From 816ea4506d3250a2bc14d752389575949399dd30 Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 12:37:38 -0700 Subject: [PATCH 1/7] experiment --- mixs6/Air.md | 133 +++ mixs6/AirMe.md | 124 +++ mixs6/AirMigsBa.md | 124 +++ mixs6/AirMigsEu.md | 124 +++ mixs6/AirMigsOrg.md | 124 +++ mixs6/AirMigsPl.md | 124 +++ mixs6/AirMigsVi.md | 124 +++ mixs6/AirMimag.md | 124 +++ mixs6/AirMimarksC.md | 124 +++ mixs6/AirMimarksS.md | 124 +++ mixs6/AirMisag.md | 124 +++ mixs6/AirMiuvig.md | 124 +++ mixs6/BuiltEnvironment.md | 673 +++++++++++++ mixs6/BuiltEnvironmentMe.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMigsBa.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMigsEu.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMigsOrg.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMigsPl.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMigsVi.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMimag.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMimarksC.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMimarksS.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMisag.md | 664 +++++++++++++ mixs6/BuiltEnvironmentMiuvig.md | 664 +++++++++++++ mixs6/Core.md | 412 ++++++++ mixs6/CoreMe.md | 403 ++++++++ mixs6/CoreMigsBa.md | 403 ++++++++ mixs6/CoreMigsEu.md | 403 ++++++++ mixs6/CoreMigsOrg.md | 403 ++++++++ mixs6/CoreMigsPl.md | 403 ++++++++ mixs6/CoreMigsVi.md | 403 ++++++++ mixs6/CoreMimag.md | 403 ++++++++ mixs6/CoreMimarksC.md | 403 ++++++++ mixs6/CoreMimarksS.md | 403 ++++++++ mixs6/CoreMisag.md | 403 ++++++++ mixs6/CoreMiuvig.md | 403 ++++++++ mixs6/Host-associated.md | 213 +++++ mixs6/Host-associatedMe.md | 204 ++++ mixs6/Host-associatedMigsBa.md | 204 ++++ mixs6/Host-associatedMigsEu.md | 204 ++++ mixs6/Host-associatedMigsOrg.md | 204 ++++ mixs6/Host-associatedMigsPl.md | 204 ++++ mixs6/Host-associatedMigsVi.md | 204 ++++ mixs6/Host-associatedMimag.md | 204 ++++ mixs6/Host-associatedMimarksC.md | 204 ++++ mixs6/Host-associatedMimarksS.md | 204 ++++ mixs6/Host-associatedMisag.md | 204 ++++ mixs6/Host-associatedMiuvig.md | 204 ++++ mixs6/Human-associated.md | 229 +++++ mixs6/Human-associatedMe.md | 220 +++++ mixs6/Human-associatedMigsBa.md | 220 +++++ mixs6/Human-associatedMigsEu.md | 220 +++++ mixs6/Human-associatedMigsOrg.md | 220 +++++ mixs6/Human-associatedMigsPl.md | 220 +++++ mixs6/Human-associatedMigsVi.md | 220 +++++ mixs6/Human-associatedMimag.md | 220 +++++ mixs6/Human-associatedMimarksC.md | 220 +++++ mixs6/Human-associatedMimarksS.md | 220 +++++ mixs6/Human-associatedMisag.md | 220 +++++ mixs6/Human-associatedMiuvig.md | 220 +++++ mixs6/Human-gut.md | 169 ++++ mixs6/Human-gutMe.md | 160 ++++ mixs6/Human-gutMigsBa.md | 160 ++++ mixs6/Human-gutMigsEu.md | 160 ++++ mixs6/Human-gutMigsOrg.md | 160 ++++ mixs6/Human-gutMigsPl.md | 160 ++++ mixs6/Human-gutMigsVi.md | 160 ++++ mixs6/Human-gutMimag.md | 160 ++++ mixs6/Human-gutMimarksC.md | 160 ++++ mixs6/Human-gutMimarksS.md | 160 ++++ mixs6/Human-gutMisag.md | 160 ++++ mixs6/Human-gutMiuvig.md | 160 ++++ mixs6/Human-oral.md | 165 ++++ mixs6/Human-oralMe.md | 156 ++++ mixs6/Human-oralMigsBa.md | 156 ++++ mixs6/Human-oralMigsEu.md | 156 ++++ mixs6/Human-oralMigsOrg.md | 156 ++++ mixs6/Human-oralMigsPl.md | 156 ++++ mixs6/Human-oralMigsVi.md | 156 ++++ mixs6/Human-oralMimag.md | 156 ++++ mixs6/Human-oralMimarksC.md | 156 ++++ mixs6/Human-oralMimarksS.md | 156 ++++ mixs6/Human-oralMisag.md | 156 ++++ mixs6/Human-oralMiuvig.md | 156 ++++ mixs6/Human-skin.md | 169 ++++ mixs6/Human-skinMe.md | 160 ++++ mixs6/Human-skinMigsBa.md | 160 ++++ mixs6/Human-skinMigsEu.md | 160 ++++ mixs6/Human-skinMigsOrg.md | 160 ++++ mixs6/Human-skinMigsPl.md | 160 ++++ mixs6/Human-skinMigsVi.md | 160 ++++ mixs6/Human-skinMimag.md | 160 ++++ mixs6/Human-skinMimarksC.md | 160 ++++ mixs6/Human-skinMimarksS.md | 160 ++++ mixs6/Human-skinMisag.md | 160 ++++ mixs6/Human-skinMiuvig.md | 160 ++++ mixs6/Human-vaginal.md | 197 ++++ mixs6/Human-vaginalMe.md | 188 ++++ mixs6/Human-vaginalMigsBa.md | 188 ++++ mixs6/Human-vaginalMigsEu.md | 188 ++++ mixs6/Human-vaginalMigsOrg.md | 188 ++++ mixs6/Human-vaginalMigsPl.md | 188 ++++ mixs6/Human-vaginalMigsVi.md | 188 ++++ mixs6/Human-vaginalMimag.md | 188 ++++ mixs6/Human-vaginalMimarksC.md | 188 ++++ mixs6/Human-vaginalMimarksS.md | 188 ++++ mixs6/Human-vaginalMisag.md | 188 ++++ mixs6/Human-vaginalMiuvig.md | 188 ++++ mixs6/HydrocarbonResources-cores.md | 349 +++++++ mixs6/HydrocarbonResources-coresMe.md | 340 +++++++ mixs6/HydrocarbonResources-coresMigsBa.md | 340 +++++++ mixs6/HydrocarbonResources-coresMigsEu.md | 340 +++++++ mixs6/HydrocarbonResources-coresMigsOrg.md | 340 +++++++ mixs6/HydrocarbonResources-coresMigsPl.md | 340 +++++++ mixs6/HydrocarbonResources-coresMigsVi.md | 340 +++++++ mixs6/HydrocarbonResources-coresMimag.md | 340 +++++++ mixs6/HydrocarbonResources-coresMimarksC.md | 340 +++++++ mixs6/HydrocarbonResources-coresMimarksS.md | 340 +++++++ mixs6/HydrocarbonResources-coresMisag.md | 340 +++++++ mixs6/HydrocarbonResources-coresMiuvig.md | 340 +++++++ mixs6/HydrocarbonResources-fluidsSwabs.md | 369 ++++++++ mixs6/HydrocarbonResources-fluidsSwabsMe.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMigsBa.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMigsEu.md | 360 +++++++ ...HydrocarbonResources-fluidsSwabsMigsOrg.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMigsPl.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMigsVi.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMimag.md | 360 +++++++ ...ydrocarbonResources-fluidsSwabsMimarksC.md | 360 +++++++ ...ydrocarbonResources-fluidsSwabsMimarksS.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMisag.md | 360 +++++++ .../HydrocarbonResources-fluidsSwabsMiuvig.md | 360 +++++++ mixs6/Me.md | 37 + mixs6/MicrobialMatBiofilm.md | 273 ++++++ mixs6/MicrobialMatBiofilmMe.md | 264 ++++++ mixs6/MicrobialMatBiofilmMigsBa.md | 264 ++++++ mixs6/MicrobialMatBiofilmMigsEu.md | 264 ++++++ mixs6/MicrobialMatBiofilmMigsOrg.md | 264 ++++++ mixs6/MicrobialMatBiofilmMigsPl.md | 264 ++++++ mixs6/MicrobialMatBiofilmMigsVi.md | 264 ++++++ mixs6/MicrobialMatBiofilmMimag.md | 264 ++++++ mixs6/MicrobialMatBiofilmMimarksC.md | 264 ++++++ mixs6/MicrobialMatBiofilmMimarksS.md | 264 ++++++ mixs6/MicrobialMatBiofilmMisag.md | 264 ++++++ mixs6/MicrobialMatBiofilmMiuvig.md | 264 ++++++ mixs6/MigsBa.md | 37 + mixs6/MigsEu.md | 37 + mixs6/MigsOrg.md | 37 + mixs6/MigsPl.md | 37 + mixs6/MigsVi.md | 37 + mixs6/Mimag.md | 37 + mixs6/MimarksC.md | 37 + mixs6/MimarksS.md | 37 + mixs6/Misag.md | 37 + ...ellaneousNaturalOrArtificialEnvironment.md | 197 ++++ ...laneousNaturalOrArtificialEnvironmentMe.md | 188 ++++ ...ousNaturalOrArtificialEnvironmentMigsBa.md | 188 ++++ ...ousNaturalOrArtificialEnvironmentMigsEu.md | 188 ++++ ...usNaturalOrArtificialEnvironmentMigsOrg.md | 188 ++++ ...ousNaturalOrArtificialEnvironmentMigsPl.md | 188 ++++ ...ousNaturalOrArtificialEnvironmentMigsVi.md | 188 ++++ ...eousNaturalOrArtificialEnvironmentMimag.md | 188 ++++ ...sNaturalOrArtificialEnvironmentMimarksC.md | 188 ++++ ...sNaturalOrArtificialEnvironmentMimarksS.md | 188 ++++ ...eousNaturalOrArtificialEnvironmentMisag.md | 188 ++++ ...ousNaturalOrArtificialEnvironmentMiuvig.md | 188 ++++ mixs6/Miuvig.md | 37 + mixs6/Plant-associated.md | 317 +++++++ mixs6/Plant-associatedMe.md | 308 ++++++ mixs6/Plant-associatedMigsBa.md | 308 ++++++ mixs6/Plant-associatedMigsEu.md | 308 ++++++ mixs6/Plant-associatedMigsOrg.md | 308 ++++++ mixs6/Plant-associatedMigsPl.md | 308 ++++++ mixs6/Plant-associatedMigsVi.md | 308 ++++++ mixs6/Plant-associatedMimag.md | 308 ++++++ mixs6/Plant-associatedMimarksC.md | 308 ++++++ mixs6/Plant-associatedMimarksS.md | 308 ++++++ mixs6/Plant-associatedMisag.md | 308 ++++++ mixs6/Plant-associatedMiuvig.md | 308 ++++++ mixs6/Sediment.md | 297 ++++++ mixs6/SedimentMe.md | 288 ++++++ mixs6/SedimentMigsBa.md | 288 ++++++ mixs6/SedimentMigsEu.md | 288 ++++++ mixs6/SedimentMigsOrg.md | 288 ++++++ mixs6/SedimentMigsPl.md | 288 ++++++ mixs6/SedimentMigsVi.md | 288 ++++++ mixs6/SedimentMimag.md | 288 ++++++ mixs6/SedimentMimarksC.md | 288 ++++++ mixs6/SedimentMimarksS.md | 288 ++++++ mixs6/SedimentMisag.md | 288 ++++++ mixs6/SedimentMiuvig.md | 288 ++++++ mixs6/Soil.md | 241 +++++ mixs6/SoilMe.md | 232 +++++ mixs6/SoilMigsBa.md | 232 +++++ mixs6/SoilMigsEu.md | 232 +++++ mixs6/SoilMigsOrg.md | 232 +++++ mixs6/SoilMigsPl.md | 232 +++++ mixs6/SoilMigsVi.md | 232 +++++ mixs6/SoilMimag.md | 232 +++++ mixs6/SoilMimarksC.md | 232 +++++ mixs6/SoilMimarksS.md | 232 +++++ mixs6/SoilMisag.md | 232 +++++ mixs6/SoilMiuvig.md | 232 +++++ mixs6/WastewaterSludge.md | 181 ++++ mixs6/WastewaterSludgeMe.md | 172 ++++ mixs6/WastewaterSludgeMigsBa.md | 172 ++++ mixs6/WastewaterSludgeMigsEu.md | 172 ++++ mixs6/WastewaterSludgeMigsOrg.md | 172 ++++ mixs6/WastewaterSludgeMigsPl.md | 172 ++++ mixs6/WastewaterSludgeMigsVi.md | 172 ++++ mixs6/WastewaterSludgeMimag.md | 172 ++++ mixs6/WastewaterSludgeMimarksC.md | 172 ++++ mixs6/WastewaterSludgeMimarksS.md | 172 ++++ mixs6/WastewaterSludgeMisag.md | 172 ++++ mixs6/WastewaterSludgeMiuvig.md | 172 ++++ mixs6/Water.md | 357 +++++++ mixs6/WaterMe.md | 348 +++++++ mixs6/WaterMigsBa.md | 348 +++++++ mixs6/WaterMigsEu.md | 348 +++++++ mixs6/WaterMigsOrg.md | 348 +++++++ mixs6/WaterMigsPl.md | 348 +++++++ mixs6/WaterMigsVi.md | 348 +++++++ mixs6/WaterMimag.md | 348 +++++++ mixs6/WaterMimarksC.md | 348 +++++++ mixs6/WaterMimarksS.md | 348 +++++++ mixs6/WaterMisag.md | 348 +++++++ mixs6/WaterMiuvig.md | 348 +++++++ mixs6/abs_air_humidity.md | 48 + mixs6/adapters.md | 56 ++ mixs6/add_recov_method.md | 48 + mixs6/additional_info.md | 60 ++ mixs6/address.md | 48 + mixs6/adj_room.md | 48 + mixs6/aero_struc.md | 48 + mixs6/agrochem_addition.md | 48 + mixs6/air_temp.md | 48 + mixs6/air_temp_regm.md | 48 + mixs6/al_sat.md | 48 + mixs6/al_sat_meth.md | 48 + mixs6/alkalinity.md | 120 +++ mixs6/alkalinity_method.md | 72 ++ mixs6/alkyl_diethers.md | 72 ++ mixs6/alt.md | 57 ++ mixs6/aminopept_act.md | 72 ++ mixs6/ammonium.md | 108 +++ mixs6/amniotic_fluid_color.md | 48 + mixs6/amount_light.md | 48 + mixs6/ances_data.md | 60 ++ mixs6/annot.md | 56 ++ mixs6/annual_precpt.md | 48 + mixs6/annual_temp.md | 48 + mixs6/antibiotic_regm.md | 48 + mixs6/api.md | 60 ++ mixs6/arch_struc.md | 48 + mixs6/aromatics_pc.md | 60 ++ mixs6/asphaltenes_pc.md | 60 ++ mixs6/assembly_name.md | 56 ++ mixs6/assembly_qual.md | 56 ++ mixs6/assembly_software.md | 56 ++ mixs6/atmospheric_data.md | 48 + mixs6/avg_dew_point.md | 48 + mixs6/avg_occup.md | 48 + mixs6/avg_temp.md | 48 + mixs6/bac_prod.md | 48 + mixs6/bac_resp.md | 48 + mixs6/bacteria_carb_prod.md | 72 ++ mixs6/barometric_press.md | 48 + mixs6/basin.md | 60 ++ mixs6/bathroom_count.md | 48 + mixs6/bedroom_count.md | 48 + mixs6/benzene.md | 60 ++ mixs6/bin_param.md | 56 ++ mixs6/bin_software.md | 56 ++ mixs6/biochem_oxygen_dem.md | 48 + mixs6/biocide.md | 48 + mixs6/biocide_admin_method.md | 48 + mixs6/biol_stat.md | 60 ++ mixs6/biomass.md | 84 ++ mixs6/biotic_regm.md | 48 + mixs6/biotic_relationship.md | 56 ++ mixs6/birth_control.md | 48 + mixs6/bishomohopanol.md | 72 ++ mixs6/blood_blood_disord.md | 48 + mixs6/bromide.md | 84 ++ mixs6/build_docs.md | 48 + mixs6/build_occup_type.md | 48 + mixs6/building_setting.md | 48 + mixs6/built_struc_age.md | 48 + mixs6/built_struc_set.md | 48 + mixs6/built_struc_type.md | 48 + mixs6/calcium.md | 108 +++ mixs6/carb_dioxide.md | 60 ++ mixs6/carb_monoxide.md | 48 + mixs6/carb_nitro_ratio.md | 72 ++ mixs6/ceil_area.md | 48 + mixs6/ceil_cond.md | 48 + mixs6/ceil_finish_mat.md | 48 + mixs6/ceil_struc.md | 48 + mixs6/ceil_texture.md | 48 + mixs6/ceil_thermal_mass.md | 48 + mixs6/ceil_type.md | 48 + mixs6/ceil_water_mold.md | 48 + mixs6/chem_administration.md | 192 ++++ mixs6/chem_mutagen.md | 48 + mixs6/chem_oxygen_dem.md | 48 + mixs6/chem_treatment.md | 48 + mixs6/chem_treatment_method.md | 48 + mixs6/chimera_check.md | 56 ++ mixs6/chloride.md | 108 +++ mixs6/chlorophyll.md | 84 ++ mixs6/climate_environment.md | 48 + mixs6/collection_date.md | 56 ++ mixs6/compl_appr.md | 56 ++ mixs6/compl_score.md | 56 ++ mixs6/compl_software.md | 56 ++ mixs6/conduc.md | 48 + mixs6/contam_score.md | 56 ++ mixs6/contam_screen_input.md | 56 ++ mixs6/contam_screen_param.md | 56 ++ mixs6/cool_syst_id.md | 48 + mixs6/core_field.md | 22 + mixs6/crop_rotation.md | 48 + mixs6/cult_root_med.md | 48 + mixs6/cur_land_use.md | 48 + mixs6/cur_vegetation.md | 48 + mixs6/cur_vegetation_meth.md | 48 + mixs6/date_last_rain.md | 48 + mixs6/decontam_software.md | 56 ++ mixs6/density.md | 96 ++ mixs6/depos_env.md | 60 ++ mixs6/depth.md | 57 ++ mixs6/dermatology_disord.md | 48 + mixs6/detec_type.md | 56 ++ mixs6/dew_point.md | 48 + mixs6/diet_last_six_month.md | 48 + mixs6/diether_lipids.md | 84 ++ mixs6/diss_carb_dioxide.md | 108 +++ mixs6/diss_hydrogen.md | 84 ++ mixs6/diss_inorg_carb.md | 108 +++ mixs6/diss_inorg_nitro.md | 48 + mixs6/diss_inorg_phosp.md | 72 ++ mixs6/diss_iron.md | 60 ++ mixs6/diss_org_carb.md | 96 ++ mixs6/diss_org_nitro.md | 84 ++ mixs6/diss_oxygen.md | 84 ++ mixs6/diss_oxygen_fluid.md | 60 ++ mixs6/dominant_hand.md | 48 + mixs6/door_comp_type.md | 48 + mixs6/door_cond.md | 48 + mixs6/door_direct.md | 48 + mixs6/door_loc.md | 48 + mixs6/door_mat.md | 48 + mixs6/door_move.md | 48 + mixs6/door_size.md | 48 + mixs6/door_type.md | 48 + mixs6/door_type_metal.md | 48 + mixs6/door_type_wood.md | 48 + mixs6/door_water_mold.md | 48 + mixs6/douche.md | 48 + mixs6/down_par.md | 48 + mixs6/drainage_class.md | 48 + mixs6/drawings.md | 48 + mixs6/drug_usage.md | 48 + mixs6/efficiency_percent.md | 48 + mixs6/elev.md | 57 ++ mixs6/elevator.md | 48 + mixs6/emulsions.md | 48 + mixs6/encoded_traits.md | 56 ++ mixs6/env_broad_scale.md | 56 ++ mixs6/env_local_scale.md | 56 ++ mixs6/env_medium.md | 56 ++ mixs6/env_package.md | 56 ++ mixs6/environment_field.md | 535 +++++++++++ mixs6/escalator.md | 48 + mixs6/estimated_size.md | 56 ++ mixs6/ethylbenzene.md | 60 ++ mixs6/exp_duct.md | 48 + mixs6/exp_pipe.md | 48 + mixs6/experimental_factor.md | 56 ++ mixs6/ext_door.md | 48 + mixs6/ext_wall_orient.md | 48 + mixs6/ext_window_orient.md | 48 + mixs6/extrachrom_elements.md | 56 ++ mixs6/extreme_event.md | 48 + mixs6/extreme_salinity.md | 48 + mixs6/fao_class.md | 48 + mixs6/feat_pred.md | 56 ++ mixs6/fertilizer_regm.md | 48 + mixs6/field.md | 60 ++ mixs6/filter_type.md | 48 + mixs6/fire.md | 48 + mixs6/fireplace_type.md | 48 + mixs6/flooding.md | 48 + mixs6/floor_age.md | 48 + mixs6/floor_area.md | 48 + mixs6/floor_cond.md | 48 + mixs6/floor_count.md | 48 + mixs6/floor_finish_mat.md | 48 + mixs6/floor_struc.md | 48 + mixs6/floor_thermal_mass.md | 48 + mixs6/floor_water_mold.md | 48 + mixs6/fluor.md | 48 + mixs6/foetal_health_stat.md | 48 + mixs6/freq_clean.md | 48 + mixs6/freq_cook.md | 48 + mixs6/fungicide_regm.md | 48 + mixs6/furniture.md | 48 + mixs6/gaseous_environment.md | 48 + mixs6/gaseous_substances.md | 48 + mixs6/gastrointest_disord.md | 48 + mixs6/gender_restroom.md | 48 + mixs6/genetic_mod.md | 60 ++ mixs6/geo_loc_name.md | 56 ++ mixs6/gestation_state.md | 48 + mixs6/glucosidase_act.md | 72 ++ mixs6/gravidity.md | 48 + mixs6/gravity.md | 48 + mixs6/growth_facil.md | 48 + mixs6/growth_habit.md | 48 + mixs6/growth_hormone_regm.md | 48 + mixs6/gynecologic_disord.md | 48 + mixs6/hall_count.md | 48 + mixs6/handidness.md | 48 + mixs6/hc_produced.md | 60 ++ mixs6/hcr.md | 60 ++ mixs6/hcr_fw_salinity.md | 60 ++ mixs6/hcr_geol_age.md | 60 ++ mixs6/hcr_pressure.md | 60 ++ mixs6/hcr_temp.md | 60 ++ mixs6/health_disease_stat.md | 56 ++ mixs6/heat_cool_type.md | 48 + mixs6/heat_deliv_loc.md | 48 + mixs6/heat_system_deliv_meth.md | 48 + mixs6/heat_system_id.md | 48 + mixs6/heavy_metals.md | 48 + mixs6/heavy_metals_meth.md | 48 + mixs6/height_carper_fiber.md | 48 + mixs6/herbicide_regm.md | 48 + mixs6/horizon.md | 48 + mixs6/horizon_meth.md | 48 + mixs6/host_age.md | 120 +++ mixs6/host_blood_press_diast.md | 48 + mixs6/host_blood_press_syst.md | 48 + mixs6/host_body_habitat.md | 48 + mixs6/host_body_mass_index.md | 96 ++ mixs6/host_body_product.md | 108 +++ mixs6/host_body_site.md | 108 +++ mixs6/host_body_temp.md | 108 +++ mixs6/host_color.md | 48 + mixs6/host_common_name.md | 60 ++ mixs6/host_diet.md | 108 +++ mixs6/host_disease_stat.md | 120 +++ mixs6/host_dry_mass.md | 60 ++ mixs6/host_family_relationship.md | 108 +++ mixs6/host_genotype.md | 120 +++ mixs6/host_growth_cond.md | 48 + mixs6/host_height.md | 120 +++ mixs6/host_hiv_stat.md | 48 + mixs6/host_infra_specific_name.md | 60 ++ mixs6/host_infra_specific_rank.md | 60 ++ mixs6/host_last_meal.md | 108 +++ mixs6/host_length.md | 60 ++ mixs6/host_life_stage.md | 60 ++ mixs6/host_occupation.md | 96 ++ mixs6/host_phenotype.md | 120 +++ mixs6/host_pred_appr.md | 56 ++ mixs6/host_pred_est_acc.md | 56 ++ mixs6/host_pulse.md | 96 ++ mixs6/host_sex.md | 108 +++ mixs6/host_shape.md | 48 + mixs6/host_spec_range.md | 56 ++ mixs6/host_subject_id.md | 108 +++ mixs6/host_substrate.md | 48 + mixs6/host_taxid.md | 60 ++ mixs6/host_tot_mass.md | 120 +++ mixs6/host_wet_mass.md | 48 + mixs6/hrt.md | 48 + mixs6/humidity.md | 48 + mixs6/humidity_regm.md | 48 + mixs6/hysterectomy.md | 48 + mixs6/ihmc_ethnicity.md | 96 ++ mixs6/ihmc_medication_code.md | 96 ++ mixs6/index.md | 884 ++++++++++++++++++ mixs6/indoor_space.md | 48 + mixs6/indoor_surf.md | 48 + mixs6/indust_eff_percent.md | 48 + mixs6/inorg_particles.md | 48 + mixs6/inside_lux.md | 48 + mixs6/int_wall_cond.md | 48 + mixs6/investigation_field.md | 25 + mixs6/investigation_type.md | 56 ++ mixs6/isol_growth_condt.md | 56 ++ mixs6/iw_bt_date_well.md | 48 + mixs6/iwf.md | 48 + mixs6/last_clean.md | 48 + mixs6/lat_lon.md | 56 ++ mixs6/lib_layout.md | 56 ++ mixs6/lib_reads_seqd.md | 56 ++ mixs6/lib_screen.md | 56 ++ mixs6/lib_size.md | 56 ++ mixs6/lib_vector.md | 56 ++ mixs6/light_intensity.md | 48 + mixs6/light_regm.md | 48 + mixs6/light_type.md | 48 + mixs6/link_addit_analys.md | 48 + mixs6/link_class_info.md | 48 + mixs6/link_climate_info.md | 48 + mixs6/lithology.md | 60 ++ mixs6/liver_disord.md | 48 + mixs6/local_class.md | 48 + mixs6/local_class_meth.md | 48 + mixs6/mag_cov_software.md | 56 ++ mixs6/magnesium.md | 96 ++ mixs6/maternal_health_stat.md | 48 + mixs6/max_occup.md | 48 + mixs6/mean_frict_vel.md | 72 ++ mixs6/mean_peak_frict_vel.md | 72 ++ mixs6/mech_struc.md | 48 + mixs6/mechanical_damage.md | 48 + mixs6/medic_hist_perform.md | 96 ++ mixs6/menarche.md | 48 + mixs6/menopause.md | 48 + mixs6/methane.md | 72 ++ mixs6/microbial_biomass.md | 48 + mixs6/microbial_biomass_meth.md | 48 + mixs6/mid.md | 56 ++ mixs6/mineral_nutr_regm.md | 48 + mixs6/misc_param.md | 228 +++++ mixs6/mixs_extension_field.md | 22 + mixs6/n_alkanes.md | 72 ++ mixs6/nitrate.md | 120 +++ mixs6/nitrite.md | 108 +++ mixs6/nitro.md | 84 ++ mixs6/non_mineral_nutr_regm.md | 48 + mixs6/nose_mouth_teeth_throat_disord.md | 48 + mixs6/nose_throat_disord.md | 48 + mixs6/nucl_acid_amp.md | 56 ++ mixs6/nucl_acid_ext.md | 56 ++ mixs6/nucleic_acid_sequence_source_field.md | 44 + mixs6/num_replicons.md | 56 ++ mixs6/number_contig.md | 56 ++ mixs6/number_pets.md | 48 + mixs6/number_plants.md | 48 + mixs6/number_resident.md | 48 + mixs6/occup_density_samp.md | 48 + mixs6/occup_document.md | 48 + mixs6/occup_samp.md | 48 + mixs6/org_carb.md | 84 ++ mixs6/org_matter.md | 84 ++ mixs6/org_nitro.md | 84 ++ mixs6/org_particles.md | 48 + mixs6/organism_count.md | 228 +++++ mixs6/organism_count_qpcr_info.md | 60 ++ mixs6/owc_tvdss.md | 48 + mixs6/oxy_stat_samp.md | 216 +++++ mixs6/oxygen.md | 48 + mixs6/part_org_carb.md | 72 ++ mixs6/part_org_nitro.md | 48 + mixs6/particle_class.md | 48 + mixs6/pathogenicity.md | 56 ++ mixs6/pcr_cond.md | 56 ++ mixs6/pcr_primers.md | 56 ++ mixs6/permeability.md | 48 + mixs6/perturbation.md | 192 ++++ mixs6/pesticide_regm.md | 48 + mixs6/pet_farm_animal.md | 48 + mixs6/petroleum_hydrocarb.md | 72 ++ mixs6/ph.md | 132 +++ mixs6/ph_meth.md | 48 + mixs6/ph_regm.md | 48 + mixs6/phaeopigments.md | 72 ++ mixs6/phosphate.md | 96 ++ mixs6/phosplipid_fatt_acid.md | 84 ++ mixs6/photon_flux.md | 48 + mixs6/plant_growth_med.md | 48 + mixs6/plant_product.md | 48 + mixs6/plant_sex.md | 48 + mixs6/plant_struc.md | 48 + mixs6/ploidy.md | 56 ++ mixs6/pollutants.md | 48 + mixs6/pool_dna_extracts.md | 48 + mixs6/porosity.md | 60 ++ mixs6/potassium.md | 108 +++ mixs6/pour_point.md | 60 ++ mixs6/pre_treatment.md | 48 + mixs6/pred_genome_struc.md | 56 ++ mixs6/pred_genome_type.md | 56 ++ mixs6/pregnancy.md | 48 + mixs6/pres_animal.md | 48 + mixs6/pressure.md | 108 +++ mixs6/previous_land_use.md | 48 + mixs6/previous_land_use_meth.md | 48 + mixs6/primary_prod.md | 48 + mixs6/primary_treatment.md | 48 + mixs6/prod_rate.md | 48 + mixs6/prod_start_date.md | 48 + mixs6/profile_position.md | 48 + mixs6/project_name.md | 56 ++ mixs6/propagation.md | 56 ++ mixs6/pulmonary_disord.md | 48 + mixs6/quad_pos.md | 48 + mixs6/radiation_regm.md | 48 + mixs6/rainfall_regm.md | 48 + mixs6/reactor_type.md | 48 + mixs6/reassembly_bin.md | 56 ++ mixs6/redox_potential.md | 72 ++ mixs6/ref_biomaterial.md | 56 ++ mixs6/ref_db.md | 56 ++ mixs6/rel_air_humidity.md | 48 + mixs6/rel_humidity_out.md | 48 + mixs6/rel_samp_loc.md | 48 + mixs6/rel_to_oxygen.md | 56 ++ mixs6/reservoir.md | 60 ++ mixs6/resins_pc.md | 60 ++ mixs6/resp_part_matter.md | 48 + mixs6/room_air_exch_rate.md | 48 + mixs6/room_architec_element.md | 48 + mixs6/room_condt.md | 48 + mixs6/room_connected.md | 48 + mixs6/room_count.md | 48 + mixs6/room_dim.md | 48 + mixs6/room_door_dist.md | 48 + mixs6/room_door_share.md | 48 + mixs6/room_hallway.md | 48 + mixs6/room_loc.md | 48 + mixs6/room_moist_damage_hist.md | 48 + mixs6/room_net_area.md | 48 + mixs6/room_occup.md | 48 + mixs6/room_samp_pos.md | 48 + mixs6/room_type.md | 48 + mixs6/room_vol.md | 48 + mixs6/room_wall_share.md | 48 + mixs6/room_window_count.md | 48 + mixs6/root_cond.md | 48 + mixs6/root_med_carbon.md | 48 + mixs6/root_med_macronutr.md | 48 + mixs6/root_med_micronutr.md | 48 + mixs6/root_med_ph.md | 48 + mixs6/root_med_regl.md | 48 + mixs6/root_med_solid.md | 48 + mixs6/root_med_suppl.md | 48 + mixs6/salinity.md | 84 ++ mixs6/salinity_meth.md | 48 + mixs6/salt_regm.md | 48 + mixs6/samp_capt_status.md | 60 ++ mixs6/samp_collect_device.md | 56 ++ mixs6/samp_collection_point.md | 48 + mixs6/samp_dis_stage.md | 60 ++ mixs6/samp_floor.md | 48 + mixs6/samp_loc_corr_rate.md | 48 + mixs6/samp_mat_process.md | 56 ++ mixs6/samp_md.md | 48 + mixs6/samp_preserv.md | 48 + mixs6/samp_room_id.md | 48 + mixs6/samp_salinity.md | 168 ++++ mixs6/samp_size.md | 56 ++ mixs6/samp_sort_meth.md | 48 + mixs6/samp_store_dur.md | 216 +++++ mixs6/samp_store_loc.md | 216 +++++ mixs6/samp_store_temp.md | 216 +++++ mixs6/samp_subtype.md | 60 ++ mixs6/samp_time_out.md | 48 + mixs6/samp_transport_cond.md | 60 ++ mixs6/samp_tvdss.md | 48 + mixs6/samp_type.md | 60 ++ mixs6/samp_vol_we_dna_ext.md | 228 +++++ mixs6/samp_weather.md | 48 + mixs6/samp_well_name.md | 60 ++ mixs6/sample_name.md | 56 ++ mixs6/saturates_pc.md | 60 ++ mixs6/season.md | 48 + mixs6/season_environment.md | 48 + mixs6/season_precpt.md | 48 + mixs6/season_temp.md | 48 + mixs6/season_use.md | 48 + mixs6/secondary_treatment.md | 48 + mixs6/sediment_type.md | 48 + mixs6/seq_meth.md | 56 ++ mixs6/seq_quality_check.md | 56 ++ mixs6/sequencing_field.md | 78 ++ mixs6/sewage_type.md | 48 + mixs6/sexual_act.md | 48 + mixs6/shading_device_cond.md | 48 + mixs6/shading_device_loc.md | 48 + mixs6/shading_device_mat.md | 48 + mixs6/shading_device_type.md | 48 + mixs6/shading_device_water_mold.md | 48 + mixs6/sieving.md | 48 + mixs6/silicate.md | 84 ++ mixs6/sim_search_meth.md | 56 ++ mixs6/single_cell_lysis_appr.md | 56 ++ mixs6/single_cell_lysis_prot.md | 56 ++ mixs6/size_frac.md | 56 ++ mixs6/size_frac_low.md | 48 + mixs6/size_frac_up.md | 48 + mixs6/slope_aspect.md | 48 + mixs6/slope_gradient.md | 48 + mixs6/sludge_retent_time.md | 48 + mixs6/smoker.md | 48 + mixs6/sodium.md | 120 +++ mixs6/soil_type.md | 48 + mixs6/soil_type_meth.md | 48 + mixs6/solar_irradiance.md | 48 + mixs6/soluble_inorg_mat.md | 48 + mixs6/soluble_org_mat.md | 48 + mixs6/soluble_react_phosp.md | 48 + mixs6/sop.md | 56 ++ mixs6/sort_tech.md | 56 ++ mixs6/source_mat_id.md | 56 ++ mixs6/source_uvig.md | 56 ++ mixs6/space_typ_state.md | 48 + mixs6/special_diet.md | 48 + mixs6/specific.md | 48 + mixs6/specific_host.md | 56 ++ mixs6/specific_humidity.md | 48 + mixs6/sr_dep_env.md | 48 + mixs6/sr_geol_age.md | 48 + mixs6/sr_kerog_type.md | 48 + mixs6/sr_lithology.md | 48 + mixs6/standing_water_regm.md | 48 + mixs6/store_cond.md | 48 + mixs6/study_complt_stat.md | 48 + mixs6/submitted_to_insdc.md | 56 ++ mixs6/subspecf_gen_lin.md | 56 ++ mixs6/substructure_type.md | 48 + mixs6/sulfate.md | 108 +++ mixs6/sulfate_fw.md | 60 ++ mixs6/sulfide.md | 108 +++ mixs6/surf_air_cont.md | 48 + mixs6/surf_humidity.md | 48 + mixs6/surf_material.md | 48 + mixs6/surf_moisture.md | 48 + mixs6/surf_moisture_ph.md | 48 + mixs6/surf_temp.md | 48 + mixs6/suspend_part_matter.md | 48 + mixs6/suspend_solids.md | 72 ++ mixs6/tan.md | 60 ++ mixs6/target_gene.md | 56 ++ mixs6/target_subfragment.md | 56 ++ mixs6/tax_class.md | 56 ++ mixs6/tax_ident.md | 56 ++ mixs6/temp.md | 216 +++++ mixs6/temp_out.md | 48 + mixs6/tertiary_treatment.md | 48 + mixs6/texture.md | 48 + mixs6/texture_meth.md | 48 + mixs6/tidal_stage.md | 60 ++ mixs6/tillage.md | 48 + mixs6/time_last_toothbrush.md | 48 + mixs6/time_since_last_wash.md | 48 + mixs6/tiss_cult_growth_med.md | 48 + mixs6/toluene.md | 60 ++ mixs6/tot_carb.md | 60 ++ mixs6/tot_depth_water_col.md | 60 ++ mixs6/tot_diss_nitro.md | 48 + mixs6/tot_inorg_nitro.md | 48 + mixs6/tot_iron.md | 60 ++ mixs6/tot_nitro.md | 84 ++ mixs6/tot_nitro_content.md | 72 ++ mixs6/tot_nitro_content_meth.md | 48 + mixs6/tot_org_c_meth.md | 48 + mixs6/tot_org_carb.md | 72 ++ mixs6/tot_part_carb.md | 48 + mixs6/tot_phosp.md | 72 ++ mixs6/tot_phosphate.md | 48 + mixs6/tot_sulfur.md | 60 ++ mixs6/train_line.md | 48 + mixs6/train_stat_loc.md | 48 + mixs6/train_stop_loc.md | 48 + mixs6/travel_out_six_month.md | 48 + mixs6/trna_ext_software.md | 56 ++ mixs6/trnas.md | 56 ++ mixs6/trophic_level.md | 56 ++ mixs6/turbidity.md | 72 ++ mixs6/tvdss_of_hcr_pressure.md | 60 ++ mixs6/tvdss_of_hcr_temp.md | 60 ++ mixs6/twin_sibling.md | 48 + mixs6/typ_occup_density.md | 48 + mixs6/urine_collect_meth.md | 48 + mixs6/url.md | 56 ++ mixs6/urogenit_disord.md | 48 + mixs6/urogenit_tract_disor.md | 48 + mixs6/ventilation_rate.md | 48 + mixs6/ventilation_type.md | 60 ++ mixs6/vfa.md | 60 ++ mixs6/vfa_fw.md | 60 ++ mixs6/vir_ident_software.md | 56 ++ mixs6/virus_enrich_appr.md | 56 ++ mixs6/vis_media.md | 48 + mixs6/viscosity.md | 60 ++ mixs6/volatile_org_comp.md | 48 + mixs6/votu_class_appr.md | 56 ++ mixs6/votu_db.md | 56 ++ mixs6/votu_seq_comp_appr.md | 56 ++ mixs6/wall_area.md | 48 + mixs6/wall_const_type.md | 48 + mixs6/wall_finish_mat.md | 48 + mixs6/wall_height.md | 48 + mixs6/wall_loc.md | 48 + mixs6/wall_surf_treatment.md | 48 + mixs6/wall_texture.md | 48 + mixs6/wall_thermal_mass.md | 48 + mixs6/wall_water_mold.md | 48 + mixs6/wastewater_type.md | 48 + mixs6/water_content.md | 72 ++ mixs6/water_content_soil_meth.md | 48 + mixs6/water_current.md | 60 ++ mixs6/water_cut.md | 48 + mixs6/water_feat_size.md | 48 + mixs6/water_feat_type.md | 48 + mixs6/water_production_rate.md | 48 + mixs6/water_temp_regm.md | 48 + mixs6/watering_regm.md | 48 + mixs6/weekday.md | 48 + mixs6/weight_loss_3_month.md | 48 + mixs6/wga_amp_appr.md | 56 ++ mixs6/wga_amp_kit.md | 56 ++ mixs6/win.md | 60 ++ mixs6/wind_direction.md | 48 + mixs6/wind_speed.md | 48 + mixs6/window_cond.md | 48 + mixs6/window_cover.md | 48 + mixs6/window_horiz_pos.md | 48 + mixs6/window_loc.md | 48 + mixs6/window_mat.md | 48 + mixs6/window_open_freq.md | 48 + mixs6/window_size.md | 48 + mixs6/window_status.md | 48 + mixs6/window_type.md | 48 + mixs6/window_vert_pos.md | 48 + mixs6/window_water_mold.md | 48 + mixs6/x_16s_recover.md | 56 ++ mixs6/x_16s_recover_software.md | 56 ++ mixs6/xylene.md | 60 ++ 834 files changed, 94934 insertions(+) create mode 100644 mixs6/Air.md create mode 100644 mixs6/AirMe.md create mode 100644 mixs6/AirMigsBa.md create mode 100644 mixs6/AirMigsEu.md create mode 100644 mixs6/AirMigsOrg.md create mode 100644 mixs6/AirMigsPl.md create mode 100644 mixs6/AirMigsVi.md create mode 100644 mixs6/AirMimag.md create mode 100644 mixs6/AirMimarksC.md create mode 100644 mixs6/AirMimarksS.md create mode 100644 mixs6/AirMisag.md create mode 100644 mixs6/AirMiuvig.md create mode 100644 mixs6/BuiltEnvironment.md create mode 100644 mixs6/BuiltEnvironmentMe.md create mode 100644 mixs6/BuiltEnvironmentMigsBa.md create mode 100644 mixs6/BuiltEnvironmentMigsEu.md create mode 100644 mixs6/BuiltEnvironmentMigsOrg.md create mode 100644 mixs6/BuiltEnvironmentMigsPl.md create mode 100644 mixs6/BuiltEnvironmentMigsVi.md create mode 100644 mixs6/BuiltEnvironmentMimag.md create mode 100644 mixs6/BuiltEnvironmentMimarksC.md create mode 100644 mixs6/BuiltEnvironmentMimarksS.md create mode 100644 mixs6/BuiltEnvironmentMisag.md create mode 100644 mixs6/BuiltEnvironmentMiuvig.md create mode 100644 mixs6/Core.md create mode 100644 mixs6/CoreMe.md create mode 100644 mixs6/CoreMigsBa.md create mode 100644 mixs6/CoreMigsEu.md create mode 100644 mixs6/CoreMigsOrg.md create mode 100644 mixs6/CoreMigsPl.md create mode 100644 mixs6/CoreMigsVi.md create mode 100644 mixs6/CoreMimag.md create mode 100644 mixs6/CoreMimarksC.md create mode 100644 mixs6/CoreMimarksS.md create mode 100644 mixs6/CoreMisag.md create mode 100644 mixs6/CoreMiuvig.md create mode 100644 mixs6/Host-associated.md create mode 100644 mixs6/Host-associatedMe.md create mode 100644 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mixs6/single_cell_lysis_prot.md create mode 100644 mixs6/size_frac.md create mode 100644 mixs6/size_frac_low.md create mode 100644 mixs6/size_frac_up.md create mode 100644 mixs6/slope_aspect.md create mode 100644 mixs6/slope_gradient.md create mode 100644 mixs6/sludge_retent_time.md create mode 100644 mixs6/smoker.md create mode 100644 mixs6/sodium.md create mode 100644 mixs6/soil_type.md create mode 100644 mixs6/soil_type_meth.md create mode 100644 mixs6/solar_irradiance.md create mode 100644 mixs6/soluble_inorg_mat.md create mode 100644 mixs6/soluble_org_mat.md create mode 100644 mixs6/soluble_react_phosp.md create mode 100644 mixs6/sop.md create mode 100644 mixs6/sort_tech.md create mode 100644 mixs6/source_mat_id.md create mode 100644 mixs6/source_uvig.md create mode 100644 mixs6/space_typ_state.md create mode 100644 mixs6/special_diet.md create mode 100644 mixs6/specific.md create mode 100644 mixs6/specific_host.md create mode 100644 mixs6/specific_humidity.md create mode 100644 mixs6/sr_dep_env.md create mode 100644 mixs6/sr_geol_age.md create mode 100644 mixs6/sr_kerog_type.md create mode 100644 mixs6/sr_lithology.md create mode 100644 mixs6/standing_water_regm.md create mode 100644 mixs6/store_cond.md create mode 100644 mixs6/study_complt_stat.md create mode 100644 mixs6/submitted_to_insdc.md create mode 100644 mixs6/subspecf_gen_lin.md create mode 100644 mixs6/substructure_type.md create mode 100644 mixs6/sulfate.md create mode 100644 mixs6/sulfate_fw.md create mode 100644 mixs6/sulfide.md create mode 100644 mixs6/surf_air_cont.md create mode 100644 mixs6/surf_humidity.md create mode 100644 mixs6/surf_material.md create mode 100644 mixs6/surf_moisture.md create mode 100644 mixs6/surf_moisture_ph.md create mode 100644 mixs6/surf_temp.md create mode 100644 mixs6/suspend_part_matter.md create mode 100644 mixs6/suspend_solids.md create mode 100644 mixs6/tan.md create mode 100644 mixs6/target_gene.md create mode 100644 mixs6/target_subfragment.md create mode 100644 mixs6/tax_class.md create mode 100644 mixs6/tax_ident.md create mode 100644 mixs6/temp.md create mode 100644 mixs6/temp_out.md create mode 100644 mixs6/tertiary_treatment.md create mode 100644 mixs6/texture.md create mode 100644 mixs6/texture_meth.md create mode 100644 mixs6/tidal_stage.md create mode 100644 mixs6/tillage.md create mode 100644 mixs6/time_last_toothbrush.md create mode 100644 mixs6/time_since_last_wash.md create mode 100644 mixs6/tiss_cult_growth_med.md create mode 100644 mixs6/toluene.md create mode 100644 mixs6/tot_carb.md create mode 100644 mixs6/tot_depth_water_col.md create mode 100644 mixs6/tot_diss_nitro.md create mode 100644 mixs6/tot_inorg_nitro.md create mode 100644 mixs6/tot_iron.md create mode 100644 mixs6/tot_nitro.md create mode 100644 mixs6/tot_nitro_content.md create mode 100644 mixs6/tot_nitro_content_meth.md create mode 100644 mixs6/tot_org_c_meth.md create mode 100644 mixs6/tot_org_carb.md create mode 100644 mixs6/tot_part_carb.md create mode 100644 mixs6/tot_phosp.md create mode 100644 mixs6/tot_phosphate.md create mode 100644 mixs6/tot_sulfur.md create mode 100644 mixs6/train_line.md create mode 100644 mixs6/train_stat_loc.md create mode 100644 mixs6/train_stop_loc.md create mode 100644 mixs6/travel_out_six_month.md create mode 100644 mixs6/trna_ext_software.md create mode 100644 mixs6/trnas.md create mode 100644 mixs6/trophic_level.md create mode 100644 mixs6/turbidity.md create mode 100644 mixs6/tvdss_of_hcr_pressure.md create mode 100644 mixs6/tvdss_of_hcr_temp.md create mode 100644 mixs6/twin_sibling.md create mode 100644 mixs6/typ_occup_density.md create mode 100644 mixs6/urine_collect_meth.md create mode 100644 mixs6/url.md create mode 100644 mixs6/urogenit_disord.md create mode 100644 mixs6/urogenit_tract_disor.md create mode 100644 mixs6/ventilation_rate.md create mode 100644 mixs6/ventilation_type.md create mode 100644 mixs6/vfa.md create mode 100644 mixs6/vfa_fw.md create mode 100644 mixs6/vir_ident_software.md create mode 100644 mixs6/virus_enrich_appr.md create mode 100644 mixs6/vis_media.md create mode 100644 mixs6/viscosity.md create mode 100644 mixs6/volatile_org_comp.md create mode 100644 mixs6/votu_class_appr.md create mode 100644 mixs6/votu_db.md create mode 100644 mixs6/votu_seq_comp_appr.md create mode 100644 mixs6/wall_area.md create mode 100644 mixs6/wall_const_type.md create mode 100644 mixs6/wall_finish_mat.md create mode 100644 mixs6/wall_height.md create mode 100644 mixs6/wall_loc.md create mode 100644 mixs6/wall_surf_treatment.md create mode 100644 mixs6/wall_texture.md create mode 100644 mixs6/wall_thermal_mass.md create mode 100644 mixs6/wall_water_mold.md create mode 100644 mixs6/wastewater_type.md create mode 100644 mixs6/water_content.md create mode 100644 mixs6/water_content_soil_meth.md create mode 100644 mixs6/water_current.md create mode 100644 mixs6/water_cut.md create mode 100644 mixs6/water_feat_size.md create mode 100644 mixs6/water_feat_type.md create mode 100644 mixs6/water_production_rate.md create mode 100644 mixs6/water_temp_regm.md create mode 100644 mixs6/watering_regm.md create mode 100644 mixs6/weekday.md create mode 100644 mixs6/weight_loss_3_month.md create mode 100644 mixs6/wga_amp_appr.md create mode 100644 mixs6/wga_amp_kit.md create mode 100644 mixs6/win.md create mode 100644 mixs6/wind_direction.md create mode 100644 mixs6/wind_speed.md create mode 100644 mixs6/window_cond.md create mode 100644 mixs6/window_cover.md create mode 100644 mixs6/window_horiz_pos.md create mode 100644 mixs6/window_loc.md create mode 100644 mixs6/window_mat.md create mode 100644 mixs6/window_open_freq.md create mode 100644 mixs6/window_size.md create mode 100644 mixs6/window_status.md create mode 100644 mixs6/window_type.md create mode 100644 mixs6/window_vert_pos.md create mode 100644 mixs6/window_water_mold.md create mode 100644 mixs6/x_16s_recover.md create mode 100644 mixs6/x_16s_recover_software.md create mode 100644 mixs6/xylene.md diff --git a/mixs6/Air.md b/mixs6/Air.md new file mode 100644 index 00000000..1bbc0f52 --- /dev/null +++ b/mixs6/Air.md @@ -0,0 +1,133 @@ + +# Class: Air + + +air + +URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[AirMiuvig],[AirMisag],[AirMimarksS],[AirMimarksC],[AirMimag],[AirMigsVi],[AirMigsPl],[AirMigsOrg],[AirMigsEu],[AirMigsBa],[AirMe],[Air|barometric_press:string%20%3F;carb_dioxide:string%20%3F;carb_monoxide:string%20%3F;chem_administration:string%20%3F;humidity:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;organism_count:organism_count_enum%20%3F;oxygen:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;perturbation:string%20%3F;pollutants:string%20%3F;resp_part_matter:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;solar_irradiance:string%20%3F;temp:string%20%3F;ventilation_rate:string%20%3F;ventilation_type:string%20%3F;volatile_org_comp:string%20%3F;wind_direction:string%20%3F;wind_speed:string%20%3F]^-[AirMiuvig],[Air]^-[AirMisag],[Air]^-[AirMimarksS],[Air]^-[AirMimarksC],[Air]^-[AirMimag],[Air]^-[AirMigsVi],[Air]^-[AirMigsPl],[Air]^-[AirMigsOrg],[Air]^-[AirMigsEu],[Air]^-[AirMigsBa],[Air]^-[AirMe]) + +## Children + + * [AirMe](AirMe.md) - Combinatorial checklist for air with me + * [AirMigsBa](AirMigsBa.md) - Combinatorial checklist for air with migs_ba + * [AirMigsEu](AirMigsEu.md) - Combinatorial checklist for air with migs_eu + * [AirMigsOrg](AirMigsOrg.md) - Combinatorial checklist for air with migs_org + * [AirMigsPl](AirMigsPl.md) - Combinatorial checklist for air with migs_pl + * [AirMigsVi](AirMigsVi.md) - Combinatorial checklist for air with migs_vi + * [AirMimag](AirMimag.md) - Combinatorial checklist for air with mimag + * [AirMimarksC](AirMimarksC.md) - Combinatorial checklist for air with mimarks_c + * [AirMimarksS](AirMimarksS.md) - Combinatorial checklist for air with mimarks_s + * [AirMisag](AirMisag.md) - Combinatorial checklist for air with misag + * [AirMiuvig](AirMiuvig.md) - Combinatorial checklist for air with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md new file mode 100644 index 00000000..dcaddab5 --- /dev/null +++ b/mixs6/AirMe.md @@ -0,0 +1,124 @@ + +# Class: AirMe + + +Combinatorial checklist for air with me + +URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[AirMe|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Me],[Air]^-[AirMe],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMigsBa.md b/mixs6/AirMigsBa.md new file mode 100644 index 00000000..85ad2916 --- /dev/null +++ b/mixs6/AirMigsBa.md @@ -0,0 +1,124 @@ + +# Class: AirMigsBa + + +Combinatorial checklist for air with migs_ba + +URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[AirMigsBa|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsBa],[Air]^-[AirMigsBa],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMigsEu.md b/mixs6/AirMigsEu.md new file mode 100644 index 00000000..4c797eee --- /dev/null +++ b/mixs6/AirMigsEu.md @@ -0,0 +1,124 @@ + +# Class: AirMigsEu + + +Combinatorial checklist for air with migs_eu + +URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[AirMigsEu|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsEu],[Air]^-[AirMigsEu],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md new file mode 100644 index 00000000..8f239c30 --- /dev/null +++ b/mixs6/AirMigsOrg.md @@ -0,0 +1,124 @@ + +# Class: AirMigsOrg + + +Combinatorial checklist for air with migs_org + +URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[AirMigsOrg|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsOrg],[Air]^-[AirMigsOrg],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMigsPl.md b/mixs6/AirMigsPl.md new file mode 100644 index 00000000..54f8f531 --- /dev/null +++ b/mixs6/AirMigsPl.md @@ -0,0 +1,124 @@ + +# Class: AirMigsPl + + +Combinatorial checklist for air with migs_pl + +URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[AirMigsPl|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsPl],[Air]^-[AirMigsPl],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMigsVi.md b/mixs6/AirMigsVi.md new file mode 100644 index 00000000..5c84c69a --- /dev/null +++ b/mixs6/AirMigsVi.md @@ -0,0 +1,124 @@ + +# Class: AirMigsVi + + +Combinatorial checklist for air with migs_vi + +URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[AirMigsVi|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsVi],[Air]^-[AirMigsVi],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md new file mode 100644 index 00000000..9888fc5e --- /dev/null +++ b/mixs6/AirMimag.md @@ -0,0 +1,124 @@ + +# Class: AirMimag + + +Combinatorial checklist for air with mimag + +URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[AirMimag|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Mimag],[Air]^-[AirMimag],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMimarksC.md b/mixs6/AirMimarksC.md new file mode 100644 index 00000000..0c094042 --- /dev/null +++ b/mixs6/AirMimarksC.md @@ -0,0 +1,124 @@ + +# Class: AirMimarksC + + +Combinatorial checklist for air with mimarks_c + +URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[AirMimarksC|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MimarksC],[Air]^-[AirMimarksC],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMimarksS.md b/mixs6/AirMimarksS.md new file mode 100644 index 00000000..e3b35698 --- /dev/null +++ b/mixs6/AirMimarksS.md @@ -0,0 +1,124 @@ + +# Class: AirMimarksS + + +Combinatorial checklist for air with mimarks_s + +URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[AirMimarksS|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MimarksS],[Air]^-[AirMimarksS],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md new file mode 100644 index 00000000..e15023af --- /dev/null +++ b/mixs6/AirMisag.md @@ -0,0 +1,124 @@ + +# Class: AirMisag + + +Combinatorial checklist for air with misag + +URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[AirMisag|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Misag],[Air]^-[AirMisag],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md new file mode 100644 index 00000000..2cea0619 --- /dev/null +++ b/mixs6/AirMiuvig.md @@ -0,0 +1,124 @@ + +# Class: AirMiuvig + + +Combinatorial checklist for air with miuvig + +URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[AirMiuvig|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Miuvig],[Air]^-[AirMiuvig],[Air]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from air: + + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [String](types/String.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [String](types/String.md) + * Example: 25 gram per cubic meter None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [String](types/String.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [String](types/String.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [String](types/String.md) + * Example: 21 kilometer per hour None diff --git a/mixs6/BuiltEnvironment.md b/mixs6/BuiltEnvironment.md new file mode 100644 index 00000000..3d637627 --- /dev/null +++ b/mixs6/BuiltEnvironment.md @@ -0,0 +1,673 @@ + +# Class: BuiltEnvironment + + +built environment + +URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[BuiltEnvironmentMiuvig],[BuiltEnvironmentMisag],[BuiltEnvironmentMimarksS],[BuiltEnvironmentMimarksC],[BuiltEnvironmentMimag],[BuiltEnvironmentMigsVi],[BuiltEnvironmentMigsPl],[BuiltEnvironmentMigsOrg],[BuiltEnvironmentMigsEu],[BuiltEnvironmentMigsBa],[BuiltEnvironmentMe],[BuiltEnvironment|surf_material:surf_material_enum%20%3F;surf_air_cont:surf_air_cont_enum%20%3F;rel_air_humidity:string%20%3F;abs_air_humidity:string%20%3F;surf_humidity:string%20%3F;air_temp:string%20%3F;surf_temp:string%20%3F;surf_moisture_ph:string%20%3F;build_occup_type:build_occup_type_enum%20%3F;surf_moisture:string%20%3F;dew_point:string%20%3F;carb_dioxide:string%20%3F;ventilation_type:string%20%3F;organism_count:organism_count_enum%20%3F;indoor_space:indoor_space_enum%20%3F;indoor_surf:indoor_surf_enum%20%3F;filter_type:filter_type_enum%20%3F;heat_cool_type:heat_cool_type_enum%20%3F;substructure_type:substructure_type_enum%20%3F;building_setting:building_setting_enum%20%3F;light_type:light_type_enum%20%3F;samp_sort_meth:string%20%3F;space_typ_state:string%20%3F;typ_occup_density:string%20%3F;occup_samp:string%20%3F;occup_density_samp:string%20%3F;address:string%20%3F;adj_room:string%20%3F;aero_struc:string%20%3F;amount_light:string%20%3F;arch_struc:arch_struc_enum%20%3F;avg_occup:string%20%3F;avg_dew_point:string%20%3F;avg_temp:string%20%3F;bathroom_count:string%20%3F;bedroom_count:string%20%3F;built_struc_age:string%20%3F;built_struc_set:string%20%3F;built_struc_type:string%20%3F;ceil_area:string%20%3F;ceil_cond:ceil_cond_enum%20%3F;ceil_finish_mat:ceil_finish_mat_enum%20%3F;ceil_water_mold:string%20%3F;ceil_struc:string%20%3F;ceil_texture:ceil_texture_enum%20%3F;ceil_thermal_mass:string%20%3F;ceil_type:ceil_type_enum%20%3F;cool_syst_id:string%20%3F;date_last_rain:string%20%3F;build_docs:build_docs_enum%20%3F;door_size:string%20%3F;door_cond:door_cond_enum%20%3F;door_direct:door_direct_enum%20%3F;door_loc:door_loc_enum%20%3F;door_mat:door_mat_enum%20%3F;door_move:door_move_enum%20%3F;door_water_mold:string%20%3F;door_type:door_type_enum%20%3F;door_comp_type:door_comp_type_enum%20%3F;door_type_metal:door_type_metal_enum%20%3F;door_type_wood:door_type_wood_enum%20%3F;drawings:drawings_enum%20%3F;elevator:string%20%3F;escalator:string%20%3F;exp_duct:string%20%3F;exp_pipe:string%20%3F;ext_door:string%20%3F;fireplace_type:string%20%3F;floor_age:string%20%3F;floor_area:string%20%3F;floor_cond:floor_cond_enum%20%3F;floor_count:string%20%3F;floor_finish_mat:floor_finish_mat_enum%20%3F;floor_water_mold:floor_water_mold_enum%20%3F;floor_struc:floor_struc_enum%20%3F;floor_thermal_mass:string%20%3F;freq_clean:string%20%3F;freq_cook:string%20%3F;furniture:furniture_enum%20%3F;gender_restroom:string%20%3F;hall_count:string%20%3F;handidness:handidness_enum%20%3F;heat_deliv_loc:heat_deliv_loc_enum%20%3F;heat_system_deliv_meth:string%20%3F;heat_system_id:string%20%3F;height_carper_fiber:string%20%3F;inside_lux:string%20%3F;int_wall_cond:int_wall_cond_enum%20%3F;last_clean:string%20%3F;max_occup:string%20%3F;mech_struc:mech_struc_enum%20%3F;number_plants:string%20%3F;number_pets:string%20%3F;number_resident:string%20%3F;occup_document:occup_document_enum%20%3F;ext_wall_orient:ext_wall_orient_enum%20%3F;ext_window_orient:ext_window_orient_enum%20%3F;rel_humidity_out:string%20%3F;pres_animal:pres_animal_enum%20%3F;quad_pos:quad_pos_enum%20%3F;rel_samp_loc:rel_samp_loc_enum%20%3F;room_air_exch_rate:string%20%3F;room_architec_element:string%20%3F;room_condt:room_condt_enum%20%3F;room_count:string%20%3F;room_dim:string%20%3F;room_door_dist:string%20%3F;room_loc:room_loc_enum%20%3F;room_moist_damage_hist:string%20%3F;room_net_area:string%20%3F;room_occup:string%20%3F;room_samp_pos:room_samp_pos_enum%20%3F;room_type:room_type_enum%20%3F;room_vol:string%20%3F;room_window_count:string%20%3F;room_connected:room_connected_enum%20%3F;room_hallway:string%20%3F;room_door_share:string%20%3F;room_wall_share:string%20%3F;samp_weather:samp_weather_enum%20%3F;samp_floor:samp_floor_enum%20%3F;samp_room_id:string%20%3F;samp_time_out:string%20%3F;season:string%20%3F;season_use:season_use_enum%20%3F;shading_device_cond:shading_device_cond_enum%20%3F;shading_device_loc:string%20%3F;shading_device_mat:string%20%3F;shading_device_water_mold:string%20%3F;shading_device_type:shading_device_type_enum%20%3F;specific_humidity:string%20%3F;specific:specific_enum%20%3F;temp_out:string%20%3F;train_line:train_line_enum%20%3F;train_stat_loc:train_stat_loc_enum%20%3F;train_stop_loc:train_stop_loc_enum%20%3F;vis_media:vis_media_enum%20%3F;wall_area:string%20%3F;wall_const_type:wall_const_type_enum%20%3F;wall_finish_mat:wall_finish_mat_enum%20%3F;wall_height:string%20%3F;wall_loc:wall_loc_enum%20%3F;wall_water_mold:string%20%3F;wall_surf_treatment:wall_surf_treatment_enum%20%3F;wall_texture:wall_texture_enum%20%3F;wall_thermal_mass:string%20%3F;water_feat_size:string%20%3F;water_feat_type:water_feat_type_enum%20%3F;weekday:weekday_enum%20%3F;window_size:string%20%3F;window_cond:window_cond_enum%20%3F;window_cover:window_cover_enum%20%3F;window_horiz_pos:window_horiz_pos_enum%20%3F;window_loc:window_loc_enum%20%3F;window_mat:window_mat_enum%20%3F;window_open_freq:string%20%3F;window_water_mold:string%20%3F;window_status:string%20%3F;window_type:window_type_enum%20%3F;window_vert_pos:window_vert_pos_enum%20%3F]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMe]) + +## Children + + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - Combinatorial checklist for built environment with me + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - Combinatorial checklist for built environment with migs_ba + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - Combinatorial checklist for built environment with migs_eu + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - Combinatorial checklist for built environment with migs_org + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - Combinatorial checklist for built environment with migs_pl + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - Combinatorial checklist for built environment with migs_vi + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - Combinatorial checklist for built environment with mimag + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - Combinatorial checklist for built environment with mimarks_c + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - Combinatorial checklist for built environment with mimarks_s + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - Combinatorial checklist for built environment with misag + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) - Combinatorial checklist for built environment with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMe.md b/mixs6/BuiltEnvironmentMe.md new file mode 100644 index 00000000..70e78e19 --- /dev/null +++ b/mixs6/BuiltEnvironmentMe.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMe + + +Combinatorial checklist for built environment with me + +URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmentMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[BuiltEnvironmentMe|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Me],[BuiltEnvironment]^-[BuiltEnvironmentMe],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMigsBa.md b/mixs6/BuiltEnvironmentMigsBa.md new file mode 100644 index 00000000..f9a56c4d --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsBa.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMigsBa + + +Combinatorial checklist for built environment with migs_ba + +URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[BuiltEnvironmentMigsBa|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMigsEu.md b/mixs6/BuiltEnvironmentMigsEu.md new file mode 100644 index 00000000..24c89376 --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsEu.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMigsEu + + +Combinatorial checklist for built environment with migs_eu + +URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[BuiltEnvironmentMigsEu|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMigsOrg.md b/mixs6/BuiltEnvironmentMigsOrg.md new file mode 100644 index 00000000..e27f8237 --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsOrg.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMigsOrg + + +Combinatorial checklist for built environment with migs_org + +URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[BuiltEnvironmentMigsOrg|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMigsPl.md b/mixs6/BuiltEnvironmentMigsPl.md new file mode 100644 index 00000000..6edb111f --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsPl.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMigsPl + + +Combinatorial checklist for built environment with migs_pl + +URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[BuiltEnvironmentMigsPl|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMigsVi.md b/mixs6/BuiltEnvironmentMigsVi.md new file mode 100644 index 00000000..b47e32ec --- /dev/null +++ b/mixs6/BuiltEnvironmentMigsVi.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMigsVi + + +Combinatorial checklist for built environment with migs_vi + +URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[BuiltEnvironmentMigsVi|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMimag.md b/mixs6/BuiltEnvironmentMimag.md new file mode 100644 index 00000000..9bf0f85e --- /dev/null +++ b/mixs6/BuiltEnvironmentMimag.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMimag + + +Combinatorial checklist for built environment with mimag + +URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnvironmentMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[BuiltEnvironmentMimag|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Mimag],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMimarksC.md b/mixs6/BuiltEnvironmentMimarksC.md new file mode 100644 index 00000000..baa22c03 --- /dev/null +++ b/mixs6/BuiltEnvironmentMimarksC.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMimarksC + + +Combinatorial checklist for built environment with mimarks_c + +URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[BuiltEnvironmentMimarksC|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMimarksS.md b/mixs6/BuiltEnvironmentMimarksS.md new file mode 100644 index 00000000..c4841229 --- /dev/null +++ b/mixs6/BuiltEnvironmentMimarksS.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMimarksS + + +Combinatorial checklist for built environment with mimarks_s + +URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[BuiltEnvironmentMimarksS|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMisag.md b/mixs6/BuiltEnvironmentMisag.md new file mode 100644 index 00000000..19fd53b7 --- /dev/null +++ b/mixs6/BuiltEnvironmentMisag.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMisag + + +Combinatorial checklist for built environment with misag + +URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnvironmentMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[BuiltEnvironmentMisag|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Misag],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/BuiltEnvironmentMiuvig.md b/mixs6/BuiltEnvironmentMiuvig.md new file mode 100644 index 00000000..83e88792 --- /dev/null +++ b/mixs6/BuiltEnvironmentMiuvig.md @@ -0,0 +1,664 @@ + +# Class: BuiltEnvironmentMiuvig + + +Combinatorial checklist for built environment with miuvig + +URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnvironmentMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[BuiltEnvironmentMiuvig|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Miuvig],[BuiltEnvironment]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [String](types/String.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [String](types/String.md) + * Example: 20 degree Celsius None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [String](types/String.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [String](types/String.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [String](types/String.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [String](types/String.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [String](types/String.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [String](types/String.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [String](types/String.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [String](types/String.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [String](types/String.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [String](types/String.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [String](types/String.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [String](types/String.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [String](types/String.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [String](types/String.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [String](types/String.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [String](types/String.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [String](types/String.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [String](types/String.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [String](types/String.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [String](types/String.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [String](types/String.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [String](types/String.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [String](types/String.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [String](types/String.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [String](types/String.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [String](types/String.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [String](types/String.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [String](types/String.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None diff --git a/mixs6/Core.md b/mixs6/Core.md new file mode 100644 index 00000000..3efff02d --- /dev/null +++ b/mixs6/Core.md @@ -0,0 +1,412 @@ + +# Class: Core + + +core package + +URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[CoreMiuvig],[CoreMisag],[CoreMimarksS],[CoreMimarksC],[CoreMimag],[CoreMigsVi],[CoreMigsPl],[CoreMigsOrg],[CoreMigsEu],[CoreMigsBa],[CoreMe],[Core|submitted_to_insdc:string%20%3F;investigation_type:investigation_type_enum%20%3F;sample_name:string%20%3F;project_name:string%20%3F;experimental_factor:string%20%3F;lat_lon:string%20%3F;depth:string%20%3F;alt:string%20%3F;elev:string%20%3F;geo_loc_name:string%20%3F;collection_date:string%20%3F;env_broad_scale:string%20%3F;env_local_scale:string%20%3F;env_medium:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;samp_size:string%20%3F;source_uvig:source_uvig_enum%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string%20%3F;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum%20%3F;seq_quality_check:string%20%3F;chimera_check:string%20%3F;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;contam_score:string%20%3F;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string%20%3F;pred_genome_type:pred_genome_type_enum%20%3F;pred_genome_struc:pred_genome_struc_enum%20%3F;detec_type:string%20%3F;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F]^-[CoreMiuvig],[Core]^-[CoreMisag],[Core]^-[CoreMimarksS],[Core]^-[CoreMimarksC],[Core]^-[CoreMimag],[Core]^-[CoreMigsVi],[Core]^-[CoreMigsPl],[Core]^-[CoreMigsOrg],[Core]^-[CoreMigsEu],[Core]^-[CoreMigsBa],[Core]^-[CoreMe]) + +## Children + + * [CoreMe](CoreMe.md) - Combinatorial checklist for core with me + * [CoreMigsBa](CoreMigsBa.md) - Combinatorial checklist for core with migs_ba + * [CoreMigsEu](CoreMigsEu.md) - Combinatorial checklist for core with migs_eu + * [CoreMigsOrg](CoreMigsOrg.md) - Combinatorial checklist for core with migs_org + * [CoreMigsPl](CoreMigsPl.md) - Combinatorial checklist for core with migs_pl + * [CoreMigsVi](CoreMigsVi.md) - Combinatorial checklist for core with migs_vi + * [CoreMimag](CoreMimag.md) - Combinatorial checklist for core with mimag + * [CoreMimarksC](CoreMimarksC.md) - Combinatorial checklist for core with mimarks_c + * [CoreMimarksS](CoreMimarksS.md) - Combinatorial checklist for core with mimarks_s + * [CoreMisag](CoreMisag.md) - Combinatorial checklist for core with misag + * [CoreMiuvig](CoreMiuvig.md) - Combinatorial checklist for core with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMe.md b/mixs6/CoreMe.md new file mode 100644 index 00000000..6ade50ce --- /dev/null +++ b/mixs6/CoreMe.md @@ -0,0 +1,403 @@ + +# Class: CoreMe + + +Combinatorial checklist for core with me + +URI: [mixs.vocab:CoreMe](https://w3id.org/mixs/vocab/CoreMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[CoreMe|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Me],[Core]^-[CoreMe],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsBa.md b/mixs6/CoreMigsBa.md new file mode 100644 index 00000000..c8fa9ec9 --- /dev/null +++ b/mixs6/CoreMigsBa.md @@ -0,0 +1,403 @@ + +# Class: CoreMigsBa + + +Combinatorial checklist for core with migs_ba + +URI: [mixs.vocab:CoreMigsBa](https://w3id.org/mixs/vocab/CoreMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[CoreMigsBa|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsBa],[Core]^-[CoreMigsBa],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsEu.md b/mixs6/CoreMigsEu.md new file mode 100644 index 00000000..26ff6cd5 --- /dev/null +++ b/mixs6/CoreMigsEu.md @@ -0,0 +1,403 @@ + +# Class: CoreMigsEu + + +Combinatorial checklist for core with migs_eu + +URI: [mixs.vocab:CoreMigsEu](https://w3id.org/mixs/vocab/CoreMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[CoreMigsEu|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsEu],[Core]^-[CoreMigsEu],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsOrg.md b/mixs6/CoreMigsOrg.md new file mode 100644 index 00000000..228cacfb --- /dev/null +++ b/mixs6/CoreMigsOrg.md @@ -0,0 +1,403 @@ + +# Class: CoreMigsOrg + + +Combinatorial checklist for core with migs_org + +URI: [mixs.vocab:CoreMigsOrg](https://w3id.org/mixs/vocab/CoreMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[CoreMigsOrg|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsOrg],[Core]^-[CoreMigsOrg],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsPl.md b/mixs6/CoreMigsPl.md new file mode 100644 index 00000000..98b195db --- /dev/null +++ b/mixs6/CoreMigsPl.md @@ -0,0 +1,403 @@ + +# Class: CoreMigsPl + + +Combinatorial checklist for core with migs_pl + +URI: [mixs.vocab:CoreMigsPl](https://w3id.org/mixs/vocab/CoreMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[CoreMigsPl|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsPl],[Core]^-[CoreMigsPl],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsVi.md b/mixs6/CoreMigsVi.md new file mode 100644 index 00000000..a2e15080 --- /dev/null +++ b/mixs6/CoreMigsVi.md @@ -0,0 +1,403 @@ + +# Class: CoreMigsVi + + +Combinatorial checklist for core with migs_vi + +URI: [mixs.vocab:CoreMigsVi](https://w3id.org/mixs/vocab/CoreMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[CoreMigsVi|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsVi],[Core]^-[CoreMigsVi],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimag.md b/mixs6/CoreMimag.md new file mode 100644 index 00000000..3f4e8185 --- /dev/null +++ b/mixs6/CoreMimag.md @@ -0,0 +1,403 @@ + +# Class: CoreMimag + + +Combinatorial checklist for core with mimag + +URI: [mixs.vocab:CoreMimag](https://w3id.org/mixs/vocab/CoreMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[CoreMimag|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Mimag],[Core]^-[CoreMimag],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimarksC.md b/mixs6/CoreMimarksC.md new file mode 100644 index 00000000..32fe375b --- /dev/null +++ b/mixs6/CoreMimarksC.md @@ -0,0 +1,403 @@ + +# Class: CoreMimarksC + + +Combinatorial checklist for core with mimarks_c + +URI: [mixs.vocab:CoreMimarksC](https://w3id.org/mixs/vocab/CoreMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[CoreMimarksC|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MimarksC],[Core]^-[CoreMimarksC],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimarksS.md b/mixs6/CoreMimarksS.md new file mode 100644 index 00000000..31d9c705 --- /dev/null +++ b/mixs6/CoreMimarksS.md @@ -0,0 +1,403 @@ + +# Class: CoreMimarksS + + +Combinatorial checklist for core with mimarks_s + +URI: [mixs.vocab:CoreMimarksS](https://w3id.org/mixs/vocab/CoreMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[CoreMimarksS|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MimarksS],[Core]^-[CoreMimarksS],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMisag.md b/mixs6/CoreMisag.md new file mode 100644 index 00000000..4d4c6fae --- /dev/null +++ b/mixs6/CoreMisag.md @@ -0,0 +1,403 @@ + +# Class: CoreMisag + + +Combinatorial checklist for core with misag + +URI: [mixs.vocab:CoreMisag](https://w3id.org/mixs/vocab/CoreMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[CoreMisag|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Misag],[Core]^-[CoreMisag],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMiuvig.md b/mixs6/CoreMiuvig.md new file mode 100644 index 00000000..ac8dda6c --- /dev/null +++ b/mixs6/CoreMiuvig.md @@ -0,0 +1,403 @@ + +# Class: CoreMiuvig + + +Combinatorial checklist for core with miuvig + +URI: [mixs.vocab:CoreMiuvig](https://w3id.org/mixs/vocab/CoreMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[CoreMiuvig|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Miuvig],[Core]^-[CoreMiuvig],[Core]) + +## Parents + + * is_a: [Core](Core.md) - core package + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from core: + + * [adapters](adapters.md) OPT + * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * range: [String](types/String.md) + * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [String](types/String.md) + * Example: 100 meter None + * [annot](annot.md) OPT + * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * range: [String](types/String.md) + * Example: prokka None + * [assembly_name](assembly_name.md) OPT + * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * range: [String](types/String.md) + * Example: HuRef, JCVI_ISG_i3_1.0 None + * [assembly_qual](assembly_qual.md) OPT + * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * range: + * Example: High-quality draft genome None + * [assembly_software](assembly_software.md) OPT + * Description: Tool(s) used for assembly, including version number and parameters + * range: [String](types/String.md) + * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None + * [bin_param](bin_param.md) OPT + * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + * range: + * Example: coverage and kmer None + * [bin_software](bin_software.md) OPT + * Description: Tool(s) used for the extraction of genomes from metagenomic datasets + * range: + * Example: concoct and maxbin None + * [biotic_relationship](biotic_relationship.md) OPT + * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * range: + * Example: free living None + * [chimera_check](chimera_check.md) OPT + * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * range: [String](types/String.md) + * Example: uchime;v4.1;default parameters None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [compl_appr](compl_appr.md) OPT + * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * range: + * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None + * [compl_score](compl_score.md) OPT + * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * range: + * Example: med;60% None + * [compl_software](compl_software.md) OPT + * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + * range: [String](types/String.md) + * Example: checkm None + * [contam_score](contam_score.md) OPT + * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * range: [String](types/String.md) + * Example: 1% None + * [contam_screen_input](contam_screen_input.md) OPT + * Description: The type of sequence data used as input + * range: [String](types/String.md) + * Example: contigs None + * [contam_screen_param](contam_screen_param.md) OPT + * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * range: + * Example: kmer None + * [decontam_software](decontam_software.md) OPT + * Description: Tool(s) used in contamination screening + * range: + * Example: anvi'o None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [detec_type](detec_type.md) OPT + * Description: Type of UViG detection + * range: [String](types/String.md) + * Example: independent sequence (UViG) None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [String](types/String.md) + * Example: 100 meter None + * [encoded_traits](encoded_traits.md) OPT + * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * range: [String](types/String.md) + * Example: beta-lactamase class A None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [env_package](env_package.md) OPT + * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * range: + * Example: soil None + * [estimated_size](estimated_size.md) OPT + * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * range: [String](types/String.md) + * Example: 300000 bp None + * [experimental_factor](experimental_factor.md) OPT + * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: time series design [EFO:EFO_0001779] None + * [extrachrom_elements](extrachrom_elements.md) OPT + * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * range: [String](types/String.md) + * Example: 5 None + * [feat_pred](feat_pred.md) OPT + * Description: Method used to predict UViGs features such as ORFs, integration site, etc. + * range: [String](types/String.md) + * Example: Prodigal;2.6.3;default parameters None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [health_disease_stat](health_disease_stat.md) OPT + * Description: Health or disease status of specific host at time of collection + * range: + * Example: dead None + * [host_pred_appr](host_pred_appr.md) OPT + * Description: Tool or approach used for host prediction + * range: + * Example: CRISPR spacer match None + * [host_pred_est_acc](host_pred_est_acc.md) OPT + * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * range: [String](types/String.md) + * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None + * [host_spec_range](host_spec_range.md) OPT + * Description: The NCBI taxonomy identifier of the specific host if it is known + * range: [String](types/String.md) + * Example: 9606 None + * [investigation_type](investigation_type.md) OPT + * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * range: + * Example: metagenome None + * [isol_growth_condt](isol_growth_condt.md) OPT + * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * range: [String](types/String.md) + * Example: doi: 10.1016/j.syapm.2018.01.009 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lib_layout](lib_layout.md) OPT + * Description: Specify whether to expect single, paired, or other configuration of reads + * range: + * Example: paired None + * [lib_reads_seqd](lib_reads_seqd.md) OPT + * Description: Total number of clones sequenced from the library + * range: [String](types/String.md) + * Example: 20 None + * [lib_screen](lib_screen.md) OPT + * Description: Specific enrichment or screening methods applied before and/or after creating libraries + * range: [String](types/String.md) + * Example: enriched, screened, normalized None + * [lib_size](lib_size.md) OPT + * Description: Total number of clones in the library prepared for the project + * range: [String](types/String.md) + * Example: 50 None + * [lib_vector](lib_vector.md) OPT + * Description: Cloning vector type(s) used in construction of libraries + * range: [String](types/String.md) + * Example: Bacteriophage P1 None + * [mag_cov_software](mag_cov_software.md) OPT + * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * range: + * Example: bbmap None + * [mid](mid.md) OPT + * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: GTGAATAT None + * [nucl_acid_amp](nucl_acid_amp.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * range: [String](types/String.md) + * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None + * [nucl_acid_ext](nucl_acid_ext.md) OPT + * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * range: [String](types/String.md) + * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None + * [num_replicons](num_replicons.md) OPT + * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * range: [String](types/String.md) + * Example: 2 None + * [number_contig](number_contig.md) OPT + * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * range: [String](types/String.md) + * Example: 40 None + * [pathogenicity](pathogenicity.md) OPT + * Description: To what is the entity pathogenic + * range: [String](types/String.md) + * Example: human, animal, plant, fungi, bacteria None + * [pcr_cond](pcr_cond.md) OPT + * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * range: [String](types/String.md) + * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None + * [pcr_primers](pcr_primers.md) OPT + * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * range: [String](types/String.md) + * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None + * [ploidy](ploidy.md) OPT + * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * range: [String](types/String.md) + * Example: allopolyploidy [PATO:0001379] None + * [pred_genome_struc](pred_genome_struc.md) OPT + * Description: Expected structure of the viral genome + * range: + * Example: non-segmented None + * [pred_genome_type](pred_genome_type.md) OPT + * Description: Type of genome predicted for the UViG + * range: + * Example: dsDNA None + * [project_name](project_name.md) OPT + * Description: Name of the project within which the sequencing was organized + * range: [String](types/String.md) + * Example: Forest soil metagenome None + * [propagation](propagation.md) OPT + * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * range: [String](types/String.md) + * Example: lytic None + * [reassembly_bin](reassembly_bin.md) OPT + * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * range: [String](types/String.md) + * Example: no None + * [ref_biomaterial](ref_biomaterial.md) OPT + * Description: Primary publication if isolated before genome publication; otherwise, primary genome report + * range: [String](types/String.md) + * Example: doi:10.1016/j.syapm.2018.01.009 None + * [ref_db](ref_db.md) OPT + * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + * range: [String](types/String.md) + * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None + * [rel_to_oxygen](rel_to_oxygen.md) OPT + * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * range: + * Example: aerobe None + * [samp_collect_device](samp_collect_device.md) OPT + * Description: The method or device employed for collecting the sample + * range: [String](types/String.md) + * Example: environmental swab sampling, biopsy, niskin bottle, push core None + * [samp_mat_process](samp_mat_process.md) OPT + * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * range: [String](types/String.md) + * Example: filtering of seawater, storing samples in ethanol None + * [samp_size](samp_size.md) OPT + * Description: Amount or size of sample (volume, mass or area) that was collected + * range: [String](types/String.md) + * Example: 5 liter None + * [sample_name](sample_name.md) OPT + * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * range: [String](types/String.md) + * Example: None + * [seq_meth](seq_meth.md) OPT + * Description: Sequencing method used; e.g. Sanger, ABI-solid + * range: + * Example: Illumina HiSeq 1500 None + * [seq_quality_check](seq_quality_check.md) OPT + * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * range: [String](types/String.md) + * Example: none None + * [sim_search_meth](sim_search_meth.md) OPT + * Description: Tool used to compare ORFs with database, along with version and cutoffs used + * range: [String](types/String.md) + * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None + * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT + * Description: Method used to free DNA from interior of the cell(s) or particle(s) + * range: + * Example: enzymatic None + * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT + * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * range: [String](types/String.md) + * Example: ambion single cell lysis kit None + * [size_frac](size_frac.md) OPT + * Description: Filtering pore size used in sample preparation + * range: [String](types/String.md) + * Example: 0-0.22 micrometer None + * [sop](sop.md) OPT + * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * range: [String](types/String.md) + * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None + * [sort_tech](sort_tech.md) OPT + * Description: Method used to sort/isolate cells or particles of interest + * range: + * Example: optical manipulation None + * [source_mat_id](source_mat_id.md) OPT + * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * range: [String](types/String.md) + * Example: MPI012345 None + * [source_uvig](source_uvig.md) OPT + * Description: Type of dataset from which the UViG was obtained + * range: + * Example: viral fraction metagenome (virome) None + * [specific_host](specific_host.md) OPT + * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * range: [String](types/String.md) + * Example: 9606 None + * [submitted_to_insdc](submitted_to_insdc.md) OPT + * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * range: [String](types/String.md) + * Example: yes None + * [subspecf_gen_lin](subspecf_gen_lin.md) OPT + * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * range: [String](types/String.md) + * Example: serovar:Newport None + * [target_gene](target_gene.md) OPT + * Description: Targeted gene or locus name for marker gene studies + * range: [String](types/String.md) + * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None + * [target_subfragment](target_subfragment.md) OPT + * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * range: [String](types/String.md) + * Example: V6, V9, ITS None + * [tax_class](tax_class.md) OPT + * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * range: [String](types/String.md) + * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None + * [tax_ident](tax_ident.md) OPT + * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * range: + * Example: other: rpoB gene None + * [trna_ext_software](trna_ext_software.md) OPT + * Description: Tools used for tRNA identification + * range: [String](types/String.md) + * Example: infernal;v2;default parameters None + * [trnas](trnas.md) OPT + * Description: The total number of tRNAs identified from the SAG or MAG + * range: [String](types/String.md) + * Example: 18 None + * [trophic_level](trophic_level.md) OPT + * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * range: + * Example: heterotroph None + * [url](url.md) OPT + * range: [String](types/String.md) + * Example: http://www.earthmicrobiome.org/ None + * [vir_ident_software](vir_ident_software.md) OPT + * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * range: [String](types/String.md) + * Example: VirSorter; 1.0.4; Virome database, category 2 None + * [virus_enrich_appr](virus_enrich_appr.md) OPT + * Description: List of approaches used to enrich the sample for viruses, if any + * range: + * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None + * [votu_class_appr](votu_class_appr.md) OPT + * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * range: [String](types/String.md) + * Example: 95% ANI;85% AF; greedy incremental clustering None + * [votu_db](votu_db.md) OPT + * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * range: [String](types/String.md) + * Example: NCBI Viral RefSeq;83 None + * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT + * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * range: [String](types/String.md) + * Example: blastn;2.6.0+;e-value cutoff: 0.001 None + * [wga_amp_appr](wga_amp_appr.md) OPT + * Description: Method used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: mda based None + * [wga_amp_kit](wga_amp_kit.md) OPT + * Description: Kit used to amplify genomic DNA in preparation for sequencing + * range: [String](types/String.md) + * Example: qiagen repli-g None + * [x_16s_recover](x_16s_recover.md) OPT + * Description: Can a 16S gene be recovered from the submitted SAG or MAG? + * range: [String](types/String.md) + * Example: yes None + * [x_16s_recover_software](x_16s_recover_software.md) OPT + * Description: Tools used for 16S rRNA gene extraction + * range: [String](types/String.md) + * Example: rambl;v2;default parameters None diff --git a/mixs6/Host-associated.md b/mixs6/Host-associated.md new file mode 100644 index 00000000..a107b9f9 --- /dev/null +++ b/mixs6/Host-associated.md @@ -0,0 +1,213 @@ + +# Class: Host-associated + + +host-associated + +URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Host-associatedMiuvig],[Host-associatedMisag],[Host-associatedMimarksS],[Host-associatedMimarksC],[Host-associatedMimag],[Host-associatedMigsVi],[Host-associatedMigsPl],[Host-associatedMigsOrg],[Host-associatedMigsEu],[Host-associatedMigsBa],[Host-associatedMe],[Host-associated|ances_data:string%20%3F;biol_stat:biol_stat_enum%20%3F;genetic_mod:string%20%3F;host_common_name:string%20%3F;samp_capt_status:samp_capt_status_enum%20%3F;samp_dis_stage:string%20%3F;host_taxid:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_life_stage:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;chem_administration:string%20%3F;host_body_habitat:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_length:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_growth_cond:string%20%3F;host_substrate:string%20%3F;host_family_relationship:string%20%3F;host_infra_specific_name:string%20%3F;host_infra_specific_rank:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_dry_mass:string%20%3F;host_blood_press_diast:string%20%3F;host_blood_press_syst:string%20%3F;host_color:string%20%3F;host_shape:string%20%3F;gravidity:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Host-associatedMiuvig],[Host-associated]^-[Host-associatedMisag],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]^-[Host-associatedMimag],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]^-[Host-associatedMe]) + +## Children + + * [Host-associatedMe](Host-associatedMe.md) - Combinatorial checklist for host-associated with me + * [Host-associatedMigsBa](Host-associatedMigsBa.md) - Combinatorial checklist for host-associated with migs_ba + * [Host-associatedMigsEu](Host-associatedMigsEu.md) - Combinatorial checklist for host-associated with migs_eu + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - Combinatorial checklist for host-associated with migs_org + * [Host-associatedMigsPl](Host-associatedMigsPl.md) - Combinatorial checklist for host-associated with migs_pl + * [Host-associatedMigsVi](Host-associatedMigsVi.md) - Combinatorial checklist for host-associated with migs_vi + * [Host-associatedMimag](Host-associatedMimag.md) - Combinatorial checklist for host-associated with mimag + * [Host-associatedMimarksC](Host-associatedMimarksC.md) - Combinatorial checklist for host-associated with mimarks_c + * [Host-associatedMimarksS](Host-associatedMimarksS.md) - Combinatorial checklist for host-associated with mimarks_s + * [Host-associatedMisag](Host-associatedMisag.md) - Combinatorial checklist for host-associated with misag + * [Host-associatedMiuvig](Host-associatedMiuvig.md) - Combinatorial checklist for host-associated with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMe.md b/mixs6/Host-associatedMe.md new file mode 100644 index 00000000..dbc9599a --- /dev/null +++ b/mixs6/Host-associatedMe.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMe + + +Combinatorial checklist for host-associated with me + +URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Host-associatedMe|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Host-associated]^-[Host-associatedMe],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMigsBa.md b/mixs6/Host-associatedMigsBa.md new file mode 100644 index 00000000..dc57b474 --- /dev/null +++ b/mixs6/Host-associatedMigsBa.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMigsBa + + +Combinatorial checklist for host-associated with migs_ba + +URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associatedMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Host-associatedMigsBa|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMigsEu.md b/mixs6/Host-associatedMigsEu.md new file mode 100644 index 00000000..91e06a04 --- /dev/null +++ b/mixs6/Host-associatedMigsEu.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMigsEu + + +Combinatorial checklist for host-associated with migs_eu + +URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associatedMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Host-associatedMigsEu|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMigsOrg.md b/mixs6/Host-associatedMigsOrg.md new file mode 100644 index 00000000..063ba237 --- /dev/null +++ b/mixs6/Host-associatedMigsOrg.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMigsOrg + + +Combinatorial checklist for host-associated with migs_org + +URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associatedMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Host-associatedMigsOrg|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMigsPl.md b/mixs6/Host-associatedMigsPl.md new file mode 100644 index 00000000..aeb1ddef --- /dev/null +++ b/mixs6/Host-associatedMigsPl.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMigsPl + + +Combinatorial checklist for host-associated with migs_pl + +URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associatedMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Host-associatedMigsPl|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMigsVi.md b/mixs6/Host-associatedMigsVi.md new file mode 100644 index 00000000..0cece668 --- /dev/null +++ b/mixs6/Host-associatedMigsVi.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMigsVi + + +Combinatorial checklist for host-associated with migs_vi + +URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associatedMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Host-associatedMigsVi|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMimag.md b/mixs6/Host-associatedMimag.md new file mode 100644 index 00000000..569540b3 --- /dev/null +++ b/mixs6/Host-associatedMimag.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMimag + + +Combinatorial checklist for host-associated with mimag + +URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associatedMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Host-associatedMimag|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Host-associated]^-[Host-associatedMimag],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMimarksC.md b/mixs6/Host-associatedMimarksC.md new file mode 100644 index 00000000..e06f7e49 --- /dev/null +++ b/mixs6/Host-associatedMimarksC.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMimarksC + + +Combinatorial checklist for host-associated with mimarks_c + +URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-associatedMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Host-associatedMimarksC|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMimarksS.md b/mixs6/Host-associatedMimarksS.md new file mode 100644 index 00000000..32088ebe --- /dev/null +++ b/mixs6/Host-associatedMimarksS.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMimarksS + + +Combinatorial checklist for host-associated with mimarks_s + +URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-associatedMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Host-associatedMimarksS|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMisag.md b/mixs6/Host-associatedMisag.md new file mode 100644 index 00000000..abcac9a8 --- /dev/null +++ b/mixs6/Host-associatedMisag.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMisag + + +Combinatorial checklist for host-associated with misag + +URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associatedMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Host-associatedMisag|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Host-associated]^-[Host-associatedMisag],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMiuvig.md b/mixs6/Host-associatedMiuvig.md new file mode 100644 index 00000000..df915e36 --- /dev/null +++ b/mixs6/Host-associatedMiuvig.md @@ -0,0 +1,204 @@ + +# Class: Host-associatedMiuvig + + +Combinatorial checklist for host-associated with miuvig + +URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associatedMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Host-associatedMiuvig|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Host-associated]^-[Host-associatedMiuvig],[Host-associated]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from host-associated: + + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [String](types/String.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-associated.md b/mixs6/Human-associated.md new file mode 100644 index 00000000..a2d7a21d --- /dev/null +++ b/mixs6/Human-associated.md @@ -0,0 +1,229 @@ + +# Class: Human-associated + + +human-associated + +URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-associatedMiuvig],[Human-associatedMisag],[Human-associatedMimarksS],[Human-associatedMimarksC],[Human-associatedMimag],[Human-associatedMigsVi],[Human-associatedMigsPl],[Human-associatedMigsOrg],[Human-associatedMigsEu],[Human-associatedMigsBa],[Human-associatedMe],[Human-associated|host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;smoker:string%20%3F;host_hiv_stat:string%20%3F;drug_usage:drug_usage_enum%20%3F;host_body_mass_index:string%20%3F;diet_last_six_month:string%20%3F;weight_loss_3_month:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;pet_farm_animal:string%20%3F;travel_out_six_month:string%20%3F;twin_sibling:string%20%3F;medic_hist_perform:string%20%3F;study_complt_stat:study_complt_stat_enum%20%3F;pulmonary_disord:string%20%3F;nose_throat_disord:string%20%3F;blood_blood_disord:string%20%3F;host_pulse:string%20%3F;gestation_state:string%20%3F;maternal_health_stat:string%20%3F;foetal_health_stat:string%20%3F;amniotic_fluid_color:string%20%3F;urogenit_tract_disor:string%20%3F;urine_collect_meth:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-associatedMiuvig],[Human-associated]^-[Human-associatedMisag],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]^-[Human-associatedMimag],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]^-[Human-associatedMe]) + +## Children + + * [Human-associatedMe](Human-associatedMe.md) - Combinatorial checklist for human-associated with me + * [Human-associatedMigsBa](Human-associatedMigsBa.md) - Combinatorial checklist for human-associated with migs_ba + * [Human-associatedMigsEu](Human-associatedMigsEu.md) - Combinatorial checklist for human-associated with migs_eu + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - Combinatorial checklist for human-associated with migs_org + * [Human-associatedMigsPl](Human-associatedMigsPl.md) - Combinatorial checklist for human-associated with migs_pl + * [Human-associatedMigsVi](Human-associatedMigsVi.md) - Combinatorial checklist for human-associated with migs_vi + * [Human-associatedMimag](Human-associatedMimag.md) - Combinatorial checklist for human-associated with mimag + * [Human-associatedMimarksC](Human-associatedMimarksC.md) - Combinatorial checklist for human-associated with mimarks_c + * [Human-associatedMimarksS](Human-associatedMimarksS.md) - Combinatorial checklist for human-associated with mimarks_s + * [Human-associatedMisag](Human-associatedMisag.md) - Combinatorial checklist for human-associated with misag + * [Human-associatedMiuvig](Human-associatedMiuvig.md) - Combinatorial checklist for human-associated with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMe.md b/mixs6/Human-associatedMe.md new file mode 100644 index 00000000..f44940f5 --- /dev/null +++ b/mixs6/Human-associatedMe.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMe + + +Combinatorial checklist for human-associated with me + +URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associatedMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-associatedMe|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-associated]^-[Human-associatedMe],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMigsBa.md b/mixs6/Human-associatedMigsBa.md new file mode 100644 index 00000000..520a2585 --- /dev/null +++ b/mixs6/Human-associatedMigsBa.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMigsBa + + +Combinatorial checklist for human-associated with migs_ba + +URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-associatedMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-associatedMigsBa|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMigsEu.md b/mixs6/Human-associatedMigsEu.md new file mode 100644 index 00000000..0c982d86 --- /dev/null +++ b/mixs6/Human-associatedMigsEu.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMigsEu + + +Combinatorial checklist for human-associated with migs_eu + +URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-associatedMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-associatedMigsEu|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMigsOrg.md b/mixs6/Human-associatedMigsOrg.md new file mode 100644 index 00000000..78babe13 --- /dev/null +++ b/mixs6/Human-associatedMigsOrg.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMigsOrg + + +Combinatorial checklist for human-associated with migs_org + +URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-associatedMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-associatedMigsOrg|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMigsPl.md b/mixs6/Human-associatedMigsPl.md new file mode 100644 index 00000000..a887224d --- /dev/null +++ b/mixs6/Human-associatedMigsPl.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMigsPl + + +Combinatorial checklist for human-associated with migs_pl + +URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-associatedMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-associatedMigsPl|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMigsVi.md b/mixs6/Human-associatedMigsVi.md new file mode 100644 index 00000000..03fbe9ea --- /dev/null +++ b/mixs6/Human-associatedMigsVi.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMigsVi + + +Combinatorial checklist for human-associated with migs_vi + +URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-associatedMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-associatedMigsVi|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMimag.md b/mixs6/Human-associatedMimag.md new file mode 100644 index 00000000..0757320c --- /dev/null +++ b/mixs6/Human-associatedMimag.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMimag + + +Combinatorial checklist for human-associated with mimag + +URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associatedMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-associatedMimag|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-associated]^-[Human-associatedMimag],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMimarksC.md b/mixs6/Human-associatedMimarksC.md new file mode 100644 index 00000000..f7d67ec3 --- /dev/null +++ b/mixs6/Human-associatedMimarksC.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMimarksC + + +Combinatorial checklist for human-associated with mimarks_c + +URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-associatedMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-associatedMimarksC|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMimarksS.md b/mixs6/Human-associatedMimarksS.md new file mode 100644 index 00000000..6e169013 --- /dev/null +++ b/mixs6/Human-associatedMimarksS.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMimarksS + + +Combinatorial checklist for human-associated with mimarks_s + +URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-associatedMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-associatedMimarksS|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMisag.md b/mixs6/Human-associatedMisag.md new file mode 100644 index 00000000..ed066b20 --- /dev/null +++ b/mixs6/Human-associatedMisag.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMisag + + +Combinatorial checklist for human-associated with misag + +URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associatedMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-associatedMisag|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-associated]^-[Human-associatedMisag],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-associatedMiuvig.md b/mixs6/Human-associatedMiuvig.md new file mode 100644 index 00000000..76b11e4f --- /dev/null +++ b/mixs6/Human-associatedMiuvig.md @@ -0,0 +1,220 @@ + +# Class: Human-associatedMiuvig + + +Combinatorial checklist for human-associated with miuvig + +URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-associatedMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-associatedMiuvig|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-associated]^-[Human-associatedMiuvig],[Human-associated]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from human-associated: + + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None diff --git a/mixs6/Human-gut.md b/mixs6/Human-gut.md new file mode 100644 index 00000000..5770d8c8 --- /dev/null +++ b/mixs6/Human-gut.md @@ -0,0 +1,169 @@ + +# Class: Human-gut + + +human-gut + +URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-gutMiuvig],[Human-gutMisag],[Human-gutMimarksS],[Human-gutMimarksC],[Human-gutMimag],[Human-gutMigsVi],[Human-gutMigsPl],[Human-gutMigsOrg],[Human-gutMigsEu],[Human-gutMigsBa],[Human-gutMe],[Human-gut|gastrointest_disord:string%20%3F;liver_disord:string%20%3F;special_diet:special_diet_enum%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-gutMiuvig],[Human-gut]^-[Human-gutMisag],[Human-gut]^-[Human-gutMimarksS],[Human-gut]^-[Human-gutMimarksC],[Human-gut]^-[Human-gutMimag],[Human-gut]^-[Human-gutMigsVi],[Human-gut]^-[Human-gutMigsPl],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]^-[Human-gutMigsEu],[Human-gut]^-[Human-gutMigsBa],[Human-gut]^-[Human-gutMe]) + +## Children + + * [Human-gutMe](Human-gutMe.md) - Combinatorial checklist for human-gut with me + * [Human-gutMigsBa](Human-gutMigsBa.md) - Combinatorial checklist for human-gut with migs_ba + * [Human-gutMigsEu](Human-gutMigsEu.md) - Combinatorial checklist for human-gut with migs_eu + * [Human-gutMigsOrg](Human-gutMigsOrg.md) - Combinatorial checklist for human-gut with migs_org + * [Human-gutMigsPl](Human-gutMigsPl.md) - Combinatorial checklist for human-gut with migs_pl + * [Human-gutMigsVi](Human-gutMigsVi.md) - Combinatorial checklist for human-gut with migs_vi + * [Human-gutMimag](Human-gutMimag.md) - Combinatorial checklist for human-gut with mimag + * [Human-gutMimarksC](Human-gutMimarksC.md) - Combinatorial checklist for human-gut with mimarks_c + * [Human-gutMimarksS](Human-gutMimarksS.md) - Combinatorial checklist for human-gut with mimarks_s + * [Human-gutMisag](Human-gutMisag.md) - Combinatorial checklist for human-gut with misag + * [Human-gutMiuvig](Human-gutMiuvig.md) - Combinatorial checklist for human-gut with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMe.md b/mixs6/Human-gutMe.md new file mode 100644 index 00000000..5fa750a8 --- /dev/null +++ b/mixs6/Human-gutMe.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMe + + +Combinatorial checklist for human-gut with me + +URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-gutMe|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-gut]^-[Human-gutMe],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMigsBa.md b/mixs6/Human-gutMigsBa.md new file mode 100644 index 00000000..985d991d --- /dev/null +++ b/mixs6/Human-gutMigsBa.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMigsBa + + +Combinatorial checklist for human-gut with migs_ba + +URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-gutMigsBa|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-gut]^-[Human-gutMigsBa],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMigsEu.md b/mixs6/Human-gutMigsEu.md new file mode 100644 index 00000000..96db2503 --- /dev/null +++ b/mixs6/Human-gutMigsEu.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMigsEu + + +Combinatorial checklist for human-gut with migs_eu + +URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-gutMigsEu|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-gut]^-[Human-gutMigsEu],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMigsOrg.md b/mixs6/Human-gutMigsOrg.md new file mode 100644 index 00000000..1fff7b95 --- /dev/null +++ b/mixs6/Human-gutMigsOrg.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMigsOrg + + +Combinatorial checklist for human-gut with migs_org + +URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-gutMigsOrg|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMigsPl.md b/mixs6/Human-gutMigsPl.md new file mode 100644 index 00000000..0b03d981 --- /dev/null +++ b/mixs6/Human-gutMigsPl.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMigsPl + + +Combinatorial checklist for human-gut with migs_pl + +URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-gutMigsPl|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-gut]^-[Human-gutMigsPl],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMigsVi.md b/mixs6/Human-gutMigsVi.md new file mode 100644 index 00000000..7b6fab31 --- /dev/null +++ b/mixs6/Human-gutMigsVi.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMigsVi + + +Combinatorial checklist for human-gut with migs_vi + +URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-gutMigsVi|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-gut]^-[Human-gutMigsVi],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMimag.md b/mixs6/Human-gutMimag.md new file mode 100644 index 00000000..9fc8df7b --- /dev/null +++ b/mixs6/Human-gutMimag.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMimag + + +Combinatorial checklist for human-gut with mimag + +URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-gutMimag|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-gut]^-[Human-gutMimag],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMimarksC.md b/mixs6/Human-gutMimarksC.md new file mode 100644 index 00000000..e74fba54 --- /dev/null +++ b/mixs6/Human-gutMimarksC.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMimarksC + + +Combinatorial checklist for human-gut with mimarks_c + +URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-gutMimarksC|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-gut]^-[Human-gutMimarksC],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMimarksS.md b/mixs6/Human-gutMimarksS.md new file mode 100644 index 00000000..a760ab33 --- /dev/null +++ b/mixs6/Human-gutMimarksS.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMimarksS + + +Combinatorial checklist for human-gut with mimarks_s + +URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-gutMimarksS|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-gut]^-[Human-gutMimarksS],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMisag.md b/mixs6/Human-gutMisag.md new file mode 100644 index 00000000..f86d9401 --- /dev/null +++ b/mixs6/Human-gutMisag.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMisag + + +Combinatorial checklist for human-gut with misag + +URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-gutMisag|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-gut]^-[Human-gutMisag],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMiuvig.md b/mixs6/Human-gutMiuvig.md new file mode 100644 index 00000000..b89a1b87 --- /dev/null +++ b/mixs6/Human-gutMiuvig.md @@ -0,0 +1,160 @@ + +# Class: Human-gutMiuvig + + +Combinatorial checklist for human-gut with miuvig + +URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-gutMiuvig|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-gut]^-[Human-gutMiuvig],[Human-gut]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from human-gut: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None diff --git a/mixs6/Human-oral.md b/mixs6/Human-oral.md new file mode 100644 index 00000000..80d0deb6 --- /dev/null +++ b/mixs6/Human-oral.md @@ -0,0 +1,165 @@ + +# Class: Human-oral + + +human-oral + +URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-oralMiuvig],[Human-oralMisag],[Human-oralMimarksS],[Human-oralMimarksC],[Human-oralMimag],[Human-oralMigsVi],[Human-oralMigsPl],[Human-oralMigsOrg],[Human-oralMigsEu],[Human-oralMigsBa],[Human-oralMe],[Human-oral|nose_mouth_teeth_throat_disord:string%20%3F;time_last_toothbrush:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-oralMiuvig],[Human-oral]^-[Human-oralMisag],[Human-oral]^-[Human-oralMimarksS],[Human-oral]^-[Human-oralMimarksC],[Human-oral]^-[Human-oralMimag],[Human-oral]^-[Human-oralMigsVi],[Human-oral]^-[Human-oralMigsPl],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]^-[Human-oralMigsEu],[Human-oral]^-[Human-oralMigsBa],[Human-oral]^-[Human-oralMe]) + +## Children + + * [Human-oralMe](Human-oralMe.md) - Combinatorial checklist for human-oral with me + * [Human-oralMigsBa](Human-oralMigsBa.md) - Combinatorial checklist for human-oral with migs_ba + * [Human-oralMigsEu](Human-oralMigsEu.md) - Combinatorial checklist for human-oral with migs_eu + * [Human-oralMigsOrg](Human-oralMigsOrg.md) - Combinatorial checklist for human-oral with migs_org + * [Human-oralMigsPl](Human-oralMigsPl.md) - Combinatorial checklist for human-oral with migs_pl + * [Human-oralMigsVi](Human-oralMigsVi.md) - Combinatorial checklist for human-oral with migs_vi + * [Human-oralMimag](Human-oralMimag.md) - Combinatorial checklist for human-oral with mimag + * [Human-oralMimarksC](Human-oralMimarksC.md) - Combinatorial checklist for human-oral with mimarks_c + * [Human-oralMimarksS](Human-oralMimarksS.md) - Combinatorial checklist for human-oral with mimarks_s + * [Human-oralMisag](Human-oralMisag.md) - Combinatorial checklist for human-oral with misag + * [Human-oralMiuvig](Human-oralMiuvig.md) - Combinatorial checklist for human-oral with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMe.md b/mixs6/Human-oralMe.md new file mode 100644 index 00000000..6f821d81 --- /dev/null +++ b/mixs6/Human-oralMe.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMe + + +Combinatorial checklist for human-oral with me + +URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-oralMe|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-oral]^-[Human-oralMe],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMigsBa.md b/mixs6/Human-oralMigsBa.md new file mode 100644 index 00000000..61bf01c9 --- /dev/null +++ b/mixs6/Human-oralMigsBa.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMigsBa + + +Combinatorial checklist for human-oral with migs_ba + +URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-oralMigsBa|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-oral]^-[Human-oralMigsBa],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMigsEu.md b/mixs6/Human-oralMigsEu.md new file mode 100644 index 00000000..edffa206 --- /dev/null +++ b/mixs6/Human-oralMigsEu.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMigsEu + + +Combinatorial checklist for human-oral with migs_eu + +URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-oralMigsEu|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-oral]^-[Human-oralMigsEu],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMigsOrg.md b/mixs6/Human-oralMigsOrg.md new file mode 100644 index 00000000..7f07e232 --- /dev/null +++ b/mixs6/Human-oralMigsOrg.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMigsOrg + + +Combinatorial checklist for human-oral with migs_org + +URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-oralMigsOrg|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMigsPl.md b/mixs6/Human-oralMigsPl.md new file mode 100644 index 00000000..a7f22b21 --- /dev/null +++ b/mixs6/Human-oralMigsPl.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMigsPl + + +Combinatorial checklist for human-oral with migs_pl + +URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-oralMigsPl|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-oral]^-[Human-oralMigsPl],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMigsVi.md b/mixs6/Human-oralMigsVi.md new file mode 100644 index 00000000..8c18d896 --- /dev/null +++ b/mixs6/Human-oralMigsVi.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMigsVi + + +Combinatorial checklist for human-oral with migs_vi + +URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-oralMigsVi|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-oral]^-[Human-oralMigsVi],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMimag.md b/mixs6/Human-oralMimag.md new file mode 100644 index 00000000..ba3ca9ab --- /dev/null +++ b/mixs6/Human-oralMimag.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMimag + + +Combinatorial checklist for human-oral with mimag + +URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-oralMimag|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-oral]^-[Human-oralMimag],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMimarksC.md b/mixs6/Human-oralMimarksC.md new file mode 100644 index 00000000..e6157f95 --- /dev/null +++ b/mixs6/Human-oralMimarksC.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMimarksC + + +Combinatorial checklist for human-oral with mimarks_c + +URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-oralMimarksC|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-oral]^-[Human-oralMimarksC],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMimarksS.md b/mixs6/Human-oralMimarksS.md new file mode 100644 index 00000000..911d4fc6 --- /dev/null +++ b/mixs6/Human-oralMimarksS.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMimarksS + + +Combinatorial checklist for human-oral with mimarks_s + +URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-oralMimarksS|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-oral]^-[Human-oralMimarksS],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMisag.md b/mixs6/Human-oralMisag.md new file mode 100644 index 00000000..7f71fd62 --- /dev/null +++ b/mixs6/Human-oralMisag.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMisag + + +Combinatorial checklist for human-oral with misag + +URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-oralMisag|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-oral]^-[Human-oralMisag],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-oralMiuvig.md b/mixs6/Human-oralMiuvig.md new file mode 100644 index 00000000..d2eabedc --- /dev/null +++ b/mixs6/Human-oralMiuvig.md @@ -0,0 +1,156 @@ + +# Class: Human-oralMiuvig + + +Combinatorial checklist for human-oral with miuvig + +URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-oralMiuvig|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-oral]^-[Human-oralMiuvig],[Human-oral]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from human-oral: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None diff --git a/mixs6/Human-skin.md b/mixs6/Human-skin.md new file mode 100644 index 00000000..43f170f0 --- /dev/null +++ b/mixs6/Human-skin.md @@ -0,0 +1,169 @@ + +# Class: Human-skin + + +human-skin + +URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-skinMiuvig],[Human-skinMisag],[Human-skinMimarksS],[Human-skinMimarksC],[Human-skinMimag],[Human-skinMigsVi],[Human-skinMigsPl],[Human-skinMigsOrg],[Human-skinMigsEu],[Human-skinMigsBa],[Human-skinMe],[Human-skin|dermatology_disord:string%20%3F;time_since_last_wash:string%20%3F;dominant_hand:dominant_hand_enum%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-skinMiuvig],[Human-skin]^-[Human-skinMisag],[Human-skin]^-[Human-skinMimarksS],[Human-skin]^-[Human-skinMimarksC],[Human-skin]^-[Human-skinMimag],[Human-skin]^-[Human-skinMigsVi],[Human-skin]^-[Human-skinMigsPl],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]^-[Human-skinMigsEu],[Human-skin]^-[Human-skinMigsBa],[Human-skin]^-[Human-skinMe]) + +## Children + + * [Human-skinMe](Human-skinMe.md) - Combinatorial checklist for human-skin with me + * [Human-skinMigsBa](Human-skinMigsBa.md) - Combinatorial checklist for human-skin with migs_ba + * [Human-skinMigsEu](Human-skinMigsEu.md) - Combinatorial checklist for human-skin with migs_eu + * [Human-skinMigsOrg](Human-skinMigsOrg.md) - Combinatorial checklist for human-skin with migs_org + * [Human-skinMigsPl](Human-skinMigsPl.md) - Combinatorial checklist for human-skin with migs_pl + * [Human-skinMigsVi](Human-skinMigsVi.md) - Combinatorial checklist for human-skin with migs_vi + * [Human-skinMimag](Human-skinMimag.md) - Combinatorial checklist for human-skin with mimag + * [Human-skinMimarksC](Human-skinMimarksC.md) - Combinatorial checklist for human-skin with mimarks_c + * [Human-skinMimarksS](Human-skinMimarksS.md) - Combinatorial checklist for human-skin with mimarks_s + * [Human-skinMisag](Human-skinMisag.md) - Combinatorial checklist for human-skin with misag + * [Human-skinMiuvig](Human-skinMiuvig.md) - Combinatorial checklist for human-skin with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMe.md b/mixs6/Human-skinMe.md new file mode 100644 index 00000000..c33dd8b3 --- /dev/null +++ b/mixs6/Human-skinMe.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMe + + +Combinatorial checklist for human-skin with me + +URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-skinMe|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-skin]^-[Human-skinMe],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMigsBa.md b/mixs6/Human-skinMigsBa.md new file mode 100644 index 00000000..f96bc46c --- /dev/null +++ b/mixs6/Human-skinMigsBa.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMigsBa + + +Combinatorial checklist for human-skin with migs_ba + +URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-skinMigsBa|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-skin]^-[Human-skinMigsBa],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMigsEu.md b/mixs6/Human-skinMigsEu.md new file mode 100644 index 00000000..dc67a32c --- /dev/null +++ b/mixs6/Human-skinMigsEu.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMigsEu + + +Combinatorial checklist for human-skin with migs_eu + +URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-skinMigsEu|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-skin]^-[Human-skinMigsEu],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMigsOrg.md b/mixs6/Human-skinMigsOrg.md new file mode 100644 index 00000000..9df122d4 --- /dev/null +++ b/mixs6/Human-skinMigsOrg.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMigsOrg + + +Combinatorial checklist for human-skin with migs_org + +URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-skinMigsOrg|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMigsPl.md b/mixs6/Human-skinMigsPl.md new file mode 100644 index 00000000..7eb286e0 --- /dev/null +++ b/mixs6/Human-skinMigsPl.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMigsPl + + +Combinatorial checklist for human-skin with migs_pl + +URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-skinMigsPl|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-skin]^-[Human-skinMigsPl],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMigsVi.md b/mixs6/Human-skinMigsVi.md new file mode 100644 index 00000000..6ad8768c --- /dev/null +++ b/mixs6/Human-skinMigsVi.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMigsVi + + +Combinatorial checklist for human-skin with migs_vi + +URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-skinMigsVi|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-skin]^-[Human-skinMigsVi],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMimag.md b/mixs6/Human-skinMimag.md new file mode 100644 index 00000000..2b7c3fb8 --- /dev/null +++ b/mixs6/Human-skinMimag.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMimag + + +Combinatorial checklist for human-skin with mimag + +URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-skinMimag|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-skin]^-[Human-skinMimag],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMimarksC.md b/mixs6/Human-skinMimarksC.md new file mode 100644 index 00000000..99a68d5e --- /dev/null +++ b/mixs6/Human-skinMimarksC.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMimarksC + + +Combinatorial checklist for human-skin with mimarks_c + +URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-skinMimarksC|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-skin]^-[Human-skinMimarksC],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMimarksS.md b/mixs6/Human-skinMimarksS.md new file mode 100644 index 00000000..fe708229 --- /dev/null +++ b/mixs6/Human-skinMimarksS.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMimarksS + + +Combinatorial checklist for human-skin with mimarks_s + +URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-skinMimarksS|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-skin]^-[Human-skinMimarksS],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMisag.md b/mixs6/Human-skinMisag.md new file mode 100644 index 00000000..0099bc06 --- /dev/null +++ b/mixs6/Human-skinMisag.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMisag + + +Combinatorial checklist for human-skin with misag + +URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-skinMisag|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-skin]^-[Human-skinMisag],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-skinMiuvig.md b/mixs6/Human-skinMiuvig.md new file mode 100644 index 00000000..dde7af07 --- /dev/null +++ b/mixs6/Human-skinMiuvig.md @@ -0,0 +1,160 @@ + +# Class: Human-skinMiuvig + + +Combinatorial checklist for human-skin with miuvig + +URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-skinMiuvig|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-skin]^-[Human-skinMiuvig],[Human-skin]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from human-skin: + + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None diff --git a/mixs6/Human-vaginal.md b/mixs6/Human-vaginal.md new file mode 100644 index 00000000..58e4bc26 --- /dev/null +++ b/mixs6/Human-vaginal.md @@ -0,0 +1,197 @@ + +# Class: Human-vaginal + + +human-vaginal + +URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-vaginalMiuvig],[Human-vaginalMisag],[Human-vaginalMimarksS],[Human-vaginalMimarksC],[Human-vaginalMimag],[Human-vaginalMigsVi],[Human-vaginalMigsPl],[Human-vaginalMigsOrg],[Human-vaginalMigsEu],[Human-vaginalMigsBa],[Human-vaginalMe],[Human-vaginal|menarche:string%20%3F;sexual_act:string%20%3F;pregnancy:string%20%3F;douche:string%20%3F;birth_control:string%20%3F;menopause:string%20%3F;hrt:string%20%3F;hysterectomy:string%20%3F;gynecologic_disord:string%20%3F;urogenit_disord:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_loc:string%20%3F;samp_store_dur:string%20%3F;misc_param:string%20%3F]^-[Human-vaginalMiuvig],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]^-[Human-vaginalMe]) + +## Children + + * [Human-vaginalMe](Human-vaginalMe.md) - Combinatorial checklist for human-vaginal with me + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - Combinatorial checklist for human-vaginal with migs_ba + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - Combinatorial checklist for human-vaginal with migs_eu + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - Combinatorial checklist for human-vaginal with migs_org + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - Combinatorial checklist for human-vaginal with migs_pl + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - Combinatorial checklist for human-vaginal with migs_vi + * [Human-vaginalMimag](Human-vaginalMimag.md) - Combinatorial checklist for human-vaginal with mimag + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - Combinatorial checklist for human-vaginal with mimarks_c + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - Combinatorial checklist for human-vaginal with mimarks_s + * [Human-vaginalMisag](Human-vaginalMisag.md) - Combinatorial checklist for human-vaginal with misag + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) - Combinatorial checklist for human-vaginal with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMe.md b/mixs6/Human-vaginalMe.md new file mode 100644 index 00000000..eaf2ac89 --- /dev/null +++ b/mixs6/Human-vaginalMe.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMe + + +Combinatorial checklist for human-vaginal with me + +URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-vaginalMe|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-vaginal]^-[Human-vaginalMe],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMigsBa.md b/mixs6/Human-vaginalMigsBa.md new file mode 100644 index 00000000..d6c948ca --- /dev/null +++ b/mixs6/Human-vaginalMigsBa.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMigsBa + + +Combinatorial checklist for human-vaginal with migs_ba + +URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-vaginalMigsBa|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMigsEu.md b/mixs6/Human-vaginalMigsEu.md new file mode 100644 index 00000000..a488e056 --- /dev/null +++ b/mixs6/Human-vaginalMigsEu.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMigsEu + + +Combinatorial checklist for human-vaginal with migs_eu + +URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-vaginalMigsEu|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMigsOrg.md b/mixs6/Human-vaginalMigsOrg.md new file mode 100644 index 00000000..fa48b833 --- /dev/null +++ b/mixs6/Human-vaginalMigsOrg.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMigsOrg + + +Combinatorial checklist for human-vaginal with migs_org + +URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginalMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-vaginalMigsOrg|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMigsPl.md b/mixs6/Human-vaginalMigsPl.md new file mode 100644 index 00000000..31100692 --- /dev/null +++ b/mixs6/Human-vaginalMigsPl.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMigsPl + + +Combinatorial checklist for human-vaginal with migs_pl + +URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-vaginalMigsPl|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMigsVi.md b/mixs6/Human-vaginalMigsVi.md new file mode 100644 index 00000000..52ab6228 --- /dev/null +++ b/mixs6/Human-vaginalMigsVi.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMigsVi + + +Combinatorial checklist for human-vaginal with migs_vi + +URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-vaginalMigsVi|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMimag.md b/mixs6/Human-vaginalMimag.md new file mode 100644 index 00000000..b162860b --- /dev/null +++ b/mixs6/Human-vaginalMimag.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMimag + + +Combinatorial checklist for human-vaginal with mimag + +URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-vaginalMimag|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMimarksC.md b/mixs6/Human-vaginalMimarksC.md new file mode 100644 index 00000000..5ca86e03 --- /dev/null +++ b/mixs6/Human-vaginalMimarksC.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMimarksC + + +Combinatorial checklist for human-vaginal with mimarks_c + +URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vaginalMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-vaginalMimarksC|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMimarksS.md b/mixs6/Human-vaginalMimarksS.md new file mode 100644 index 00000000..75341ab1 --- /dev/null +++ b/mixs6/Human-vaginalMimarksS.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMimarksS + + +Combinatorial checklist for human-vaginal with mimarks_s + +URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vaginalMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-vaginalMimarksS|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMisag.md b/mixs6/Human-vaginalMisag.md new file mode 100644 index 00000000..46b09f83 --- /dev/null +++ b/mixs6/Human-vaginalMisag.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMisag + + +Combinatorial checklist for human-vaginal with misag + +URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-vaginalMisag|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Human-vaginalMiuvig.md b/mixs6/Human-vaginalMiuvig.md new file mode 100644 index 00000000..78cad60b --- /dev/null +++ b/mixs6/Human-vaginalMiuvig.md @@ -0,0 +1,188 @@ + +# Class: Human-vaginalMiuvig + + +Combinatorial checklist for human-vaginal with miuvig + +URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-vaginalMiuvig|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-vaginal]^-[Human-vaginalMiuvig],[Human-vaginal]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from human-vaginal: + + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [String](types/String.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [String](types/String.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [String](types/String.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-cores.md b/mixs6/HydrocarbonResources-cores.md new file mode 100644 index 00000000..a110479f --- /dev/null +++ b/mixs6/HydrocarbonResources-cores.md @@ -0,0 +1,349 @@ + +# Class: HydrocarbonResources-cores + + +hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/HydrocarbonResources-cores) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-coresMisag],[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-coresMimag],[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-coresMe],[HydrocarbonResources-cores|hcr:hcr_enum%20%3F;hc_produced:hc_produced_enum%20%3F;basin:string%20%3F;field:string%20%3F;reservoir:string%20%3F;hcr_temp:string%20%3F;tvdss_of_hcr_temp:string%20%3F;hcr_pressure:string%20%3F;tvdss_of_hcr_pressure:string%20%3F;permeability:string%20%3F;porosity:string%20%3F;lithology:lithology_enum%20%3F;depos_env:depos_env_enum%20%3F;hcr_geol_age:hcr_geol_age_enum%20%3F;owc_tvdss:string%20%3F;hcr_fw_salinity:string%20%3F;sulfate_fw:string%20%3F;vfa_fw:string%20%3F;sr_kerog_type:sr_kerog_type_enum%20%3F;sr_lithology:sr_lithology_enum%20%3F;sr_dep_env:sr_dep_env_enum%20%3F;sr_geol_age:sr_geol_age_enum%20%3F;samp_well_name:string%20%3F;win:string%20%3F;samp_type:samp_type_enum%20%3F;samp_subtype:samp_subtype_enum%20%3F;temp:string%20%3F;pressure:string%20%3F;samp_tvdss:string%20%3F;samp_md:samp_md_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;samp_transport_cond:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_vol_we_dna_ext:string%20%3F;organism_count:organism_count_enum%20%3F;organism_count_qpcr_info:string%20%3F;ph:string%20%3F;samp_salinity:string%20%3F;alkalinity:string%20%3F;alkalinity_method:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;tot_sulfur:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;ammonium:string%20%3F;tot_nitro:string%20%3F;diss_iron:string%20%3F;sodium:string%20%3F;chloride:string%20%3F;potassium:string%20%3F;magnesium:string%20%3F;calcium:string%20%3F;tot_iron:string%20%3F;diss_org_carb:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_phosp:string%20%3F;tot_phosp:string%20%3F;suspend_solids:string%20%3F;density:string%20%3F;diss_carb_dioxide:string%20%3F;diss_oxygen_fluid:string%20%3F;vfa:string%20%3F;benzene:string%20%3F;toluene:string%20%3F;ethylbenzene:string%20%3F;xylene:string%20%3F;api:string%20%3F;tan:string%20%3F;viscosity:string%20%3F;pour_point:string%20%3F;saturates_pc:string%20%3F;aromatics_pc:string%20%3F;resins_pc:string%20%3F;asphaltenes_pc:string%20%3F;misc_param:string%20%3F;additional_info:string%20%3F]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe]) + +## Children + + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - Combinatorial checklist for hydrocarbon resources-cores with me + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_ba + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_eu + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_org + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_pl + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_vi + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - Combinatorial checklist for hydrocarbon resources-cores with mimag + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_c + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_s + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - Combinatorial checklist for hydrocarbon resources-cores with misag + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) - Combinatorial checklist for hydrocarbon resources-cores with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMe.md b/mixs6/HydrocarbonResources-coresMe.md new file mode 100644 index 00000000..ae868b8a --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMe.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMe + + +Combinatorial checklist for hydrocarbon resources-cores with me + +URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[HydrocarbonResources-coresMe|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMigsBa.md b/mixs6/HydrocarbonResources-coresMigsBa.md new file mode 100644 index 00000000..b6c618af --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsBa.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMigsBa + + +Combinatorial checklist for hydrocarbon resources-cores with migs_ba + +URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[HydrocarbonResources-coresMigsBa|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMigsEu.md b/mixs6/HydrocarbonResources-coresMigsEu.md new file mode 100644 index 00000000..0f016aff --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsEu.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMigsEu + + +Combinatorial checklist for hydrocarbon resources-cores with migs_eu + +URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[HydrocarbonResources-coresMigsEu|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMigsOrg.md b/mixs6/HydrocarbonResources-coresMigsOrg.md new file mode 100644 index 00000000..2fe36db2 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsOrg.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMigsOrg + + +Combinatorial checklist for hydrocarbon resources-cores with migs_org + +URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[HydrocarbonResources-coresMigsOrg|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMigsPl.md b/mixs6/HydrocarbonResources-coresMigsPl.md new file mode 100644 index 00000000..383dee09 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsPl.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMigsPl + + +Combinatorial checklist for hydrocarbon resources-cores with migs_pl + +URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[HydrocarbonResources-coresMigsPl|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMigsVi.md b/mixs6/HydrocarbonResources-coresMigsVi.md new file mode 100644 index 00000000..cb25267f --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMigsVi.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMigsVi + + +Combinatorial checklist for hydrocarbon resources-cores with migs_vi + +URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[HydrocarbonResources-coresMigsVi|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMimag.md b/mixs6/HydrocarbonResources-coresMimag.md new file mode 100644 index 00000000..f23986e1 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMimag.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMimag + + +Combinatorial checklist for hydrocarbon resources-cores with mimag + +URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[HydrocarbonResources-coresMimag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMimarksC.md b/mixs6/HydrocarbonResources-coresMimarksC.md new file mode 100644 index 00000000..f99e8687 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMimarksC.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMimarksC + + +Combinatorial checklist for hydrocarbon resources-cores with mimarks_c + +URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[HydrocarbonResources-coresMimarksC|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMimarksS.md b/mixs6/HydrocarbonResources-coresMimarksS.md new file mode 100644 index 00000000..521bcae5 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMimarksS.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMimarksS + + +Combinatorial checklist for hydrocarbon resources-cores with mimarks_s + +URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[HydrocarbonResources-coresMimarksS|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMisag.md b/mixs6/HydrocarbonResources-coresMisag.md new file mode 100644 index 00000000..16413e68 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMisag.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMisag + + +Combinatorial checklist for hydrocarbon resources-cores with misag + +URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[HydrocarbonResources-coresMisag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-coresMiuvig.md b/mixs6/HydrocarbonResources-coresMiuvig.md new file mode 100644 index 00000000..836030d7 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMiuvig.md @@ -0,0 +1,340 @@ + +# Class: HydrocarbonResources-coresMiuvig + + +Combinatorial checklist for hydrocarbon resources-cores with miuvig + +URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[HydrocarbonResources-coresMiuvig|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabs.md b/mixs6/HydrocarbonResources-fluidsSwabs.md new file mode 100644 index 00000000..1c5414f0 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabs.md @@ -0,0 +1,369 @@ + +# Class: HydrocarbonResources-fluidsSwabs + + +hydrocarbon resources-fluids/swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabs) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs|hcr:hcr_enum%20%3F;hc_produced:hc_produced_enum%20%3F;basin:string%20%3F;field:string%20%3F;reservoir:string%20%3F;hcr_temp:string%20%3F;tvdss_of_hcr_temp:string%20%3F;hcr_pressure:string%20%3F;tvdss_of_hcr_pressure:string%20%3F;lithology:lithology_enum%20%3F;depos_env:depos_env_enum%20%3F;hcr_geol_age:hcr_geol_age_enum%20%3F;hcr_fw_salinity:string%20%3F;sulfate_fw:string%20%3F;vfa_fw:string%20%3F;prod_start_date:string%20%3F;prod_rate:string%20%3F;water_production_rate:string%20%3F;water_cut:string%20%3F;iwf:string%20%3F;add_recov_method:add_recov_method_enum%20%3F;iw_bt_date_well:string%20%3F;biocide:string%20%3F;biocide_admin_method:string%20%3F;chem_treatment:string%20%3F;chem_treatment_method:string%20%3F;samp_loc_corr_rate:string%20%3F;samp_well_name:string%20%3F;win:string%20%3F;samp_type:samp_type_enum%20%3F;samp_subtype:samp_subtype_enum%20%3F;samp_collection_point:samp_collection_point_enum%20%3F;temp:string%20%3F;pressure:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;samp_preserv:string%20%3F;samp_transport_cond:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_vol_we_dna_ext:string%20%3F;organism_count:organism_count_enum%20%3F;organism_count_qpcr_info:string%20%3F;ph:string%20%3F;samp_salinity:string%20%3F;alkalinity:string%20%3F;alkalinity_method:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;tot_sulfur:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;ammonium:string%20%3F;tot_nitro:string%20%3F;diss_iron:string%20%3F;sodium:string%20%3F;chloride:string%20%3F;potassium:string%20%3F;magnesium:string%20%3F;calcium:string%20%3F;tot_iron:string%20%3F;diss_org_carb:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_phosp:string%20%3F;tot_phosp:string%20%3F;suspend_solids:string%20%3F;density:string%20%3F;diss_carb_dioxide:string%20%3F;diss_oxygen_fluid:string%20%3F;vfa:string%20%3F;benzene:string%20%3F;toluene:string%20%3F;ethylbenzene:string%20%3F;xylene:string%20%3F;api:string%20%3F;tan:string%20%3F;viscosity:string%20%3F;pour_point:string%20%3F;saturates_pc:string%20%3F;aromatics_pc:string%20%3F;resins_pc:string%20%3F;asphaltenes_pc:string%20%3F;misc_param:string%20%3F;additional_info:string%20%3F]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe]) + +## Children + + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with me + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMe.md b/mixs6/HydrocarbonResources-fluidsSwabsMe.md new file mode 100644 index 00000000..da9af04e --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMe.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMe + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with me + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[HydrocarbonResources-fluidsSwabsMe|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md new file mode 100644 index 00000000..220f2ac8 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMigsBa + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md new file mode 100644 index 00000000..f48329b8 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMigsEu + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md new file mode 100644 index 00000000..abc25b2f --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMigsOrg + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md new file mode 100644 index 00000000..f59aa331 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMigsPl + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md new file mode 100644 index 00000000..6fc7cbf2 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMigsVi + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md new file mode 100644 index 00000000..3a5c223a --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMimag + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[HydrocarbonResources-fluidsSwabsMimag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md new file mode 100644 index 00000000..ea23f581 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMimarksC + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md new file mode 100644 index 00000000..719b8571 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMimarksS + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md new file mode 100644 index 00000000..fe6519d3 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMisag + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[HydrocarbonResources-fluidsSwabsMisag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md new file mode 100644 index 00000000..cd2dcc74 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md @@ -0,0 +1,360 @@ + +# Class: HydrocarbonResources-fluidsSwabsMiuvig + + +Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) + * range: [String](types/String.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [String](types/String.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [String](types/String.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [String](types/String.md) + * Example: None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [String](types/String.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [String](types/String.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [String](types/String.md) + * Example: None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [String](types/String.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [String](types/String.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [String](types/String.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [String](types/String.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [String](types/String.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [String](types/String.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [String](types/String.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Me.md b/mixs6/Me.md new file mode 100644 index 00000000..4d7a762e --- /dev/null +++ b/mixs6/Me.md @@ -0,0 +1,37 @@ + +# Class: Me + + +me Checklist + +URI: [mixs.vocab:Me](https://w3id.org/mixs/vocab/Me) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe]uses%20-.->[Me],[WastewaterSludgeMe]uses%20-.->[Me],[SoilMe]uses%20-.->[Me],[SedimentMe]uses%20-.->[Me],[Plant-associatedMe]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironmentMe]uses%20-.->[Me],[MicrobialMatBiofilmMe]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabsMe]uses%20-.->[Me],[HydrocarbonResources-coresMe]uses%20-.->[Me],[Human-vaginalMe]uses%20-.->[Me],[Human-skinMe]uses%20-.->[Me],[Human-oralMe]uses%20-.->[Me],[Human-gutMe]uses%20-.->[Me],[Human-associatedMe]uses%20-.->[Me],[Host-associatedMe]uses%20-.->[Me],[CoreMe]uses%20-.->[Me],[BuiltEnvironmentMe]uses%20-.->[Me],[AirMe]uses%20-.->[Me],[WaterMe],[WastewaterSludgeMe],[SoilMe],[SedimentMe],[Plant-associatedMe],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MicrobialMatBiofilmMe],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-coresMe],[Human-vaginalMe],[Human-skinMe],[Human-oralMe],[Human-gutMe],[Human-associatedMe],[Host-associatedMe],[CoreMe],[BuiltEnvironmentMe],[AirMe]) + +## Mixin for + + * [AirMe](AirMe.md) (mixin) - Combinatorial checklist for air with me + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) (mixin) - Combinatorial checklist for built environment with me + * [CoreMe](CoreMe.md) (mixin) - Combinatorial checklist for core with me + * [Host-associatedMe](Host-associatedMe.md) (mixin) - Combinatorial checklist for host-associated with me + * [Human-associatedMe](Human-associatedMe.md) (mixin) - Combinatorial checklist for human-associated with me + * [Human-gutMe](Human-gutMe.md) (mixin) - Combinatorial checklist for human-gut with me + * [Human-oralMe](Human-oralMe.md) (mixin) - Combinatorial checklist for human-oral with me + * [Human-skinMe](Human-skinMe.md) (mixin) - Combinatorial checklist for human-skin with me + * [Human-vaginalMe](Human-vaginalMe.md) (mixin) - Combinatorial checklist for human-vaginal with me + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with me + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with me + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with me + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with me + * [Plant-associatedMe](Plant-associatedMe.md) (mixin) - Combinatorial checklist for plant-associated with me + * [SedimentMe](SedimentMe.md) (mixin) - Combinatorial checklist for sediment with me + * [SoilMe](SoilMe.md) (mixin) - Combinatorial checklist for soil with me + * [WastewaterSludgeMe](WastewaterSludgeMe.md) (mixin) - Combinatorial checklist for wastewater_sludge with me + * [WaterMe](WaterMe.md) (mixin) - Combinatorial checklist for water with me + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MicrobialMatBiofilm.md b/mixs6/MicrobialMatBiofilm.md new file mode 100644 index 00000000..46bceaed --- /dev/null +++ b/mixs6/MicrobialMatBiofilm.md @@ -0,0 +1,273 @@ + +# Class: MicrobialMatBiofilm + + +microbial mat/biofilm + +URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBiofilm) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilmMisag],[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilmMimag],[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilmMe],[MicrobialMatBiofilm|alkalinity:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;bacteria_carb_prod:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;glucosidase_act:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;part_org_carb:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;tot_carb:string%20%3F;tot_nitro_content:string%20%3F;tot_org_carb:string%20%3F;turbidity:string%20%3F;water_content:string%20%3F]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe]) + +## Children + + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - Combinatorial checklist for microbial mat_biofilm with me + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - Combinatorial checklist for microbial mat_biofilm with migs_ba + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - Combinatorial checklist for microbial mat_biofilm with migs_eu + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - Combinatorial checklist for microbial mat_biofilm with migs_org + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - Combinatorial checklist for microbial mat_biofilm with migs_pl + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - Combinatorial checklist for microbial mat_biofilm with migs_vi + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - Combinatorial checklist for microbial mat_biofilm with mimag + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_c + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_s + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - Combinatorial checklist for microbial mat_biofilm with misag + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) - Combinatorial checklist for microbial mat_biofilm with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMe.md b/mixs6/MicrobialMatBiofilmMe.md new file mode 100644 index 00000000..2a70f29c --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMe.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMe + + +Combinatorial checklist for microbial mat_biofilm with me + +URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MicrobialMatBiofilmMe|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Me],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe],[MicrobialMatBiofilm],[Me]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMigsBa.md b/mixs6/MicrobialMatBiofilmMigsBa.md new file mode 100644 index 00000000..71e56501 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsBa.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMigsBa + + +Combinatorial checklist for microbial mat_biofilm with migs_ba + +URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[MicrobialMatBiofilmMigsBa|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMigsEu.md b/mixs6/MicrobialMatBiofilmMigsEu.md new file mode 100644 index 00000000..ac85c75d --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsEu.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMigsEu + + +Combinatorial checklist for microbial mat_biofilm with migs_eu + +URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[MicrobialMatBiofilmMigsEu|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMigsOrg.md b/mixs6/MicrobialMatBiofilmMigsOrg.md new file mode 100644 index 00000000..23e637d0 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsOrg.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMigsOrg + + +Combinatorial checklist for microbial mat_biofilm with migs_org + +URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[MicrobialMatBiofilmMigsOrg|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMigsPl.md b/mixs6/MicrobialMatBiofilmMigsPl.md new file mode 100644 index 00000000..71e8c22e --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsPl.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMigsPl + + +Combinatorial checklist for microbial mat_biofilm with migs_pl + +URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[MicrobialMatBiofilmMigsPl|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMigsVi.md b/mixs6/MicrobialMatBiofilmMigsVi.md new file mode 100644 index 00000000..b3cffdd9 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMigsVi.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMigsVi + + +Combinatorial checklist for microbial mat_biofilm with migs_vi + +URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[MicrobialMatBiofilmMigsVi|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMimag.md b/mixs6/MicrobialMatBiofilmMimag.md new file mode 100644 index 00000000..e3c05a38 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMimag.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMimag + + +Combinatorial checklist for microbial mat_biofilm with mimag + +URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[MicrobialMatBiofilmMimag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Mimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMimarksC.md b/mixs6/MicrobialMatBiofilmMimarksC.md new file mode 100644 index 00000000..96c7872b --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMimarksC.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMimarksC + + +Combinatorial checklist for microbial mat_biofilm with mimarks_c + +URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[MicrobialMatBiofilmMimarksC|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMimarksS.md b/mixs6/MicrobialMatBiofilmMimarksS.md new file mode 100644 index 00000000..e6d8f0ab --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMimarksS.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMimarksS + + +Combinatorial checklist for microbial mat_biofilm with mimarks_s + +URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[MicrobialMatBiofilmMimarksS|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMisag.md b/mixs6/MicrobialMatBiofilmMisag.md new file mode 100644 index 00000000..aa336139 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMisag.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMisag + + +Combinatorial checklist for microbial mat_biofilm with misag + +URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[MicrobialMatBiofilmMisag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Misag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MicrobialMatBiofilmMiuvig.md b/mixs6/MicrobialMatBiofilmMiuvig.md new file mode 100644 index 00000000..f2909401 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMiuvig.md @@ -0,0 +1,264 @@ + +# Class: MicrobialMatBiofilmMiuvig + + +Combinatorial checklist for microbial mat_biofilm with miuvig + +URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[MicrobialMatBiofilmMiuvig|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Miuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/MigsBa.md b/mixs6/MigsBa.md new file mode 100644 index 00000000..9c4c2ddc --- /dev/null +++ b/mixs6/MigsBa.md @@ -0,0 +1,37 @@ + +# Class: MigsBa + + +migs_ba Checklist + +URI: [mixs.vocab:MigsBa](https://w3id.org/mixs/vocab/MigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa]uses%20-.->[MigsBa],[WastewaterSludgeMigsBa]uses%20-.->[MigsBa],[SoilMigsBa]uses%20-.->[MigsBa],[SedimentMigsBa]uses%20-.->[MigsBa],[Plant-associatedMigsBa]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa]uses%20-.->[MigsBa],[MicrobialMatBiofilmMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-coresMigsBa]uses%20-.->[MigsBa],[Human-vaginalMigsBa]uses%20-.->[MigsBa],[Human-skinMigsBa]uses%20-.->[MigsBa],[Human-oralMigsBa]uses%20-.->[MigsBa],[Human-gutMigsBa]uses%20-.->[MigsBa],[Human-associatedMigsBa]uses%20-.->[MigsBa],[Host-associatedMigsBa]uses%20-.->[MigsBa],[CoreMigsBa]uses%20-.->[MigsBa],[BuiltEnvironmentMigsBa]uses%20-.->[MigsBa],[AirMigsBa]uses%20-.->[MigsBa],[WaterMigsBa],[WastewaterSludgeMigsBa],[SoilMigsBa],[SedimentMigsBa],[Plant-associatedMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MicrobialMatBiofilmMigsBa],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-coresMigsBa],[Human-vaginalMigsBa],[Human-skinMigsBa],[Human-oralMigsBa],[Human-gutMigsBa],[Human-associatedMigsBa],[Host-associatedMigsBa],[CoreMigsBa],[BuiltEnvironmentMigsBa],[AirMigsBa]) + +## Mixin for + + * [AirMigsBa](AirMigsBa.md) (mixin) - Combinatorial checklist for air with migs_ba + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) (mixin) - Combinatorial checklist for built environment with migs_ba + * [CoreMigsBa](CoreMigsBa.md) (mixin) - Combinatorial checklist for core with migs_ba + * [Host-associatedMigsBa](Host-associatedMigsBa.md) (mixin) - Combinatorial checklist for host-associated with migs_ba + * [Human-associatedMigsBa](Human-associatedMigsBa.md) (mixin) - Combinatorial checklist for human-associated with migs_ba + * [Human-gutMigsBa](Human-gutMigsBa.md) (mixin) - Combinatorial checklist for human-gut with migs_ba + * [Human-oralMigsBa](Human-oralMigsBa.md) (mixin) - Combinatorial checklist for human-oral with migs_ba + * [Human-skinMigsBa](Human-skinMigsBa.md) (mixin) - Combinatorial checklist for human-skin with migs_ba + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) (mixin) - Combinatorial checklist for human-vaginal with migs_ba + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_ba + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_ba + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) (mixin) - Combinatorial checklist for plant-associated with migs_ba + * [SedimentMigsBa](SedimentMigsBa.md) (mixin) - Combinatorial checklist for sediment with migs_ba + * [SoilMigsBa](SoilMigsBa.md) (mixin) - Combinatorial checklist for soil with migs_ba + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_ba + * [WaterMigsBa](WaterMigsBa.md) (mixin) - Combinatorial checklist for water with migs_ba + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MigsEu.md b/mixs6/MigsEu.md new file mode 100644 index 00000000..b95bea82 --- /dev/null +++ b/mixs6/MigsEu.md @@ -0,0 +1,37 @@ + +# Class: MigsEu + + +migs_eu Checklist + +URI: [mixs.vocab:MigsEu](https://w3id.org/mixs/vocab/MigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu]uses%20-.->[MigsEu],[WastewaterSludgeMigsEu]uses%20-.->[MigsEu],[SoilMigsEu]uses%20-.->[MigsEu],[SedimentMigsEu]uses%20-.->[MigsEu],[Plant-associatedMigsEu]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu]uses%20-.->[MigsEu],[MicrobialMatBiofilmMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-coresMigsEu]uses%20-.->[MigsEu],[Human-vaginalMigsEu]uses%20-.->[MigsEu],[Human-skinMigsEu]uses%20-.->[MigsEu],[Human-oralMigsEu]uses%20-.->[MigsEu],[Human-gutMigsEu]uses%20-.->[MigsEu],[Human-associatedMigsEu]uses%20-.->[MigsEu],[Host-associatedMigsEu]uses%20-.->[MigsEu],[CoreMigsEu]uses%20-.->[MigsEu],[BuiltEnvironmentMigsEu]uses%20-.->[MigsEu],[AirMigsEu]uses%20-.->[MigsEu],[WaterMigsEu],[WastewaterSludgeMigsEu],[SoilMigsEu],[SedimentMigsEu],[Plant-associatedMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MicrobialMatBiofilmMigsEu],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-coresMigsEu],[Human-vaginalMigsEu],[Human-skinMigsEu],[Human-oralMigsEu],[Human-gutMigsEu],[Human-associatedMigsEu],[Host-associatedMigsEu],[CoreMigsEu],[BuiltEnvironmentMigsEu],[AirMigsEu]) + +## Mixin for + + * [AirMigsEu](AirMigsEu.md) (mixin) - Combinatorial checklist for air with migs_eu + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) (mixin) - Combinatorial checklist for built environment with migs_eu + * [CoreMigsEu](CoreMigsEu.md) (mixin) - Combinatorial checklist for core with migs_eu + * [Host-associatedMigsEu](Host-associatedMigsEu.md) (mixin) - Combinatorial checklist for host-associated with migs_eu + * [Human-associatedMigsEu](Human-associatedMigsEu.md) (mixin) - Combinatorial checklist for human-associated with migs_eu + * [Human-gutMigsEu](Human-gutMigsEu.md) (mixin) - Combinatorial checklist for human-gut with migs_eu + * [Human-oralMigsEu](Human-oralMigsEu.md) (mixin) - Combinatorial checklist for human-oral with migs_eu + * [Human-skinMigsEu](Human-skinMigsEu.md) (mixin) - Combinatorial checklist for human-skin with migs_eu + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) (mixin) - Combinatorial checklist for human-vaginal with migs_eu + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_eu + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_eu + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) (mixin) - Combinatorial checklist for plant-associated with migs_eu + * [SedimentMigsEu](SedimentMigsEu.md) (mixin) - Combinatorial checklist for sediment with migs_eu + * [SoilMigsEu](SoilMigsEu.md) (mixin) - Combinatorial checklist for soil with migs_eu + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_eu + * [WaterMigsEu](WaterMigsEu.md) (mixin) - Combinatorial checklist for water with migs_eu + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MigsOrg.md b/mixs6/MigsOrg.md new file mode 100644 index 00000000..63d64f6d --- /dev/null +++ b/mixs6/MigsOrg.md @@ -0,0 +1,37 @@ + +# Class: MigsOrg + + +migs_org Checklist + +URI: [mixs.vocab:MigsOrg](https://w3id.org/mixs/vocab/MigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg]uses%20-.->[MigsOrg],[WastewaterSludgeMigsOrg]uses%20-.->[MigsOrg],[SoilMigsOrg]uses%20-.->[MigsOrg],[SedimentMigsOrg]uses%20-.->[MigsOrg],[Plant-associatedMigsOrg]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg]uses%20-.->[MigsOrg],[MicrobialMatBiofilmMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-coresMigsOrg]uses%20-.->[MigsOrg],[Human-vaginalMigsOrg]uses%20-.->[MigsOrg],[Human-skinMigsOrg]uses%20-.->[MigsOrg],[Human-oralMigsOrg]uses%20-.->[MigsOrg],[Human-gutMigsOrg]uses%20-.->[MigsOrg],[Human-associatedMigsOrg]uses%20-.->[MigsOrg],[Host-associatedMigsOrg]uses%20-.->[MigsOrg],[CoreMigsOrg]uses%20-.->[MigsOrg],[BuiltEnvironmentMigsOrg]uses%20-.->[MigsOrg],[AirMigsOrg]uses%20-.->[MigsOrg],[WaterMigsOrg],[WastewaterSludgeMigsOrg],[SoilMigsOrg],[SedimentMigsOrg],[Plant-associatedMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MicrobialMatBiofilmMigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-coresMigsOrg],[Human-vaginalMigsOrg],[Human-skinMigsOrg],[Human-oralMigsOrg],[Human-gutMigsOrg],[Human-associatedMigsOrg],[Host-associatedMigsOrg],[CoreMigsOrg],[BuiltEnvironmentMigsOrg],[AirMigsOrg]) + +## Mixin for + + * [AirMigsOrg](AirMigsOrg.md) (mixin) - Combinatorial checklist for air with migs_org + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) (mixin) - Combinatorial checklist for built environment with migs_org + * [CoreMigsOrg](CoreMigsOrg.md) (mixin) - Combinatorial checklist for core with migs_org + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) (mixin) - Combinatorial checklist for host-associated with migs_org + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) (mixin) - Combinatorial checklist for human-associated with migs_org + * [Human-gutMigsOrg](Human-gutMigsOrg.md) (mixin) - Combinatorial checklist for human-gut with migs_org + * [Human-oralMigsOrg](Human-oralMigsOrg.md) (mixin) - Combinatorial checklist for human-oral with migs_org + * [Human-skinMigsOrg](Human-skinMigsOrg.md) (mixin) - Combinatorial checklist for human-skin with migs_org + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) (mixin) - Combinatorial checklist for human-vaginal with migs_org + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_org + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_org + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_org + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) (mixin) - Combinatorial checklist for plant-associated with migs_org + * [SedimentMigsOrg](SedimentMigsOrg.md) (mixin) - Combinatorial checklist for sediment with migs_org + * [SoilMigsOrg](SoilMigsOrg.md) (mixin) - Combinatorial checklist for soil with migs_org + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_org + * [WaterMigsOrg](WaterMigsOrg.md) (mixin) - Combinatorial checklist for water with migs_org + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MigsPl.md b/mixs6/MigsPl.md new file mode 100644 index 00000000..3e8fe35e --- /dev/null +++ b/mixs6/MigsPl.md @@ -0,0 +1,37 @@ + +# Class: MigsPl + + +migs_pl Checklist + +URI: [mixs.vocab:MigsPl](https://w3id.org/mixs/vocab/MigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl]uses%20-.->[MigsPl],[WastewaterSludgeMigsPl]uses%20-.->[MigsPl],[SoilMigsPl]uses%20-.->[MigsPl],[SedimentMigsPl]uses%20-.->[MigsPl],[Plant-associatedMigsPl]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl]uses%20-.->[MigsPl],[MicrobialMatBiofilmMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-coresMigsPl]uses%20-.->[MigsPl],[Human-vaginalMigsPl]uses%20-.->[MigsPl],[Human-skinMigsPl]uses%20-.->[MigsPl],[Human-oralMigsPl]uses%20-.->[MigsPl],[Human-gutMigsPl]uses%20-.->[MigsPl],[Human-associatedMigsPl]uses%20-.->[MigsPl],[Host-associatedMigsPl]uses%20-.->[MigsPl],[CoreMigsPl]uses%20-.->[MigsPl],[BuiltEnvironmentMigsPl]uses%20-.->[MigsPl],[AirMigsPl]uses%20-.->[MigsPl],[WaterMigsPl],[WastewaterSludgeMigsPl],[SoilMigsPl],[SedimentMigsPl],[Plant-associatedMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MicrobialMatBiofilmMigsPl],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-coresMigsPl],[Human-vaginalMigsPl],[Human-skinMigsPl],[Human-oralMigsPl],[Human-gutMigsPl],[Human-associatedMigsPl],[Host-associatedMigsPl],[CoreMigsPl],[BuiltEnvironmentMigsPl],[AirMigsPl]) + +## Mixin for + + * [AirMigsPl](AirMigsPl.md) (mixin) - Combinatorial checklist for air with migs_pl + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) (mixin) - Combinatorial checklist for built environment with migs_pl + * [CoreMigsPl](CoreMigsPl.md) (mixin) - Combinatorial checklist for core with migs_pl + * [Host-associatedMigsPl](Host-associatedMigsPl.md) (mixin) - Combinatorial checklist for host-associated with migs_pl + * [Human-associatedMigsPl](Human-associatedMigsPl.md) (mixin) - Combinatorial checklist for human-associated with migs_pl + * [Human-gutMigsPl](Human-gutMigsPl.md) (mixin) - Combinatorial checklist for human-gut with migs_pl + * [Human-oralMigsPl](Human-oralMigsPl.md) (mixin) - Combinatorial checklist for human-oral with migs_pl + * [Human-skinMigsPl](Human-skinMigsPl.md) (mixin) - Combinatorial checklist for human-skin with migs_pl + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) (mixin) - Combinatorial checklist for human-vaginal with migs_pl + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_pl + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_pl + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) (mixin) - Combinatorial checklist for plant-associated with migs_pl + * [SedimentMigsPl](SedimentMigsPl.md) (mixin) - Combinatorial checklist for sediment with migs_pl + * [SoilMigsPl](SoilMigsPl.md) (mixin) - Combinatorial checklist for soil with migs_pl + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_pl + * [WaterMigsPl](WaterMigsPl.md) (mixin) - Combinatorial checklist for water with migs_pl + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MigsVi.md b/mixs6/MigsVi.md new file mode 100644 index 00000000..a95a674d --- /dev/null +++ b/mixs6/MigsVi.md @@ -0,0 +1,37 @@ + +# Class: MigsVi + + +migs_vi Checklist + +URI: [mixs.vocab:MigsVi](https://w3id.org/mixs/vocab/MigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi]uses%20-.->[MigsVi],[WastewaterSludgeMigsVi]uses%20-.->[MigsVi],[SoilMigsVi]uses%20-.->[MigsVi],[SedimentMigsVi]uses%20-.->[MigsVi],[Plant-associatedMigsVi]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi]uses%20-.->[MigsVi],[MicrobialMatBiofilmMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-coresMigsVi]uses%20-.->[MigsVi],[Human-vaginalMigsVi]uses%20-.->[MigsVi],[Human-skinMigsVi]uses%20-.->[MigsVi],[Human-oralMigsVi]uses%20-.->[MigsVi],[Human-gutMigsVi]uses%20-.->[MigsVi],[Human-associatedMigsVi]uses%20-.->[MigsVi],[Host-associatedMigsVi]uses%20-.->[MigsVi],[CoreMigsVi]uses%20-.->[MigsVi],[BuiltEnvironmentMigsVi]uses%20-.->[MigsVi],[AirMigsVi]uses%20-.->[MigsVi],[WaterMigsVi],[WastewaterSludgeMigsVi],[SoilMigsVi],[SedimentMigsVi],[Plant-associatedMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MicrobialMatBiofilmMigsVi],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-coresMigsVi],[Human-vaginalMigsVi],[Human-skinMigsVi],[Human-oralMigsVi],[Human-gutMigsVi],[Human-associatedMigsVi],[Host-associatedMigsVi],[CoreMigsVi],[BuiltEnvironmentMigsVi],[AirMigsVi]) + +## Mixin for + + * [AirMigsVi](AirMigsVi.md) (mixin) - Combinatorial checklist for air with migs_vi + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) (mixin) - Combinatorial checklist for built environment with migs_vi + * [CoreMigsVi](CoreMigsVi.md) (mixin) - Combinatorial checklist for core with migs_vi + * [Host-associatedMigsVi](Host-associatedMigsVi.md) (mixin) - Combinatorial checklist for host-associated with migs_vi + * [Human-associatedMigsVi](Human-associatedMigsVi.md) (mixin) - Combinatorial checklist for human-associated with migs_vi + * [Human-gutMigsVi](Human-gutMigsVi.md) (mixin) - Combinatorial checklist for human-gut with migs_vi + * [Human-oralMigsVi](Human-oralMigsVi.md) (mixin) - Combinatorial checklist for human-oral with migs_vi + * [Human-skinMigsVi](Human-skinMigsVi.md) (mixin) - Combinatorial checklist for human-skin with migs_vi + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) (mixin) - Combinatorial checklist for human-vaginal with migs_vi + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_vi + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_vi + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) (mixin) - Combinatorial checklist for plant-associated with migs_vi + * [SedimentMigsVi](SedimentMigsVi.md) (mixin) - Combinatorial checklist for sediment with migs_vi + * [SoilMigsVi](SoilMigsVi.md) (mixin) - Combinatorial checklist for soil with migs_vi + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_vi + * [WaterMigsVi](WaterMigsVi.md) (mixin) - Combinatorial checklist for water with migs_vi + +## Referenced by class + + +## Attributes + diff --git a/mixs6/Mimag.md b/mixs6/Mimag.md new file mode 100644 index 00000000..52e0c140 --- /dev/null +++ b/mixs6/Mimag.md @@ -0,0 +1,37 @@ + +# Class: Mimag + + +mimag Checklist + +URI: [mixs.vocab:Mimag](https://w3id.org/mixs/vocab/Mimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag]uses%20-.->[Mimag],[WastewaterSludgeMimag]uses%20-.->[Mimag],[SoilMimag]uses%20-.->[Mimag],[SedimentMimag]uses%20-.->[Mimag],[Plant-associatedMimag]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag]uses%20-.->[Mimag],[MicrobialMatBiofilmMimag]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabsMimag]uses%20-.->[Mimag],[HydrocarbonResources-coresMimag]uses%20-.->[Mimag],[Human-vaginalMimag]uses%20-.->[Mimag],[Human-skinMimag]uses%20-.->[Mimag],[Human-oralMimag]uses%20-.->[Mimag],[Human-gutMimag]uses%20-.->[Mimag],[Human-associatedMimag]uses%20-.->[Mimag],[Host-associatedMimag]uses%20-.->[Mimag],[CoreMimag]uses%20-.->[Mimag],[BuiltEnvironmentMimag]uses%20-.->[Mimag],[AirMimag]uses%20-.->[Mimag],[WaterMimag],[WastewaterSludgeMimag],[SoilMimag],[SedimentMimag],[Plant-associatedMimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MicrobialMatBiofilmMimag],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-coresMimag],[Human-vaginalMimag],[Human-skinMimag],[Human-oralMimag],[Human-gutMimag],[Human-associatedMimag],[Host-associatedMimag],[CoreMimag],[BuiltEnvironmentMimag],[AirMimag]) + +## Mixin for + + * [AirMimag](AirMimag.md) (mixin) - Combinatorial checklist for air with mimag + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) (mixin) - Combinatorial checklist for built environment with mimag + * [CoreMimag](CoreMimag.md) (mixin) - Combinatorial checklist for core with mimag + * [Host-associatedMimag](Host-associatedMimag.md) (mixin) - Combinatorial checklist for host-associated with mimag + * [Human-associatedMimag](Human-associatedMimag.md) (mixin) - Combinatorial checklist for human-associated with mimag + * [Human-gutMimag](Human-gutMimag.md) (mixin) - Combinatorial checklist for human-gut with mimag + * [Human-oralMimag](Human-oralMimag.md) (mixin) - Combinatorial checklist for human-oral with mimag + * [Human-skinMimag](Human-skinMimag.md) (mixin) - Combinatorial checklist for human-skin with mimag + * [Human-vaginalMimag](Human-vaginalMimag.md) (mixin) - Combinatorial checklist for human-vaginal with mimag + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimag + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimag + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimag + * [Plant-associatedMimag](Plant-associatedMimag.md) (mixin) - Combinatorial checklist for plant-associated with mimag + * [SedimentMimag](SedimentMimag.md) (mixin) - Combinatorial checklist for sediment with mimag + * [SoilMimag](SoilMimag.md) (mixin) - Combinatorial checklist for soil with mimag + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimag + * [WaterMimag](WaterMimag.md) (mixin) - Combinatorial checklist for water with mimag + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MimarksC.md b/mixs6/MimarksC.md new file mode 100644 index 00000000..39ab66e3 --- /dev/null +++ b/mixs6/MimarksC.md @@ -0,0 +1,37 @@ + +# Class: MimarksC + + +mimarks_c Checklist + +URI: [mixs.vocab:MimarksC](https://w3id.org/mixs/vocab/MimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC]uses%20-.->[MimarksC],[WastewaterSludgeMimarksC]uses%20-.->[MimarksC],[SoilMimarksC]uses%20-.->[MimarksC],[SedimentMimarksC]uses%20-.->[MimarksC],[Plant-associatedMimarksC]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC]uses%20-.->[MimarksC],[MicrobialMatBiofilmMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-coresMimarksC]uses%20-.->[MimarksC],[Human-vaginalMimarksC]uses%20-.->[MimarksC],[Human-skinMimarksC]uses%20-.->[MimarksC],[Human-oralMimarksC]uses%20-.->[MimarksC],[Human-gutMimarksC]uses%20-.->[MimarksC],[Human-associatedMimarksC]uses%20-.->[MimarksC],[Host-associatedMimarksC]uses%20-.->[MimarksC],[CoreMimarksC]uses%20-.->[MimarksC],[BuiltEnvironmentMimarksC]uses%20-.->[MimarksC],[AirMimarksC]uses%20-.->[MimarksC],[WaterMimarksC],[WastewaterSludgeMimarksC],[SoilMimarksC],[SedimentMimarksC],[Plant-associatedMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MicrobialMatBiofilmMimarksC],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-coresMimarksC],[Human-vaginalMimarksC],[Human-skinMimarksC],[Human-oralMimarksC],[Human-gutMimarksC],[Human-associatedMimarksC],[Host-associatedMimarksC],[CoreMimarksC],[BuiltEnvironmentMimarksC],[AirMimarksC]) + +## Mixin for + + * [AirMimarksC](AirMimarksC.md) (mixin) - Combinatorial checklist for air with mimarks_c + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) (mixin) - Combinatorial checklist for built environment with mimarks_c + * [CoreMimarksC](CoreMimarksC.md) (mixin) - Combinatorial checklist for core with mimarks_c + * [Host-associatedMimarksC](Host-associatedMimarksC.md) (mixin) - Combinatorial checklist for host-associated with mimarks_c + * [Human-associatedMimarksC](Human-associatedMimarksC.md) (mixin) - Combinatorial checklist for human-associated with mimarks_c + * [Human-gutMimarksC](Human-gutMimarksC.md) (mixin) - Combinatorial checklist for human-gut with mimarks_c + * [Human-oralMimarksC](Human-oralMimarksC.md) (mixin) - Combinatorial checklist for human-oral with mimarks_c + * [Human-skinMimarksC](Human-skinMimarksC.md) (mixin) - Combinatorial checklist for human-skin with mimarks_c + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) (mixin) - Combinatorial checklist for human-vaginal with mimarks_c + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_c + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimarks_c + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) (mixin) - Combinatorial checklist for plant-associated with mimarks_c + * [SedimentMimarksC](SedimentMimarksC.md) (mixin) - Combinatorial checklist for sediment with mimarks_c + * [SoilMimarksC](SoilMimarksC.md) (mixin) - Combinatorial checklist for soil with mimarks_c + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimarks_c + * [WaterMimarksC](WaterMimarksC.md) (mixin) - Combinatorial checklist for water with mimarks_c + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MimarksS.md b/mixs6/MimarksS.md new file mode 100644 index 00000000..eb4ebef4 --- /dev/null +++ b/mixs6/MimarksS.md @@ -0,0 +1,37 @@ + +# Class: MimarksS + + +mimarks_s Checklist + +URI: [mixs.vocab:MimarksS](https://w3id.org/mixs/vocab/MimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS]uses%20-.->[MimarksS],[WastewaterSludgeMimarksS]uses%20-.->[MimarksS],[SoilMimarksS]uses%20-.->[MimarksS],[SedimentMimarksS]uses%20-.->[MimarksS],[Plant-associatedMimarksS]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS]uses%20-.->[MimarksS],[MicrobialMatBiofilmMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-coresMimarksS]uses%20-.->[MimarksS],[Human-vaginalMimarksS]uses%20-.->[MimarksS],[Human-skinMimarksS]uses%20-.->[MimarksS],[Human-oralMimarksS]uses%20-.->[MimarksS],[Human-gutMimarksS]uses%20-.->[MimarksS],[Human-associatedMimarksS]uses%20-.->[MimarksS],[Host-associatedMimarksS]uses%20-.->[MimarksS],[CoreMimarksS]uses%20-.->[MimarksS],[BuiltEnvironmentMimarksS]uses%20-.->[MimarksS],[AirMimarksS]uses%20-.->[MimarksS],[WaterMimarksS],[WastewaterSludgeMimarksS],[SoilMimarksS],[SedimentMimarksS],[Plant-associatedMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MicrobialMatBiofilmMimarksS],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-coresMimarksS],[Human-vaginalMimarksS],[Human-skinMimarksS],[Human-oralMimarksS],[Human-gutMimarksS],[Human-associatedMimarksS],[Host-associatedMimarksS],[CoreMimarksS],[BuiltEnvironmentMimarksS],[AirMimarksS]) + +## Mixin for + + * [AirMimarksS](AirMimarksS.md) (mixin) - Combinatorial checklist for air with mimarks_s + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) (mixin) - Combinatorial checklist for built environment with mimarks_s + * [CoreMimarksS](CoreMimarksS.md) (mixin) - Combinatorial checklist for core with mimarks_s + * [Host-associatedMimarksS](Host-associatedMimarksS.md) (mixin) - Combinatorial checklist for host-associated with mimarks_s + * [Human-associatedMimarksS](Human-associatedMimarksS.md) (mixin) - Combinatorial checklist for human-associated with mimarks_s + * [Human-gutMimarksS](Human-gutMimarksS.md) (mixin) - Combinatorial checklist for human-gut with mimarks_s + * [Human-oralMimarksS](Human-oralMimarksS.md) (mixin) - Combinatorial checklist for human-oral with mimarks_s + * [Human-skinMimarksS](Human-skinMimarksS.md) (mixin) - Combinatorial checklist for human-skin with mimarks_s + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) (mixin) - Combinatorial checklist for human-vaginal with mimarks_s + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_s + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimarks_s + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) (mixin) - Combinatorial checklist for plant-associated with mimarks_s + * [SedimentMimarksS](SedimentMimarksS.md) (mixin) - Combinatorial checklist for sediment with mimarks_s + * [SoilMimarksS](SoilMimarksS.md) (mixin) - Combinatorial checklist for soil with mimarks_s + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimarks_s + * [WaterMimarksS](WaterMimarksS.md) (mixin) - Combinatorial checklist for water with mimarks_s + +## Referenced by class + + +## Attributes + diff --git a/mixs6/Misag.md b/mixs6/Misag.md new file mode 100644 index 00000000..149f3453 --- /dev/null +++ b/mixs6/Misag.md @@ -0,0 +1,37 @@ + +# Class: Misag + + +misag Checklist + +URI: [mixs.vocab:Misag](https://w3id.org/mixs/vocab/Misag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag]uses%20-.->[Misag],[WastewaterSludgeMisag]uses%20-.->[Misag],[SoilMisag]uses%20-.->[Misag],[SedimentMisag]uses%20-.->[Misag],[Plant-associatedMisag]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironmentMisag]uses%20-.->[Misag],[MicrobialMatBiofilmMisag]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabsMisag]uses%20-.->[Misag],[HydrocarbonResources-coresMisag]uses%20-.->[Misag],[Human-vaginalMisag]uses%20-.->[Misag],[Human-skinMisag]uses%20-.->[Misag],[Human-oralMisag]uses%20-.->[Misag],[Human-gutMisag]uses%20-.->[Misag],[Human-associatedMisag]uses%20-.->[Misag],[Host-associatedMisag]uses%20-.->[Misag],[CoreMisag]uses%20-.->[Misag],[BuiltEnvironmentMisag]uses%20-.->[Misag],[AirMisag]uses%20-.->[Misag],[WaterMisag],[WastewaterSludgeMisag],[SoilMisag],[SedimentMisag],[Plant-associatedMisag],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MicrobialMatBiofilmMisag],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-coresMisag],[Human-vaginalMisag],[Human-skinMisag],[Human-oralMisag],[Human-gutMisag],[Human-associatedMisag],[Host-associatedMisag],[CoreMisag],[BuiltEnvironmentMisag],[AirMisag]) + +## Mixin for + + * [AirMisag](AirMisag.md) (mixin) - Combinatorial checklist for air with misag + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) (mixin) - Combinatorial checklist for built environment with misag + * [CoreMisag](CoreMisag.md) (mixin) - Combinatorial checklist for core with misag + * [Host-associatedMisag](Host-associatedMisag.md) (mixin) - Combinatorial checklist for host-associated with misag + * [Human-associatedMisag](Human-associatedMisag.md) (mixin) - Combinatorial checklist for human-associated with misag + * [Human-gutMisag](Human-gutMisag.md) (mixin) - Combinatorial checklist for human-gut with misag + * [Human-oralMisag](Human-oralMisag.md) (mixin) - Combinatorial checklist for human-oral with misag + * [Human-skinMisag](Human-skinMisag.md) (mixin) - Combinatorial checklist for human-skin with misag + * [Human-vaginalMisag](Human-vaginalMisag.md) (mixin) - Combinatorial checklist for human-vaginal with misag + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with misag + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with misag + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with misag + * [Plant-associatedMisag](Plant-associatedMisag.md) (mixin) - Combinatorial checklist for plant-associated with misag + * [SedimentMisag](SedimentMisag.md) (mixin) - Combinatorial checklist for sediment with misag + * [SoilMisag](SoilMisag.md) (mixin) - Combinatorial checklist for soil with misag + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) (mixin) - Combinatorial checklist for wastewater_sludge with misag + * [WaterMisag](WaterMisag.md) (mixin) - Combinatorial checklist for water with misag + +## Referenced by class + + +## Attributes + diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md new file mode 100644 index 00000000..a0a6c132 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md @@ -0,0 +1,197 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironment + + +miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment|alkalinity:string%20%3F;ammonium:string%20%3F;biomass:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;misc_param:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;perturbation:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;water_current:string%20%3F]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe]) + +## Children + + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - Combinatorial checklist for miscellaneous natural or artificial environment with me + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_org + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimag + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with misag + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) - Combinatorial checklist for miscellaneous natural or artificial environment with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md new file mode 100644 index 00000000..9094066e --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMe + + +Combinatorial checklist for miscellaneous natural or artificial environment with me + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMe|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment],[Me]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md new file mode 100644 index 00000000..cdf4666e --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsBa + + +Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsBa|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment],[MigsBa]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md new file mode 100644 index 00000000..52c5b664 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsEu + + +Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsEu|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment],[MigsEu]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md new file mode 100644 index 00000000..5432641c --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsOrg + + +Combinatorial checklist for miscellaneous natural or artificial environment with migs_org + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MigsOrg]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md new file mode 100644 index 00000000..02f9623e --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsPl + + +Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsPl|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment],[MigsPl]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md new file mode 100644 index 00000000..b0e93ae1 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsVi + + +Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsVi|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment],[MigsVi]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md new file mode 100644 index 00000000..ebae0da5 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMimag + + +Combinatorial checklist for miscellaneous natural or artificial environment with mimag + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimag|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment],[Mimag]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md new file mode 100644 index 00000000..eddc635d --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMimarksC + + +Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimarksC|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksC]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md new file mode 100644 index 00000000..b0da0478 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMimarksS + + +Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimarksS|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksS]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md new file mode 100644 index 00000000..9951c9cc --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMisag + + +Combinatorial checklist for miscellaneous natural or artificial environment with misag + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMisag|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment],[Misag]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md new file mode 100644 index 00000000..926735a3 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md @@ -0,0 +1,188 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMiuvig + + +Combinatorial checklist for miscellaneous natural or artificial environment with miuvig + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/Miuvig.md b/mixs6/Miuvig.md new file mode 100644 index 00000000..091eb141 --- /dev/null +++ b/mixs6/Miuvig.md @@ -0,0 +1,37 @@ + +# Class: Miuvig + + +miuvig Checklist + +URI: [mixs.vocab:Miuvig](https://w3id.org/mixs/vocab/Miuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig]uses%20-.->[Miuvig],[WastewaterSludgeMiuvig]uses%20-.->[Miuvig],[SoilMiuvig]uses%20-.->[Miuvig],[SedimentMiuvig]uses%20-.->[Miuvig],[Plant-associatedMiuvig]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig]uses%20-.->[Miuvig],[MicrobialMatBiofilmMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-coresMiuvig]uses%20-.->[Miuvig],[Human-vaginalMiuvig]uses%20-.->[Miuvig],[Human-skinMiuvig]uses%20-.->[Miuvig],[Human-oralMiuvig]uses%20-.->[Miuvig],[Human-gutMiuvig]uses%20-.->[Miuvig],[Human-associatedMiuvig]uses%20-.->[Miuvig],[Host-associatedMiuvig]uses%20-.->[Miuvig],[CoreMiuvig]uses%20-.->[Miuvig],[BuiltEnvironmentMiuvig]uses%20-.->[Miuvig],[AirMiuvig]uses%20-.->[Miuvig],[WaterMiuvig],[WastewaterSludgeMiuvig],[SoilMiuvig],[SedimentMiuvig],[Plant-associatedMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MicrobialMatBiofilmMiuvig],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-coresMiuvig],[Human-vaginalMiuvig],[Human-skinMiuvig],[Human-oralMiuvig],[Human-gutMiuvig],[Human-associatedMiuvig],[Host-associatedMiuvig],[CoreMiuvig],[BuiltEnvironmentMiuvig],[AirMiuvig]) + +## Mixin for + + * [AirMiuvig](AirMiuvig.md) (mixin) - Combinatorial checklist for air with miuvig + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) (mixin) - Combinatorial checklist for built environment with miuvig + * [CoreMiuvig](CoreMiuvig.md) (mixin) - Combinatorial checklist for core with miuvig + * [Host-associatedMiuvig](Host-associatedMiuvig.md) (mixin) - Combinatorial checklist for host-associated with miuvig + * [Human-associatedMiuvig](Human-associatedMiuvig.md) (mixin) - Combinatorial checklist for human-associated with miuvig + * [Human-gutMiuvig](Human-gutMiuvig.md) (mixin) - Combinatorial checklist for human-gut with miuvig + * [Human-oralMiuvig](Human-oralMiuvig.md) (mixin) - Combinatorial checklist for human-oral with miuvig + * [Human-skinMiuvig](Human-skinMiuvig.md) (mixin) - Combinatorial checklist for human-skin with miuvig + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) (mixin) - Combinatorial checklist for human-vaginal with miuvig + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with miuvig + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with miuvig + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with miuvig + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) (mixin) - Combinatorial checklist for plant-associated with miuvig + * [SedimentMiuvig](SedimentMiuvig.md) (mixin) - Combinatorial checklist for sediment with miuvig + * [SoilMiuvig](SoilMiuvig.md) (mixin) - Combinatorial checklist for soil with miuvig + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) (mixin) - Combinatorial checklist for wastewater_sludge with miuvig + * [WaterMiuvig](WaterMiuvig.md) (mixin) - Combinatorial checklist for water with miuvig + +## Referenced by class + + +## Attributes + diff --git a/mixs6/Plant-associated.md b/mixs6/Plant-associated.md new file mode 100644 index 00000000..0b1d8e8d --- /dev/null +++ b/mixs6/Plant-associated.md @@ -0,0 +1,317 @@ + +# Class: Plant-associated + + +plant-associated + +URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMiuvig],[Plant-associatedMisag],[Plant-associatedMimarksS],[Plant-associatedMimarksC],[Plant-associatedMimag],[Plant-associatedMigsVi],[Plant-associatedMigsPl],[Plant-associatedMigsOrg],[Plant-associatedMigsEu],[Plant-associatedMigsBa],[Plant-associatedMe],[Plant-associated|air_temp_regm:string%20%3F;ances_data:string%20%3F;antibiotic_regm:string%20%3F;biol_stat:biol_stat_enum%20%3F;biotic_regm:string%20%3F;chem_administration:string%20%3F;chem_mutagen:string%20%3F;climate_environment:string%20%3F;cult_root_med:string%20%3F;fertilizer_regm:string%20%3F;fungicide_regm:string%20%3F;gaseous_environment:string%20%3F;genetic_mod:string%20%3F;gravity:string%20%3F;growth_facil:string%20%3F;growth_habit:growth_habit_enum%20%3F;growth_hormone_regm:string%20%3F;herbicide_regm:string%20%3F;host_age:string%20%3F;host_common_name:string%20%3F;host_disease_stat:string%20%3F;host_dry_mass:string%20%3F;host_genotype:string%20%3F;host_height:string%20%3F;host_infra_specific_name:string%20%3F;host_infra_specific_rank:string%20%3F;host_length:string%20%3F;host_life_stage:string%20%3F;host_phenotype:string%20%3F;host_taxid:string%20%3F;host_tot_mass:string%20%3F;host_wet_mass:string%20%3F;humidity_regm:string%20%3F;light_regm:string%20%3F;mechanical_damage:string%20%3F;mineral_nutr_regm:string%20%3F;misc_param:string%20%3F;non_mineral_nutr_regm:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph_regm:string%20%3F;perturbation:string%20%3F;pesticide_regm:string%20%3F;plant_growth_med:plant_growth_med_enum%20%3F;plant_product:string%20%3F;plant_sex:plant_sex_enum%20%3F;plant_struc:string%20%3F;radiation_regm:string%20%3F;rainfall_regm:string%20%3F;root_cond:string%20%3F;root_med_carbon:string%20%3F;root_med_macronutr:string%20%3F;root_med_micronutr:string%20%3F;root_med_suppl:string%20%3F;root_med_ph:string%20%3F;root_med_regl:string%20%3F;root_med_solid:string%20%3F;salt_regm:string%20%3F;samp_capt_status:samp_capt_status_enum%20%3F;samp_dis_stage:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;season_environment:string%20%3F;standing_water_regm:string%20%3F;temp:string%20%3F;tiss_cult_growth_med:string%20%3F;water_temp_regm:string%20%3F;watering_regm:string%20%3F]^-[Plant-associatedMiuvig],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated]^-[Plant-associatedMe]) + +## Children + + * [Plant-associatedMe](Plant-associatedMe.md) - Combinatorial checklist for plant-associated with me + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - Combinatorial checklist for plant-associated with migs_ba + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - Combinatorial checklist for plant-associated with migs_eu + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - Combinatorial checklist for plant-associated with migs_org + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - Combinatorial checklist for plant-associated with migs_pl + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - Combinatorial checklist for plant-associated with migs_vi + * [Plant-associatedMimag](Plant-associatedMimag.md) - Combinatorial checklist for plant-associated with mimag + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - Combinatorial checklist for plant-associated with mimarks_c + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - Combinatorial checklist for plant-associated with mimarks_s + * [Plant-associatedMisag](Plant-associatedMisag.md) - Combinatorial checklist for plant-associated with misag + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) - Combinatorial checklist for plant-associated with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMe.md b/mixs6/Plant-associatedMe.md new file mode 100644 index 00000000..cdc9c1d7 --- /dev/null +++ b/mixs6/Plant-associatedMe.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMe + + +Combinatorial checklist for plant-associated with me + +URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associatedMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMe|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Me],[Plant-associated]^-[Plant-associatedMe],[Plant-associated],[Me]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMigsBa.md b/mixs6/Plant-associatedMigsBa.md new file mode 100644 index 00000000..8a9f7e34 --- /dev/null +++ b/mixs6/Plant-associatedMigsBa.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMigsBa + + +Combinatorial checklist for plant-associated with migs_ba + +URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-associatedMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsBa|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsBa],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated],[MigsBa]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMigsEu.md b/mixs6/Plant-associatedMigsEu.md new file mode 100644 index 00000000..b1ca1161 --- /dev/null +++ b/mixs6/Plant-associatedMigsEu.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMigsEu + + +Combinatorial checklist for plant-associated with migs_eu + +URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-associatedMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsEu|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsEu],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated],[MigsEu]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMigsOrg.md b/mixs6/Plant-associatedMigsOrg.md new file mode 100644 index 00000000..ba9f7455 --- /dev/null +++ b/mixs6/Plant-associatedMigsOrg.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMigsOrg + + +Combinatorial checklist for plant-associated with migs_org + +URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-associatedMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsOrg|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsOrg],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated],[MigsOrg]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMigsPl.md b/mixs6/Plant-associatedMigsPl.md new file mode 100644 index 00000000..7ae6fe4e --- /dev/null +++ b/mixs6/Plant-associatedMigsPl.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMigsPl + + +Combinatorial checklist for plant-associated with migs_pl + +URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-associatedMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsPl|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsPl],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated],[MigsPl]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMigsVi.md b/mixs6/Plant-associatedMigsVi.md new file mode 100644 index 00000000..27fa98f5 --- /dev/null +++ b/mixs6/Plant-associatedMigsVi.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMigsVi + + +Combinatorial checklist for plant-associated with migs_vi + +URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-associatedMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsVi|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsVi],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated],[MigsVi]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMimag.md b/mixs6/Plant-associatedMimag.md new file mode 100644 index 00000000..04c7d1a2 --- /dev/null +++ b/mixs6/Plant-associatedMimag.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMimag + + +Combinatorial checklist for plant-associated with mimag + +URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associatedMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimag|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Mimag],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated],[Mimag]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170 milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2 milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMimarksC.md b/mixs6/Plant-associatedMimarksC.md new file mode 100644 index 00000000..08773cda --- /dev/null +++ b/mixs6/Plant-associatedMimarksC.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMimarksC + + +Combinatorial checklist for plant-associated with mimarks_c + +URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-associatedMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimarksC|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksC],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated],[MimarksC]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMimarksS.md b/mixs6/Plant-associatedMimarksS.md new file mode 100644 index 00000000..2126c285 --- /dev/null +++ b/mixs6/Plant-associatedMimarksS.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMimarksS + + +Combinatorial checklist for plant-associated with mimarks_s + +URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-associatedMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimarksS|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksS],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated],[MimarksS]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMisag.md b/mixs6/Plant-associatedMisag.md new file mode 100644 index 00000000..9b357997 --- /dev/null +++ b/mixs6/Plant-associatedMisag.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMisag + + +Combinatorial checklist for plant-associated with misag + +URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associatedMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMisag|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Misag],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated],[Misag]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Plant-associatedMiuvig.md b/mixs6/Plant-associatedMiuvig.md new file mode 100644 index 00000000..bb63fe6e --- /dev/null +++ b/mixs6/Plant-associatedMiuvig.md @@ -0,0 +1,308 @@ + +# Class: Plant-associatedMiuvig + + +Combinatorial checklist for plant-associated with miuvig + +URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-associatedMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMiuvig|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Miuvig],[Plant-associated]^-[Plant-associatedMiuvig],[Plant-associated],[Miuvig]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [String](types/String.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [String](types/String.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [String](types/String.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [String](types/String.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [String](types/String.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [String](types/String.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [String](types/String.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None diff --git a/mixs6/Sediment.md b/mixs6/Sediment.md new file mode 100644 index 00000000..b7865c01 --- /dev/null +++ b/mixs6/Sediment.md @@ -0,0 +1,297 @@ + +# Class: Sediment + + +sediment + +URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig],[SedimentMisag],[SedimentMimarksS],[SedimentMimarksC],[SedimentMimag],[SedimentMigsVi],[SedimentMigsPl],[SedimentMigsOrg],[SedimentMigsEu],[SedimentMigsBa],[SedimentMe],[Sediment|alkalinity:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;bacteria_carb_prod:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;glucosidase_act:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;particle_class:string%20%3F;part_org_carb:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;porosity:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;sediment_type:sediment_type_enum%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;tidal_stage:tidal_stage_enum%20%3F;tot_carb:string%20%3F;tot_depth_water_col:string%20%3F;tot_nitro_content:string%20%3F;tot_org_carb:string%20%3F;turbidity:string%20%3F;water_content:string%20%3F]^-[SedimentMiuvig],[Sediment]^-[SedimentMisag],[Sediment]^-[SedimentMimarksS],[Sediment]^-[SedimentMimarksC],[Sediment]^-[SedimentMimag],[Sediment]^-[SedimentMigsVi],[Sediment]^-[SedimentMigsPl],[Sediment]^-[SedimentMigsOrg],[Sediment]^-[SedimentMigsEu],[Sediment]^-[SedimentMigsBa],[Sediment]^-[SedimentMe]) + +## Children + + * [SedimentMe](SedimentMe.md) - Combinatorial checklist for sediment with me + * [SedimentMigsBa](SedimentMigsBa.md) - Combinatorial checklist for sediment with migs_ba + * [SedimentMigsEu](SedimentMigsEu.md) - Combinatorial checklist for sediment with migs_eu + * [SedimentMigsOrg](SedimentMigsOrg.md) - Combinatorial checklist for sediment with migs_org + * [SedimentMigsPl](SedimentMigsPl.md) - Combinatorial checklist for sediment with migs_pl + * [SedimentMigsVi](SedimentMigsVi.md) - Combinatorial checklist for sediment with migs_vi + * [SedimentMimag](SedimentMimag.md) - Combinatorial checklist for sediment with mimag + * [SedimentMimarksC](SedimentMimarksC.md) - Combinatorial checklist for sediment with mimarks_c + * [SedimentMimarksS](SedimentMimarksS.md) - Combinatorial checklist for sediment with mimarks_s + * [SedimentMisag](SedimentMisag.md) - Combinatorial checklist for sediment with misag + * [SedimentMiuvig](SedimentMiuvig.md) - Combinatorial checklist for sediment with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMe.md b/mixs6/SedimentMe.md new file mode 100644 index 00000000..c69a1f9d --- /dev/null +++ b/mixs6/SedimentMe.md @@ -0,0 +1,288 @@ + +# Class: SedimentMe + + +Combinatorial checklist for sediment with me + +URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMe|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Me],[Sediment]^-[SedimentMe],[Sediment],[Me]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMigsBa.md b/mixs6/SedimentMigsBa.md new file mode 100644 index 00000000..92a51e60 --- /dev/null +++ b/mixs6/SedimentMigsBa.md @@ -0,0 +1,288 @@ + +# Class: SedimentMigsBa + + +Combinatorial checklist for sediment with migs_ba + +URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsBa|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsBa],[Sediment]^-[SedimentMigsBa],[Sediment],[MigsBa]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMigsEu.md b/mixs6/SedimentMigsEu.md new file mode 100644 index 00000000..631f1299 --- /dev/null +++ b/mixs6/SedimentMigsEu.md @@ -0,0 +1,288 @@ + +# Class: SedimentMigsEu + + +Combinatorial checklist for sediment with migs_eu + +URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsEu|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsEu],[Sediment]^-[SedimentMigsEu],[Sediment],[MigsEu]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMigsOrg.md b/mixs6/SedimentMigsOrg.md new file mode 100644 index 00000000..c8b12ac8 --- /dev/null +++ b/mixs6/SedimentMigsOrg.md @@ -0,0 +1,288 @@ + +# Class: SedimentMigsOrg + + +Combinatorial checklist for sediment with migs_org + +URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsOrg|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsOrg],[Sediment]^-[SedimentMigsOrg],[Sediment],[MigsOrg]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMigsPl.md b/mixs6/SedimentMigsPl.md new file mode 100644 index 00000000..3aad22f9 --- /dev/null +++ b/mixs6/SedimentMigsPl.md @@ -0,0 +1,288 @@ + +# Class: SedimentMigsPl + + +Combinatorial checklist for sediment with migs_pl + +URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsPl|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsPl],[Sediment]^-[SedimentMigsPl],[Sediment],[MigsPl]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMigsVi.md b/mixs6/SedimentMigsVi.md new file mode 100644 index 00000000..a15cc6ea --- /dev/null +++ b/mixs6/SedimentMigsVi.md @@ -0,0 +1,288 @@ + +# Class: SedimentMigsVi + + +Combinatorial checklist for sediment with migs_vi + +URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsVi|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsVi],[Sediment]^-[SedimentMigsVi],[Sediment],[MigsVi]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMimag.md b/mixs6/SedimentMimag.md new file mode 100644 index 00000000..d43727d5 --- /dev/null +++ b/mixs6/SedimentMimag.md @@ -0,0 +1,288 @@ + +# Class: SedimentMimag + + +Combinatorial checklist for sediment with mimag + +URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Mimag],[Sediment]^-[SedimentMimag],[Sediment],[Mimag]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMimarksC.md b/mixs6/SedimentMimarksC.md new file mode 100644 index 00000000..ef0d616c --- /dev/null +++ b/mixs6/SedimentMimarksC.md @@ -0,0 +1,288 @@ + +# Class: SedimentMimarksC + + +Combinatorial checklist for sediment with mimarks_c + +URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksC|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksC],[Sediment]^-[SedimentMimarksC],[Sediment],[MimarksC]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMimarksS.md b/mixs6/SedimentMimarksS.md new file mode 100644 index 00000000..1c64cf35 --- /dev/null +++ b/mixs6/SedimentMimarksS.md @@ -0,0 +1,288 @@ + +# Class: SedimentMimarksS + + +Combinatorial checklist for sediment with mimarks_s + +URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksS|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksS],[Sediment]^-[SedimentMimarksS],[Sediment],[MimarksS]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMisag.md b/mixs6/SedimentMisag.md new file mode 100644 index 00000000..45a69ce9 --- /dev/null +++ b/mixs6/SedimentMisag.md @@ -0,0 +1,288 @@ + +# Class: SedimentMisag + + +Combinatorial checklist for sediment with misag + +URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMisag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Misag],[Sediment]^-[SedimentMisag],[Sediment],[Misag]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SedimentMiuvig.md b/mixs6/SedimentMiuvig.md new file mode 100644 index 00000000..dbb8fd22 --- /dev/null +++ b/mixs6/SedimentMiuvig.md @@ -0,0 +1,288 @@ + +# Class: SedimentMiuvig + + +Combinatorial checklist for sediment with miuvig + +URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Miuvig],[Sediment]^-[SedimentMiuvig],[Sediment],[Miuvig]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [String](types/String.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [String](types/String.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Soil.md b/mixs6/Soil.md new file mode 100644 index 00000000..fa176f3f --- /dev/null +++ b/mixs6/Soil.md @@ -0,0 +1,241 @@ + +# Class: Soil + + +soil + +URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig],[SoilMisag],[SoilMimarksS],[SoilMimarksC],[SoilMimag],[SoilMigsVi],[SoilMigsPl],[SoilMigsOrg],[SoilMigsEu],[SoilMigsBa],[SoilMe],[Soil|cur_land_use:cur_land_use_enum%20%3F;cur_vegetation:string%20%3F;cur_vegetation_meth:string%20%3F;previous_land_use:string%20%3F;previous_land_use_meth:string%20%3F;crop_rotation:string%20%3F;agrochem_addition:string%20%3F;tillage:tillage_enum%20%3F;fire:string%20%3F;flooding:string%20%3F;extreme_event:string%20%3F;horizon:horizon_enum%20%3F;horizon_meth:string%20%3F;sieving:string%20%3F;water_content:string%20%3F;water_content_soil_meth:string%20%3F;samp_vol_we_dna_ext:string%20%3F;pool_dna_extracts:string%20%3F;store_cond:string%20%3F;link_climate_info:string%20%3F;annual_temp:string%20%3F;season_temp:string%20%3F;annual_precpt:string%20%3F;season_precpt:string%20%3F;link_class_info:string%20%3F;fao_class:fao_class_enum%20%3F;local_class:string%20%3F;local_class_meth:string%20%3F;soil_type:string%20%3F;soil_type_meth:string%20%3F;slope_gradient:string%20%3F;slope_aspect:string%20%3F;profile_position:profile_position_enum%20%3F;drainage_class:drainage_class_enum%20%3F;texture:string%20%3F;texture_meth:string%20%3F;ph:string%20%3F;ph_meth:string%20%3F;tot_org_carb:string%20%3F;tot_org_c_meth:string%20%3F;tot_nitro_content:string%20%3F;tot_nitro_content_meth:string%20%3F;microbial_biomass:string%20%3F;microbial_biomass_meth:string%20%3F;link_addit_analys:string%20%3F;extreme_salinity:string%20%3F;salinity_meth:string%20%3F;heavy_metals:string%20%3F;heavy_metals_meth:string%20%3F;al_sat:string%20%3F;al_sat_meth:string%20%3F;misc_param:string%20%3F]^-[SoilMiuvig],[Soil]^-[SoilMisag],[Soil]^-[SoilMimarksS],[Soil]^-[SoilMimarksC],[Soil]^-[SoilMimag],[Soil]^-[SoilMigsVi],[Soil]^-[SoilMigsPl],[Soil]^-[SoilMigsOrg],[Soil]^-[SoilMigsEu],[Soil]^-[SoilMigsBa],[Soil]^-[SoilMe]) + +## Children + + * [SoilMe](SoilMe.md) - Combinatorial checklist for soil with me + * [SoilMigsBa](SoilMigsBa.md) - Combinatorial checklist for soil with migs_ba + * [SoilMigsEu](SoilMigsEu.md) - Combinatorial checklist for soil with migs_eu + * [SoilMigsOrg](SoilMigsOrg.md) - Combinatorial checklist for soil with migs_org + * [SoilMigsPl](SoilMigsPl.md) - Combinatorial checklist for soil with migs_pl + * [SoilMigsVi](SoilMigsVi.md) - Combinatorial checklist for soil with migs_vi + * [SoilMimag](SoilMimag.md) - Combinatorial checklist for soil with mimag + * [SoilMimarksC](SoilMimarksC.md) - Combinatorial checklist for soil with mimarks_c + * [SoilMimarksS](SoilMimarksS.md) - Combinatorial checklist for soil with mimarks_s + * [SoilMisag](SoilMisag.md) - Combinatorial checklist for soil with misag + * [SoilMiuvig](SoilMiuvig.md) - Combinatorial checklist for soil with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMe.md b/mixs6/SoilMe.md new file mode 100644 index 00000000..d5b75606 --- /dev/null +++ b/mixs6/SoilMe.md @@ -0,0 +1,232 @@ + +# Class: SoilMe + + +Combinatorial checklist for soil with me + +URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMe|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Soil]^-[SoilMe],[Soil],[Me]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMigsBa.md b/mixs6/SoilMigsBa.md new file mode 100644 index 00000000..ab04e1be --- /dev/null +++ b/mixs6/SoilMigsBa.md @@ -0,0 +1,232 @@ + +# Class: SoilMigsBa + + +Combinatorial checklist for soil with migs_ba + +URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsBa|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Soil]^-[SoilMigsBa],[Soil],[MigsBa]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMigsEu.md b/mixs6/SoilMigsEu.md new file mode 100644 index 00000000..4552ac13 --- /dev/null +++ b/mixs6/SoilMigsEu.md @@ -0,0 +1,232 @@ + +# Class: SoilMigsEu + + +Combinatorial checklist for soil with migs_eu + +URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsEu|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Soil]^-[SoilMigsEu],[Soil],[MigsEu]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMigsOrg.md b/mixs6/SoilMigsOrg.md new file mode 100644 index 00000000..15bddc18 --- /dev/null +++ b/mixs6/SoilMigsOrg.md @@ -0,0 +1,232 @@ + +# Class: SoilMigsOrg + + +Combinatorial checklist for soil with migs_org + +URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsOrg|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Soil]^-[SoilMigsOrg],[Soil],[MigsOrg]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMigsPl.md b/mixs6/SoilMigsPl.md new file mode 100644 index 00000000..88f3149b --- /dev/null +++ b/mixs6/SoilMigsPl.md @@ -0,0 +1,232 @@ + +# Class: SoilMigsPl + + +Combinatorial checklist for soil with migs_pl + +URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsPl|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Soil]^-[SoilMigsPl],[Soil],[MigsPl]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMigsVi.md b/mixs6/SoilMigsVi.md new file mode 100644 index 00000000..c90e6092 --- /dev/null +++ b/mixs6/SoilMigsVi.md @@ -0,0 +1,232 @@ + +# Class: SoilMigsVi + + +Combinatorial checklist for soil with migs_vi + +URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsVi|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Soil]^-[SoilMigsVi],[Soil],[MigsVi]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMimag.md b/mixs6/SoilMimag.md new file mode 100644 index 00000000..d4ad6c7a --- /dev/null +++ b/mixs6/SoilMimag.md @@ -0,0 +1,232 @@ + +# Class: SoilMimag + + +Combinatorial checklist for soil with mimag + +URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimag|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Soil]^-[SoilMimag],[Soil],[Mimag]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMimarksC.md b/mixs6/SoilMimarksC.md new file mode 100644 index 00000000..64e66456 --- /dev/null +++ b/mixs6/SoilMimarksC.md @@ -0,0 +1,232 @@ + +# Class: SoilMimarksC + + +Combinatorial checklist for soil with mimarks_c + +URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksC|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Soil]^-[SoilMimarksC],[Soil],[MimarksC]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMimarksS.md b/mixs6/SoilMimarksS.md new file mode 100644 index 00000000..f6e4c733 --- /dev/null +++ b/mixs6/SoilMimarksS.md @@ -0,0 +1,232 @@ + +# Class: SoilMimarksS + + +Combinatorial checklist for soil with mimarks_s + +URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksS|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Soil]^-[SoilMimarksS],[Soil],[MimarksS]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMisag.md b/mixs6/SoilMisag.md new file mode 100644 index 00000000..28d400c5 --- /dev/null +++ b/mixs6/SoilMisag.md @@ -0,0 +1,232 @@ + +# Class: SoilMisag + + +Combinatorial checklist for soil with misag + +URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMisag|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Soil]^-[SoilMisag],[Soil],[Misag]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/SoilMiuvig.md b/mixs6/SoilMiuvig.md new file mode 100644 index 00000000..a491c7bc --- /dev/null +++ b/mixs6/SoilMiuvig.md @@ -0,0 +1,232 @@ + +# Class: SoilMiuvig + + +Combinatorial checklist for soil with miuvig + +URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Soil]^-[SoilMiuvig],[Soil],[Miuvig]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [String](types/String.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [String](types/String.md) + * Example: 12.5 degree Celsius None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [String](types/String.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [String](types/String.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [String](types/String.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [String](types/String.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [String](types/String.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [String](types/String.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [String](types/String.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [String](types/String.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [String](types/String.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [String](types/String.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludge.md b/mixs6/WastewaterSludge.md new file mode 100644 index 00000000..909a1a7c --- /dev/null +++ b/mixs6/WastewaterSludge.md @@ -0,0 +1,181 @@ + +# Class: WastewaterSludge + + +wastewater/sludge + +URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig],[WastewaterSludgeMisag],[WastewaterSludgeMimarksS],[WastewaterSludgeMimarksC],[WastewaterSludgeMimag],[WastewaterSludgeMigsVi],[WastewaterSludgeMigsPl],[WastewaterSludgeMigsOrg],[WastewaterSludgeMigsEu],[WastewaterSludgeMigsBa],[WastewaterSludgeMe],[WastewaterSludge|alkalinity:string%20%3F;biochem_oxygen_dem:string%20%3F;chem_administration:string%20%3F;chem_oxygen_dem:string%20%3F;efficiency_percent:string%20%3F;emulsions:string%20%3F;gaseous_substances:string%20%3F;indust_eff_percent:string%20%3F;inorg_particles:string%20%3F;misc_param:string%20%3F;nitrate:string%20%3F;org_particles:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;perturbation:string%20%3F;phosphate:string%20%3F;pre_treatment:string%20%3F;primary_treatment:string%20%3F;reactor_type:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;secondary_treatment:string%20%3F;sewage_type:string%20%3F;sludge_retent_time:string%20%3F;sodium:string%20%3F;soluble_inorg_mat:string%20%3F;soluble_org_mat:string%20%3F;suspend_solids:string%20%3F;temp:string%20%3F;tertiary_treatment:string%20%3F;tot_nitro:string%20%3F;tot_phosphate:string%20%3F;wastewater_type:string%20%3F]^-[WastewaterSludgeMiuvig],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge]^-[WastewaterSludgeMe]) + +## Children + + * [WastewaterSludgeMe](WastewaterSludgeMe.md) - Combinatorial checklist for wastewater_sludge with me + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - Combinatorial checklist for wastewater_sludge with migs_ba + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - Combinatorial checklist for wastewater_sludge with migs_eu + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - Combinatorial checklist for wastewater_sludge with migs_org + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - Combinatorial checklist for wastewater_sludge with migs_pl + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - Combinatorial checklist for wastewater_sludge with migs_vi + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - Combinatorial checklist for wastewater_sludge with mimag + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - Combinatorial checklist for wastewater_sludge with mimarks_c + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - Combinatorial checklist for wastewater_sludge with mimarks_s + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - Combinatorial checklist for wastewater_sludge with misag + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) - Combinatorial checklist for wastewater_sludge with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMe.md b/mixs6/WastewaterSludgeMe.md new file mode 100644 index 00000000..8bad9eaf --- /dev/null +++ b/mixs6/WastewaterSludgeMe.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMe + + +Combinatorial checklist for wastewater_sludge with me + +URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludgeMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMe|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Me],[WastewaterSludge]^-[WastewaterSludgeMe],[WastewaterSludge],[Me]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMigsBa.md b/mixs6/WastewaterSludgeMigsBa.md new file mode 100644 index 00000000..c611e1f8 --- /dev/null +++ b/mixs6/WastewaterSludgeMigsBa.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMigsBa + + +Combinatorial checklist for wastewater_sludge with migs_ba + +URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterSludgeMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsBa|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsBa],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge],[MigsBa]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMigsEu.md b/mixs6/WastewaterSludgeMigsEu.md new file mode 100644 index 00000000..70a0c1ba --- /dev/null +++ b/mixs6/WastewaterSludgeMigsEu.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMigsEu + + +Combinatorial checklist for wastewater_sludge with migs_eu + +URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterSludgeMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsEu|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge],[MigsEu]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMigsOrg.md b/mixs6/WastewaterSludgeMigsOrg.md new file mode 100644 index 00000000..932a870f --- /dev/null +++ b/mixs6/WastewaterSludgeMigsOrg.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMigsOrg + + +Combinatorial checklist for wastewater_sludge with migs_org + +URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsOrg|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge],[MigsOrg]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMigsPl.md b/mixs6/WastewaterSludgeMigsPl.md new file mode 100644 index 00000000..e1184e09 --- /dev/null +++ b/mixs6/WastewaterSludgeMigsPl.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMigsPl + + +Combinatorial checklist for wastewater_sludge with migs_pl + +URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterSludgeMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsPl|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge],[MigsPl]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMigsVi.md b/mixs6/WastewaterSludgeMigsVi.md new file mode 100644 index 00000000..884f9914 --- /dev/null +++ b/mixs6/WastewaterSludgeMigsVi.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMigsVi + + +Combinatorial checklist for wastewater_sludge with migs_vi + +URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterSludgeMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsVi|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge],[MigsVi]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMimag.md b/mixs6/WastewaterSludgeMimag.md new file mode 100644 index 00000000..ac381809 --- /dev/null +++ b/mixs6/WastewaterSludgeMimag.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMimag + + +Combinatorial checklist for wastewater_sludge with mimag + +URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSludgeMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimag|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Mimag],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge],[Mimag]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMimarksC.md b/mixs6/WastewaterSludgeMimarksC.md new file mode 100644 index 00000000..f5971281 --- /dev/null +++ b/mixs6/WastewaterSludgeMimarksC.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMimarksC + + +Combinatorial checklist for wastewater_sludge with mimarks_c + +URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksC|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksC],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge],[MimarksC]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMimarksS.md b/mixs6/WastewaterSludgeMimarksS.md new file mode 100644 index 00000000..b088bdb6 --- /dev/null +++ b/mixs6/WastewaterSludgeMimarksS.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMimarksS + + +Combinatorial checklist for wastewater_sludge with mimarks_s + +URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksS|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge],[MimarksS]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMisag.md b/mixs6/WastewaterSludgeMisag.md new file mode 100644 index 00000000..87211def --- /dev/null +++ b/mixs6/WastewaterSludgeMisag.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMisag + + +Combinatorial checklist for wastewater_sludge with misag + +URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSludgeMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMisag|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Misag],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge],[Misag]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/WastewaterSludgeMiuvig.md b/mixs6/WastewaterSludgeMiuvig.md new file mode 100644 index 00000000..941c3b55 --- /dev/null +++ b/mixs6/WastewaterSludgeMiuvig.md @@ -0,0 +1,172 @@ + +# Class: WastewaterSludgeMiuvig + + +Combinatorial checklist for wastewater_sludge with miuvig + +URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterSludgeMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Miuvig],[WastewaterSludge]^-[WastewaterSludgeMiuvig],[WastewaterSludge],[Miuvig]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [String](types/String.md) + * Example: None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [String](types/String.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [String](types/String.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None diff --git a/mixs6/Water.md b/mixs6/Water.md new file mode 100644 index 00000000..1204c230 --- /dev/null +++ b/mixs6/Water.md @@ -0,0 +1,357 @@ + +# Class: Water + + +water + +URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig],[WaterMisag],[WaterMimarksS],[WaterMimarksC],[WaterMimag],[WaterMigsVi],[WaterMigsPl],[WaterMigsOrg],[WaterMigsEu],[WaterMigsBa],[WaterMe],[Water|alkalinity:string%20%3F;alkalinity_method:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;atmospheric_data:string%20%3F;bacteria_carb_prod:string%20%3F;bac_prod:string%20%3F;bac_resp:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;conduc:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_nitro:string%20%3F;diss_inorg_phosp:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;down_par:string%20%3F;fluor:string%20%3F;glucosidase_act:string%20%3F;light_intensity:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;part_org_carb:string%20%3F;part_org_nitro:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;photon_flux:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;primary_prod:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;size_frac_low:string%20%3F;size_frac_up:string%20%3F;sodium:string%20%3F;soluble_react_phosp:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;suspend_part_matter:string%20%3F;temp:string%20%3F;tidal_stage:tidal_stage_enum%20%3F;tot_depth_water_col:string%20%3F;tot_diss_nitro:string%20%3F;tot_inorg_nitro:string%20%3F;tot_nitro:string%20%3F;tot_part_carb:string%20%3F;tot_phosp:string%20%3F;turbidity:string%20%3F;water_current:string%20%3F]^-[WaterMiuvig],[Water]^-[WaterMisag],[Water]^-[WaterMimarksS],[Water]^-[WaterMimarksC],[Water]^-[WaterMimag],[Water]^-[WaterMigsVi],[Water]^-[WaterMigsPl],[Water]^-[WaterMigsOrg],[Water]^-[WaterMigsEu],[Water]^-[WaterMigsBa],[Water]^-[WaterMe]) + +## Children + + * [WaterMe](WaterMe.md) - Combinatorial checklist for water with me + * [WaterMigsBa](WaterMigsBa.md) - Combinatorial checklist for water with migs_ba + * [WaterMigsEu](WaterMigsEu.md) - Combinatorial checklist for water with migs_eu + * [WaterMigsOrg](WaterMigsOrg.md) - Combinatorial checklist for water with migs_org + * [WaterMigsPl](WaterMigsPl.md) - Combinatorial checklist for water with migs_pl + * [WaterMigsVi](WaterMigsVi.md) - Combinatorial checklist for water with migs_vi + * [WaterMimag](WaterMimag.md) - Combinatorial checklist for water with mimag + * [WaterMimarksC](WaterMimarksC.md) - Combinatorial checklist for water with mimarks_c + * [WaterMimarksS](WaterMimarksS.md) - Combinatorial checklist for water with mimarks_s + * [WaterMisag](WaterMisag.md) - Combinatorial checklist for water with misag + * [WaterMiuvig](WaterMiuvig.md) - Combinatorial checklist for water with miuvig + +## Referenced by class + + +## Attributes + + +### Own + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMe.md b/mixs6/WaterMe.md new file mode 100644 index 00000000..3cf4af09 --- /dev/null +++ b/mixs6/WaterMe.md @@ -0,0 +1,348 @@ + +# Class: WaterMe + + +Combinatorial checklist for water with me + +URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Me],[Water]^-[WaterMe],[Water],[Me]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [Me](Me.md) - me Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMigsBa.md b/mixs6/WaterMigsBa.md new file mode 100644 index 00000000..0309b2a3 --- /dev/null +++ b/mixs6/WaterMigsBa.md @@ -0,0 +1,348 @@ + +# Class: WaterMigsBa + + +Combinatorial checklist for water with migs_ba + +URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsBa],[Water]^-[WaterMigsBa],[Water],[MigsBa]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMigsEu.md b/mixs6/WaterMigsEu.md new file mode 100644 index 00000000..854489cf --- /dev/null +++ b/mixs6/WaterMigsEu.md @@ -0,0 +1,348 @@ + +# Class: WaterMigsEu + + +Combinatorial checklist for water with migs_eu + +URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsEu],[Water]^-[WaterMigsEu],[Water],[MigsEu]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMigsOrg.md b/mixs6/WaterMigsOrg.md new file mode 100644 index 00000000..dce470a1 --- /dev/null +++ b/mixs6/WaterMigsOrg.md @@ -0,0 +1,348 @@ + +# Class: WaterMigsOrg + + +Combinatorial checklist for water with migs_org + +URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsOrg],[Water]^-[WaterMigsOrg],[Water],[MigsOrg]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMigsPl.md b/mixs6/WaterMigsPl.md new file mode 100644 index 00000000..6d93bc90 --- /dev/null +++ b/mixs6/WaterMigsPl.md @@ -0,0 +1,348 @@ + +# Class: WaterMigsPl + + +Combinatorial checklist for water with migs_pl + +URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsPl],[Water]^-[WaterMigsPl],[Water],[MigsPl]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMigsVi.md b/mixs6/WaterMigsVi.md new file mode 100644 index 00000000..8909545e --- /dev/null +++ b/mixs6/WaterMigsVi.md @@ -0,0 +1,348 @@ + +# Class: WaterMigsVi + + +Combinatorial checklist for water with migs_vi + +URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsVi],[Water]^-[WaterMigsVi],[Water],[MigsVi]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMimag.md b/mixs6/WaterMimag.md new file mode 100644 index 00000000..a61d6060 --- /dev/null +++ b/mixs6/WaterMimag.md @@ -0,0 +1,348 @@ + +# Class: WaterMimag + + +Combinatorial checklist for water with mimag + +URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Mimag],[Water]^-[WaterMimag],[Water],[Mimag]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [Mimag](Mimag.md) - mimag Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMimarksC.md b/mixs6/WaterMimarksC.md new file mode 100644 index 00000000..7fed9e00 --- /dev/null +++ b/mixs6/WaterMimarksC.md @@ -0,0 +1,348 @@ + +# Class: WaterMimarksC + + +Combinatorial checklist for water with mimarks_c + +URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksC],[Water]^-[WaterMimarksC],[Water],[MimarksC]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMimarksS.md b/mixs6/WaterMimarksS.md new file mode 100644 index 00000000..500c277c --- /dev/null +++ b/mixs6/WaterMimarksS.md @@ -0,0 +1,348 @@ + +# Class: WaterMimarksS + + +Combinatorial checklist for water with mimarks_s + +URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksS],[Water]^-[WaterMimarksS],[Water],[MimarksS]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMisag.md b/mixs6/WaterMisag.md new file mode 100644 index 00000000..f02422aa --- /dev/null +++ b/mixs6/WaterMisag.md @@ -0,0 +1,348 @@ + +# Class: WaterMisag + + +Combinatorial checklist for water with misag + +URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Misag],[Water]^-[WaterMisag],[Water],[Misag]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [Misag](Misag.md) - misag Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMiuvig.md b/mixs6/WaterMiuvig.md new file mode 100644 index 00000000..e04e19fe --- /dev/null +++ b/mixs6/WaterMiuvig.md @@ -0,0 +1,348 @@ + +# Class: WaterMiuvig + + +Combinatorial checklist for water with miuvig + +URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Miuvig],[Water]^-[WaterMiuvig],[Water],[Miuvig]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [String](types/String.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [String](types/String.md) + * Example: 0.005 mole per liter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [String](types/String.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [String](types/String.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [String](types/String.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [String](types/String.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [String](types/String.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [String](types/String.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [String](types/String.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [String](types/String.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [String](types/String.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [String](types/String.md) + * Example: 5 milligram per cubic meter None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [String](types/String.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [String](types/String.md) + * Example: 1000 kilogram per cubic meter None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [String](types/String.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [String](types/String.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [String](types/String.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [String](types/String.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [String](types/String.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [String](types/String.md) + * Example: 28.71 microEinstein per square meter per second None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [String](types/String.md) + * Example: 2.5 volts None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [String](types/String.md) + * Example: 5 mol per liter per hour None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [String](types/String.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [String](types/String.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [String](types/String.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [String](types/String.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [String](types/String.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [String](types/String.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [String](types/String.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [String](types/String.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [String](types/String.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [String](types/String.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [String](types/String.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [String](types/String.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [String](types/String.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [String](types/String.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [String](types/String.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [String](types/String.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [String](types/String.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [String](types/String.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [String](types/String.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [String](types/String.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [String](types/String.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [String](types/String.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [String](types/String.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [String](types/String.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [String](types/String.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [String](types/String.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [String](types/String.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [String](types/String.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [String](types/String.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [String](types/String.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [String](types/String.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [String](types/String.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [String](types/String.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [String](types/String.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [String](types/String.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [String](types/String.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [String](types/String.md) + * Example: 10 cubic meter per second None diff --git a/mixs6/abs_air_humidity.md b/mixs6/abs_air_humidity.md new file mode 100644 index 00000000..ce7d14ab --- /dev/null +++ b/mixs6/abs_air_humidity.md @@ -0,0 +1,48 @@ + +# Slot: abs_air_humidity + + +Actual mass of water vapor - mh20 - present in the air water vapor mixture + +URI: [mixs.vocab:abs_air_humidity](https://w3id.org/mixs/vocab/abs_air_humidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | absolute air humidity | +| **Mappings:** | | MIXS:0000122 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per gram, kilogram per kilogram, kilogram, pound | +| | | Occurrence: 1 | +| | | Position: 4 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='9 gram per gram', description=None) | + diff --git a/mixs6/adapters.md b/mixs6/adapters.md new file mode 100644 index 00000000..853c935f --- /dev/null +++ b/mixs6/adapters.md @@ -0,0 +1,56 @@ + +# Slot: adapters + + +Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + +URI: [mixs.vocab:adapters](https://w3id.org/mixs/vocab/adapters) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | adapters | +| **Comments:** | | Expected value: adapter A and B sequence | +| | | Preferred unit: | +| | | Position: 48.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT', description=None) | + diff --git a/mixs6/add_recov_method.md b/mixs6/add_recov_method.md new file mode 100644 index 00000000..da1de359 --- /dev/null +++ b/mixs6/add_recov_method.md @@ -0,0 +1,48 @@ + +# Slot: add_recov_method + + +Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:add_recov_method](https://w3id.org/mixs/vocab/add_recov_method) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | secondary and tertiary recovery methods and start date | +| **Mappings:** | | MIXS:0001009 | +| **Comments:** | | Expected value: enumeration;timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 28 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Polymer Addition;2018-06-21T14:30Z', description=None) | + diff --git a/mixs6/additional_info.md b/mixs6/additional_info.md new file mode 100644 index 00000000..6fbb55ac --- /dev/null +++ b/mixs6/additional_info.md @@ -0,0 +1,60 @@ + +# Slot: additional_info + + +Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + +URI: [mixs.vocab:additional_info](https://w3id.org/mixs/vocab/additional_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | additional info | +| **Mappings:** | | MIXS:0000300 | +| **Comments:** | | Expected value: text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 94 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/address.md b/mixs6/address.md new file mode 100644 index 00000000..8291231f --- /dev/null +++ b/mixs6/address.md @@ -0,0 +1,48 @@ + +# Slot: address + + +The street name and building number where the sampling occurred. + +URI: [mixs.vocab:address](https://w3id.org/mixs/vocab/address) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | address | +| **Mappings:** | | MIXS:0000218 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 27 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/adj_room.md b/mixs6/adj_room.md new file mode 100644 index 00000000..6de39287 --- /dev/null +++ b/mixs6/adj_room.md @@ -0,0 +1,48 @@ + +# Slot: adj_room + + +List of rooms (room number, room name) immediately adjacent to the sampling room + +URI: [mixs.vocab:adj_room](https://w3id.org/mixs/vocab/adj_room) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | adjacent rooms | +| **Mappings:** | | MIXS:0000219 | +| **Comments:** | | Expected value: room name;room number | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 28 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/aero_struc.md b/mixs6/aero_struc.md new file mode 100644 index 00000000..e3ce786f --- /dev/null +++ b/mixs6/aero_struc.md @@ -0,0 +1,48 @@ + +# Slot: aero_struc + + +Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + +URI: [mixs.vocab:aero_struc](https://w3id.org/mixs/vocab/aero_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aerospace structure | +| **Mappings:** | | MIXS:0000773 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 29 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='plane', description=None) | + diff --git a/mixs6/agrochem_addition.md b/mixs6/agrochem_addition.md new file mode 100644 index 00000000..afb0af15 --- /dev/null +++ b/mixs6/agrochem_addition.md @@ -0,0 +1,48 @@ + +# Slot: agrochem_addition + + +Addition of fertilizers, pesticides, etc. - amount and time of applications + +URI: [mixs.vocab:agrochem_addition](https://w3id.org/mixs/vocab/agrochem_addition) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/agrochemical additions | +| **Mappings:** | | MIXS:0000639 | +| **Comments:** | | Expected value: agrochemical name;agrochemical amount;timestamp | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 7 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='roundup;5 milligram per liter;2018-06-21', description=None) | + diff --git a/mixs6/air_temp.md b/mixs6/air_temp.md new file mode 100644 index 00000000..ecda9ceb --- /dev/null +++ b/mixs6/air_temp.md @@ -0,0 +1,48 @@ + +# Slot: air_temp + + +Temperature of the air at the time of sampling + +URI: [mixs.vocab:air_temp](https://w3id.org/mixs/vocab/air_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | air temperature | +| **Mappings:** | | MIXS:0000124 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 6 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='20 degree Celsius', description=None) | + diff --git a/mixs6/air_temp_regm.md b/mixs6/air_temp_regm.md new file mode 100644 index 00000000..46b24fde --- /dev/null +++ b/mixs6/air_temp_regm.md @@ -0,0 +1,48 @@ + +# Slot: air_temp_regm + + +Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + +URI: [mixs.vocab:air_temp_regm](https://w3id.org/mixs/vocab/air_temp_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | air temperature regimen | +| **Mappings:** | | MIXS:0000551 | +| **Comments:** | | Expected value: temperature value;treatment interval and duration | +| | | Preferred unit: degree Celsius | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/al_sat.md b/mixs6/al_sat.md new file mode 100644 index 00000000..3e0883a7 --- /dev/null +++ b/mixs6/al_sat.md @@ -0,0 +1,48 @@ + +# Slot: al_sat + + +Aluminum saturation (esp. For tropical soils) + +URI: [mixs.vocab:al_sat](https://w3id.org/mixs/vocab/al_sat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/Al saturation | +| **Mappings:** | | MIXS:0000607 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 50 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/al_sat_meth.md b/mixs6/al_sat_meth.md new file mode 100644 index 00000000..2bf95412 --- /dev/null +++ b/mixs6/al_sat_meth.md @@ -0,0 +1,48 @@ + +# Slot: al_sat_meth + + +Reference or method used in determining Al saturation + +URI: [mixs.vocab:al_sat_meth](https://w3id.org/mixs/vocab/al_sat_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/Al saturation method | +| **Mappings:** | | MIXS:0000324 | +| **Comments:** | | Expected value: PMID,DOI or URL | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 51 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/alkalinity.md b/mixs6/alkalinity.md new file mode 100644 index 00000000..c1b83ff5 --- /dev/null +++ b/mixs6/alkalinity.md @@ -0,0 +1,120 @@ + +# Slot: alkalinity + + +Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + +URI: [mixs.vocab:alkalinity](https://w3id.org/mixs/vocab/alkalinity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkalinity | +| **Mappings:** | | MIXS:0000421 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milliequivalent per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 56 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='50 milligram per liter', description=None) | + diff --git a/mixs6/alkalinity_method.md b/mixs6/alkalinity_method.md new file mode 100644 index 00000000..879fdf80 --- /dev/null +++ b/mixs6/alkalinity_method.md @@ -0,0 +1,72 @@ + +# Slot: alkalinity_method + + +Method used for alkalinity measurement + +URI: [mixs.vocab:alkalinity_method](https://w3id.org/mixs/vocab/alkalinity_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkalinity method | +| **Mappings:** | | MIXS:0000298 | +| **Comments:** | | Expected value: description of method | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 57 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='titration', description=None) | + diff --git a/mixs6/alkyl_diethers.md b/mixs6/alkyl_diethers.md new file mode 100644 index 00000000..9e510f2c --- /dev/null +++ b/mixs6/alkyl_diethers.md @@ -0,0 +1,72 @@ + +# Slot: alkyl_diethers + + +Concentration of alkyl diethers + +URI: [mixs.vocab:alkyl_diethers](https://w3id.org/mixs/vocab/alkyl_diethers) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | alkyl diethers | +| **Mappings:** | | MIXS:0000490 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.005 mole per liter', description=None) | + diff --git a/mixs6/alt.md b/mixs6/alt.md new file mode 100644 index 00000000..cfb9e50c --- /dev/null +++ b/mixs6/alt.md @@ -0,0 +1,57 @@ + +# Slot: alt + + +Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + +URI: [mixs.vocab:alt](https://w3id.org/mixs/vocab/alt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | altitude | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Position: | +| | | CHECKLIST migs_eu: E | +| | | CHECKLIST migs_ba: E | +| | | CHECKLIST migs_pl: E | +| | | CHECKLIST migs_vi: E | +| | | CHECKLIST migs_org: E | +| | | CHECKLIST me: E | +| | | CHECKLIST mimarks_s: E | +| | | CHECKLIST mimarks_c: E | +| | | CHECKLIST misag: E | +| | | CHECKLIST mimag: E | +| | | CHECKLIST miuvig: E | +| | | This field is used in: 3 packages: air, host-associated, miscellaneous natural or artificial environment | +| **Examples:** | | Example(value='100 meter', description=None) | + diff --git a/mixs6/aminopept_act.md b/mixs6/aminopept_act.md new file mode 100644 index 00000000..18ea2b2e --- /dev/null +++ b/mixs6/aminopept_act.md @@ -0,0 +1,72 @@ + +# Slot: aminopept_act + + +Measurement of aminopeptidase activity + +URI: [mixs.vocab:aminopept_act](https://w3id.org/mixs/vocab/aminopept_act) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aminopeptidase activity | +| **Mappings:** | | MIXS:0000172 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.269 mole per liter per hour', description=None) | + diff --git a/mixs6/ammonium.md b/mixs6/ammonium.md new file mode 100644 index 00000000..79e0fdb8 --- /dev/null +++ b/mixs6/ammonium.md @@ -0,0 +1,108 @@ + +# Slot: ammonium + + +Concentration of ammonium in the sample + +URI: [mixs.vocab:ammonium](https://w3id.org/mixs/vocab/ammonium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ammonium | +| **Mappings:** | | MIXS:0000427 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 63 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.5 milligram per liter', description=None) | + diff --git a/mixs6/amniotic_fluid_color.md b/mixs6/amniotic_fluid_color.md new file mode 100644 index 00000000..acd8387c --- /dev/null +++ b/mixs6/amniotic_fluid_color.md @@ -0,0 +1,48 @@ + +# Slot: amniotic_fluid_color + + +Specification of the color of the amniotic fluid sample + +URI: [mixs.vocab:amniotic_fluid_color](https://w3id.org/mixs/vocab/amniotic_fluid_color) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/color | +| **Mappings:** | | MIXS:0000276 | +| **Comments:** | | Expected value: color | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 39 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/amount_light.md b/mixs6/amount_light.md new file mode 100644 index 00000000..7a5263e5 --- /dev/null +++ b/mixs6/amount_light.md @@ -0,0 +1,48 @@ + +# Slot: amount_light + + +The unit of illuminance and luminous emittance, measuring luminous flux per unit area + +URI: [mixs.vocab:amount_light](https://w3id.org/mixs/vocab/amount_light) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amount of light | +| **Mappings:** | | MIXS:0000140 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: lux, lumens per square meter | +| | | Occurrence: 1 | +| | | Position: 30 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ances_data.md b/mixs6/ances_data.md new file mode 100644 index 00000000..0ec8ed6b --- /dev/null +++ b/mixs6/ances_data.md @@ -0,0 +1,60 @@ + +# Slot: ances_data + + +Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + +URI: [mixs.vocab:ances_data](https://w3id.org/mixs/vocab/ances_data) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ancestral data | +| **Mappings:** | | MIXS:0000247 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='A/3*B', description=None) | + diff --git a/mixs6/annot.md b/mixs6/annot.md new file mode 100644 index 00000000..def42193 --- /dev/null +++ b/mixs6/annot.md @@ -0,0 +1,56 @@ + +# Slot: annot + + +Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + +URI: [mixs.vocab:annot](https://w3id.org/mixs/vocab/annot) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | annotation | +| **Comments:** | | Expected value: name of tool or pipeline used, or annotation source description | +| | | Preferred unit: | +| | | Position: 57.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='prokka', description=None) | + diff --git a/mixs6/annual_precpt.md b/mixs6/annual_precpt.md new file mode 100644 index 00000000..e380a5dd --- /dev/null +++ b/mixs6/annual_precpt.md @@ -0,0 +1,48 @@ + +# Slot: annual_precpt + + +The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + +URI: [mixs.vocab:annual_precpt](https://w3id.org/mixs/vocab/annual_precpt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean annual precipitation | +| **Mappings:** | | MIXS:0000644 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter | +| | | Occurrence: 1 | +| | | Position: 23 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/annual_temp.md b/mixs6/annual_temp.md new file mode 100644 index 00000000..209dd2c6 --- /dev/null +++ b/mixs6/annual_temp.md @@ -0,0 +1,48 @@ + +# Slot: annual_temp + + +Mean annual temperature + +URI: [mixs.vocab:annual_temp](https://w3id.org/mixs/vocab/annual_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean annual temperature | +| **Mappings:** | | MIXS:0000642 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 21 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='12.5 degree Celsius', description=None) | + diff --git a/mixs6/antibiotic_regm.md b/mixs6/antibiotic_regm.md new file mode 100644 index 00000000..8eb661ad --- /dev/null +++ b/mixs6/antibiotic_regm.md @@ -0,0 +1,48 @@ + +# Slot: antibiotic_regm + + +Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + +URI: [mixs.vocab:antibiotic_regm](https://w3id.org/mixs/vocab/antibiotic_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | antibiotic regimen | +| **Mappings:** | | MIXS:0000553 | +| **Comments:** | | Expected value: antibiotic name;antibiotic amount;treatment interval and duration | +| | | Preferred unit: milligram | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/api.md b/mixs6/api.md new file mode 100644 index 00000000..88bf4021 --- /dev/null +++ b/mixs6/api.md @@ -0,0 +1,60 @@ + +# Slot: api + + +API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + +URI: [mixs.vocab:api](https://w3id.org/mixs/vocab/api) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | API gravity | +| **Mappings:** | | MIXS:0000157 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degrees API | +| | | Occurrence: 1 | +| | | Position: 85 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/arch_struc.md b/mixs6/arch_struc.md new file mode 100644 index 00000000..3c887bb6 --- /dev/null +++ b/mixs6/arch_struc.md @@ -0,0 +1,48 @@ + +# Slot: arch_struc + + +An architectural structure is a human-made, free-standing, immobile outdoor construction + +URI: [mixs.vocab:arch_struc](https://w3id.org/mixs/vocab/arch_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | architectural structure | +| **Mappings:** | | MIXS:0000774 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 31 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='shed', description=None) | + diff --git a/mixs6/aromatics_pc.md b/mixs6/aromatics_pc.md new file mode 100644 index 00000000..0d1e1017 --- /dev/null +++ b/mixs6/aromatics_pc.md @@ -0,0 +1,60 @@ + +# Slot: aromatics_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:aromatics_pc](https://w3id.org/mixs/vocab/aromatics_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | aromatics wt% | +| **Mappings:** | | MIXS:0000133 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 90 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/asphaltenes_pc.md b/mixs6/asphaltenes_pc.md new file mode 100644 index 00000000..e1fd8307 --- /dev/null +++ b/mixs6/asphaltenes_pc.md @@ -0,0 +1,60 @@ + +# Slot: asphaltenes_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:asphaltenes_pc](https://w3id.org/mixs/vocab/asphaltenes_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | asphaltenes wt% | +| **Mappings:** | | MIXS:0000135 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 92 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/assembly_name.md b/mixs6/assembly_name.md new file mode 100644 index 00000000..15b59d22 --- /dev/null +++ b/mixs6/assembly_name.md @@ -0,0 +1,56 @@ + +# Slot: assembly_name + + +Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + +URI: [mixs.vocab:assembly_name](https://w3id.org/mixs/vocab/assembly_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly name | +| **Comments:** | | Expected value: name and version of assembly | +| | | Preferred unit: | +| | | Position: 55.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='HuRef, JCVI_ISG_i3_1.0', description=None) | + diff --git a/mixs6/assembly_qual.md b/mixs6/assembly_qual.md new file mode 100644 index 00000000..4a45a974 --- /dev/null +++ b/mixs6/assembly_qual.md @@ -0,0 +1,56 @@ + +# Slot: assembly_qual + + +The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + +URI: [mixs.vocab:assembly_qual](https://w3id.org/mixs/vocab/assembly_qual) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly quality | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 54.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='High-quality draft genome', description=None) | + diff --git a/mixs6/assembly_software.md b/mixs6/assembly_software.md new file mode 100644 index 00000000..d1baacb2 --- /dev/null +++ b/mixs6/assembly_software.md @@ -0,0 +1,56 @@ + +# Slot: assembly_software + + +Tool(s) used for assembly, including version number and parameters + +URI: [mixs.vocab:assembly_software](https://w3id.org/mixs/vocab/assembly_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | assembly software | +| **Comments:** | | Expected value: name and version of software, parameters used | +| | | Preferred unit: | +| | | Position: 56.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise', description=None) | + diff --git a/mixs6/atmospheric_data.md b/mixs6/atmospheric_data.md new file mode 100644 index 00000000..ea1ab1fc --- /dev/null +++ b/mixs6/atmospheric_data.md @@ -0,0 +1,48 @@ + +# Slot: atmospheric_data + + +Measurement of atmospheric data; can include multiple data + +URI: [mixs.vocab:atmospheric_data](https://w3id.org/mixs/vocab/atmospheric_data) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | atmospheric data | +| **Mappings:** | | MIXS:0001097 | +| **Comments:** | | Expected value: atmospheric data name;measurement value | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='wind speed;9 knots', description=None) | + diff --git a/mixs6/avg_dew_point.md b/mixs6/avg_dew_point.md new file mode 100644 index 00000000..80027415 --- /dev/null +++ b/mixs6/avg_dew_point.md @@ -0,0 +1,48 @@ + +# Slot: avg_dew_point + + +The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + +URI: [mixs.vocab:avg_dew_point](https://w3id.org/mixs/vocab/avg_dew_point) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average dew point | +| **Mappings:** | | MIXS:0000141 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 33 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25.5 degree Celsius', description=None) | + diff --git a/mixs6/avg_occup.md b/mixs6/avg_occup.md new file mode 100644 index 00000000..027b8cc7 --- /dev/null +++ b/mixs6/avg_occup.md @@ -0,0 +1,48 @@ + +# Slot: avg_occup + + +Daily average occupancy of room + +URI: [mixs.vocab:avg_occup](https://w3id.org/mixs/vocab/avg_occup) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average daily occupancy | +| **Mappings:** | | MIXS:0000775 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 32 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/avg_temp.md b/mixs6/avg_temp.md new file mode 100644 index 00000000..b5d8bd95 --- /dev/null +++ b/mixs6/avg_temp.md @@ -0,0 +1,48 @@ + +# Slot: avg_temp + + +The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + +URI: [mixs.vocab:avg_temp](https://w3id.org/mixs/vocab/avg_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | average temperature | +| **Mappings:** | | MIXS:0000142 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 34 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12.5 degree Celsius', description=None) | + diff --git a/mixs6/bac_prod.md b/mixs6/bac_prod.md new file mode 100644 index 00000000..26338540 --- /dev/null +++ b/mixs6/bac_prod.md @@ -0,0 +1,48 @@ + +# Slot: bac_prod + + +Bacterial production in the water column measured by isotope uptake + +URI: [mixs.vocab:bac_prod](https://w3id.org/mixs/vocab/bac_prod) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial production | +| **Mappings:** | | MIXS:0000683 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='5 milligram per cubic meter per day', description=None) | + diff --git a/mixs6/bac_resp.md b/mixs6/bac_resp.md new file mode 100644 index 00000000..2a2165fd --- /dev/null +++ b/mixs6/bac_resp.md @@ -0,0 +1,48 @@ + +# Slot: bac_resp + + +Measurement of bacterial respiration in the water column + +URI: [mixs.vocab:bac_resp](https://w3id.org/mixs/vocab/bac_resp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial respiration | +| **Mappings:** | | MIXS:0000684 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day, micromole oxygen per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='300 micromole oxygen per liter per hour', description=None) | + diff --git a/mixs6/bacteria_carb_prod.md b/mixs6/bacteria_carb_prod.md new file mode 100644 index 00000000..bf45a4c4 --- /dev/null +++ b/mixs6/bacteria_carb_prod.md @@ -0,0 +1,72 @@ + +# Slot: bacteria_carb_prod + + +Measurement of bacterial carbon production + +URI: [mixs.vocab:bacteria_carb_prod](https://w3id.org/mixs/vocab/bacteria_carb_prod) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bacterial carbon production | +| **Mappings:** | | MIXS:0000173 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: nanogram per hour | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='2.53 microgram per liter per hour', description=None) | + diff --git a/mixs6/barometric_press.md b/mixs6/barometric_press.md new file mode 100644 index 00000000..64467fb8 --- /dev/null +++ b/mixs6/barometric_press.md @@ -0,0 +1,48 @@ + +# Slot: barometric_press + + +Force per unit area exerted against a surface by the weight of air above that surface + +URI: [mixs.vocab:barometric_press](https://w3id.org/mixs/vocab/barometric_press) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | barometric pressure | +| **Mappings:** | | MIXS:0000096 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millibar | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='5 millibar', description=None) | + diff --git a/mixs6/basin.md b/mixs6/basin.md new file mode 100644 index 00000000..f4740e3c --- /dev/null +++ b/mixs6/basin.md @@ -0,0 +1,60 @@ + +# Slot: basin + + +Name of the basin (e.g. Campos) + +URI: [mixs.vocab:basin](https://w3id.org/mixs/vocab/basin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | basin name | +| **Mappings:** | | MIXS:0000290 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bathroom_count.md b/mixs6/bathroom_count.md new file mode 100644 index 00000000..357867db --- /dev/null +++ b/mixs6/bathroom_count.md @@ -0,0 +1,48 @@ + +# Slot: bathroom_count + + +The number of bathrooms in the building + +URI: [mixs.vocab:bathroom_count](https://w3id.org/mixs/vocab/bathroom_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bathroom count | +| **Mappings:** | | MIXS:0000776 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 35 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='1', description=None) | + diff --git a/mixs6/bedroom_count.md b/mixs6/bedroom_count.md new file mode 100644 index 00000000..c25ad009 --- /dev/null +++ b/mixs6/bedroom_count.md @@ -0,0 +1,48 @@ + +# Slot: bedroom_count + + +The number of bedrooms in the building + +URI: [mixs.vocab:bedroom_count](https://w3id.org/mixs/vocab/bedroom_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bedroom count | +| **Mappings:** | | MIXS:0000777 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 36 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/benzene.md b/mixs6/benzene.md new file mode 100644 index 00000000..89a322bb --- /dev/null +++ b/mixs6/benzene.md @@ -0,0 +1,60 @@ + +# Slot: benzene + + +Concentration of benzene in the sample + +URI: [mixs.vocab:benzene](https://w3id.org/mixs/vocab/benzene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | benzene | +| **Mappings:** | | MIXS:0000153 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 81 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bin_param.md b/mixs6/bin_param.md new file mode 100644 index 00000000..de1f06e6 --- /dev/null +++ b/mixs6/bin_param.md @@ -0,0 +1,56 @@ + +# Slot: bin_param + + +The parameters that have been applied during the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:bin_param](https://w3id.org/mixs/vocab/bin_param) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | binning parameters | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 79.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='coverage and kmer', description=None) | + diff --git a/mixs6/bin_software.md b/mixs6/bin_software.md new file mode 100644 index 00000000..96c0f1e9 --- /dev/null +++ b/mixs6/bin_software.md @@ -0,0 +1,56 @@ + +# Slot: bin_software + + +Tool(s) used for the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:bin_software](https://w3id.org/mixs/vocab/bin_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | binning software | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 80.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='concoct and maxbin', description=None) | + diff --git a/mixs6/biochem_oxygen_dem.md b/mixs6/biochem_oxygen_dem.md new file mode 100644 index 00000000..7da1545c --- /dev/null +++ b/mixs6/biochem_oxygen_dem.md @@ -0,0 +1,48 @@ + +# Slot: biochem_oxygen_dem + + +Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + +URI: [mixs.vocab:biochem_oxygen_dem](https://w3id.org/mixs/vocab/biochem_oxygen_dem) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biochemical oxygen demand | +| **Mappings:** | | MIXS:0000653 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/biocide.md b/mixs6/biocide.md new file mode 100644 index 00000000..5caff76b --- /dev/null +++ b/mixs6/biocide.md @@ -0,0 +1,48 @@ + +# Slot: biocide + + +List of biocides (commercial name of product and supplier) and date of administration + +URI: [mixs.vocab:biocide](https://w3id.org/mixs/vocab/biocide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biocide administration | +| **Mappings:** | | MIXS:0001011 | +| **Comments:** | | Expected value: name;name;timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 30 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='ALPHA 1427;Baker Hughes;2008-01-23', description=None) | + diff --git a/mixs6/biocide_admin_method.md b/mixs6/biocide_admin_method.md new file mode 100644 index 00000000..9df099b2 --- /dev/null +++ b/mixs6/biocide_admin_method.md @@ -0,0 +1,48 @@ + +# Slot: biocide_admin_method + + +Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + +URI: [mixs.vocab:biocide_admin_method](https://w3id.org/mixs/vocab/biocide_admin_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biocide administration method | +| **Mappings:** | | MIXS:0000456 | +| **Comments:** | | Expected value: measurement value;frequency;duration;duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 31 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/biol_stat.md b/mixs6/biol_stat.md new file mode 100644 index 00000000..c2319266 --- /dev/null +++ b/mixs6/biol_stat.md @@ -0,0 +1,60 @@ + +# Slot: biol_stat + + +The level of genome modification + +URI: [mixs.vocab:biol_stat](https://w3id.org/mixs/vocab/biol_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biological status | +| **Mappings:** | | MIXS:0000858 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='natural', description=None) | + diff --git a/mixs6/biomass.md b/mixs6/biomass.md new file mode 100644 index 00000000..c0a44fe2 --- /dev/null +++ b/mixs6/biomass.md @@ -0,0 +1,84 @@ + +# Slot: biomass + + +Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + +URI: [mixs.vocab:biomass](https://w3id.org/mixs/vocab/biomass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biomass | +| **Mappings:** | | MIXS:0000174 | +| **Comments:** | | Expected value: biomass type;measurement value | +| | | Preferred unit: ton, kilogram, gram | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='total;20 gram', description=None) | + diff --git a/mixs6/biotic_regm.md b/mixs6/biotic_regm.md new file mode 100644 index 00000000..9b823c5a --- /dev/null +++ b/mixs6/biotic_regm.md @@ -0,0 +1,48 @@ + +# Slot: biotic_regm + + +Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + +URI: [mixs.vocab:biotic_regm](https://w3id.org/mixs/vocab/biotic_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | biotic regimen | +| **Mappings:** | | MIXS:0001038 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='sample inoculated with Rhizobium spp. Culture', description=None) | + diff --git a/mixs6/biotic_relationship.md b/mixs6/biotic_relationship.md new file mode 100644 index 00000000..1bee7867 --- /dev/null +++ b/mixs6/biotic_relationship.md @@ -0,0 +1,56 @@ + +# Slot: biotic_relationship + + +Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + +URI: [mixs.vocab:biotic_relationship](https://w3id.org/mixs/vocab/biotic_relationship) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | observed biotic relationship | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 22.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='free living', description=None) | + diff --git a/mixs6/birth_control.md b/mixs6/birth_control.md new file mode 100644 index 00000000..44c30127 --- /dev/null +++ b/mixs6/birth_control.md @@ -0,0 +1,48 @@ + +# Slot: birth_control + + +Specification of birth control medication used + +URI: [mixs.vocab:birth_control](https://w3id.org/mixs/vocab/birth_control) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | birth control | +| **Mappings:** | | MIXS:0000286 | +| **Comments:** | | Expected value: medication name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 5 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bishomohopanol.md b/mixs6/bishomohopanol.md new file mode 100644 index 00000000..198f63ec --- /dev/null +++ b/mixs6/bishomohopanol.md @@ -0,0 +1,72 @@ + +# Slot: bishomohopanol + + +Concentration of bishomohopanol + +URI: [mixs.vocab:bishomohopanol](https://w3id.org/mixs/vocab/bishomohopanol) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bishomohopanol | +| **Mappings:** | | MIXS:0000175 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, microgram per gram | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='14 microgram per liter', description=None) | + diff --git a/mixs6/blood_blood_disord.md b/mixs6/blood_blood_disord.md new file mode 100644 index 00000000..601100e5 --- /dev/null +++ b/mixs6/blood_blood_disord.md @@ -0,0 +1,48 @@ + +# Slot: blood_blood_disord + + +History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + +URI: [mixs.vocab:blood_blood_disord](https://w3id.org/mixs/vocab/blood_blood_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | blood/blood disorder | +| **Mappings:** | | MIXS:0000271 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 32 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/bromide.md b/mixs6/bromide.md new file mode 100644 index 00000000..9690b7b9 --- /dev/null +++ b/mixs6/bromide.md @@ -0,0 +1,84 @@ + +# Slot: bromide + + +Concentration of bromide + +URI: [mixs.vocab:bromide](https://w3id.org/mixs/vocab/bromide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | bromide | +| **Mappings:** | | MIXS:0000176 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 parts per million', description=None) | + diff --git a/mixs6/build_docs.md b/mixs6/build_docs.md new file mode 100644 index 00000000..82ca5bbf --- /dev/null +++ b/mixs6/build_docs.md @@ -0,0 +1,48 @@ + +# Slot: build_docs + + +The building design, construction and operation documents + +URI: [mixs.vocab:build_docs](https://w3id.org/mixs/vocab/build_docs) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | design, construction, and operation documents | +| **Mappings:** | | MIXS:0000787 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 50 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='maintenance plans', description=None) | + diff --git a/mixs6/build_occup_type.md b/mixs6/build_occup_type.md new file mode 100644 index 00000000..9174bc08 --- /dev/null +++ b/mixs6/build_occup_type.md @@ -0,0 +1,48 @@ + +# Slot: build_occup_type + + +The primary function for which a building or discrete part of a building is intended to be used + +URI: [mixs.vocab:build_occup_type](https://w3id.org/mixs/vocab/build_occup_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | building occupancy type | +| **Mappings:** | | MIXS:0000761 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 9 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='market', description=None) | + diff --git a/mixs6/building_setting.md b/mixs6/building_setting.md new file mode 100644 index 00000000..fa98b086 --- /dev/null +++ b/mixs6/building_setting.md @@ -0,0 +1,48 @@ + +# Slot: building_setting + + +A location (geography) where a building is set + +URI: [mixs.vocab:building_setting](https://w3id.org/mixs/vocab/building_setting) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | building setting | +| **Mappings:** | | MIXS:0000768 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 20 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rural', description=None) | + diff --git a/mixs6/built_struc_age.md b/mixs6/built_struc_age.md new file mode 100644 index 00000000..f78d56e7 --- /dev/null +++ b/mixs6/built_struc_age.md @@ -0,0 +1,48 @@ + +# Slot: built_struc_age + + +The age of the built structure since construction + +URI: [mixs.vocab:built_struc_age](https://w3id.org/mixs/vocab/built_struc_age) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure age | +| **Mappings:** | | MIXS:0000145 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: year | +| | | Occurrence: 1 | +| | | Position: 37 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15', description=None) | + diff --git a/mixs6/built_struc_set.md b/mixs6/built_struc_set.md new file mode 100644 index 00000000..9afab716 --- /dev/null +++ b/mixs6/built_struc_set.md @@ -0,0 +1,48 @@ + +# Slot: built_struc_set + + +The characterization of the location of the built structure as high or low human density + +URI: [mixs.vocab:built_struc_set](https://w3id.org/mixs/vocab/built_struc_set) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure setting | +| **Mappings:** | | MIXS:0000778 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 38 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rural', description=None) | + diff --git a/mixs6/built_struc_type.md b/mixs6/built_struc_type.md new file mode 100644 index 00000000..78313c3a --- /dev/null +++ b/mixs6/built_struc_type.md @@ -0,0 +1,48 @@ + +# Slot: built_struc_type + + +A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + +URI: [mixs.vocab:built_struc_type](https://w3id.org/mixs/vocab/built_struc_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | built structure type | +| **Mappings:** | | MIXS:0000721 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 39 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/calcium.md b/mixs6/calcium.md new file mode 100644 index 00000000..91aaf705 --- /dev/null +++ b/mixs6/calcium.md @@ -0,0 +1,108 @@ + +# Slot: calcium + + +Concentration of calcium in the sample + +URI: [mixs.vocab:calcium](https://w3id.org/mixs/vocab/calcium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | calcium | +| **Mappings:** | | MIXS:0000432 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 70 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.2 micromole per liter', description=None) | + diff --git a/mixs6/carb_dioxide.md b/mixs6/carb_dioxide.md new file mode 100644 index 00000000..80042ded --- /dev/null +++ b/mixs6/carb_dioxide.md @@ -0,0 +1,60 @@ + +# Slot: carb_dioxide + + +Carbon dioxide (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:carb_dioxide](https://w3id.org/mixs/vocab/carb_dioxide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon dioxide | +| **Mappings:** | | MIXS:0000097 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: air, built environment | +| **Examples:** | | Example(value='410 parts per million', description=None) | + diff --git a/mixs6/carb_monoxide.md b/mixs6/carb_monoxide.md new file mode 100644 index 00000000..d551078b --- /dev/null +++ b/mixs6/carb_monoxide.md @@ -0,0 +1,48 @@ + +# Slot: carb_monoxide + + +Carbon monoxide (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:carb_monoxide](https://w3id.org/mixs/vocab/carb_monoxide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon monoxide | +| **Mappings:** | | MIXS:0000098 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='0.1 parts per million', description=None) | + diff --git a/mixs6/carb_nitro_ratio.md b/mixs6/carb_nitro_ratio.md new file mode 100644 index 00000000..26a3c3a8 --- /dev/null +++ b/mixs6/carb_nitro_ratio.md @@ -0,0 +1,72 @@ + +# Slot: carb_nitro_ratio + + +Ratio of amount or concentrations of carbon to nitrogen + +URI: [mixs.vocab:carb_nitro_ratio](https://w3id.org/mixs/vocab/carb_nitro_ratio) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | carbon/nitrogen ratio | +| **Mappings:** | | MIXS:0000310 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.417361111', description=None) | + diff --git a/mixs6/ceil_area.md b/mixs6/ceil_area.md new file mode 100644 index 00000000..e960d353 --- /dev/null +++ b/mixs6/ceil_area.md @@ -0,0 +1,48 @@ + +# Slot: ceil_area + + +The area of the ceiling space within the room + +URI: [mixs.vocab:ceil_area](https://w3id.org/mixs/vocab/ceil_area) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling area | +| **Mappings:** | | MIXS:0000148 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 40 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25 square meter', description=None) | + diff --git a/mixs6/ceil_cond.md b/mixs6/ceil_cond.md new file mode 100644 index 00000000..39fe60d0 --- /dev/null +++ b/mixs6/ceil_cond.md @@ -0,0 +1,48 @@ + +# Slot: ceil_cond + + +The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:ceil_cond](https://w3id.org/mixs/vocab/ceil_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling condition | +| **Mappings:** | | MIXS:0000779 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 41 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='damaged', description=None) | + diff --git a/mixs6/ceil_finish_mat.md b/mixs6/ceil_finish_mat.md new file mode 100644 index 00000000..336aaa09 --- /dev/null +++ b/mixs6/ceil_finish_mat.md @@ -0,0 +1,48 @@ + +# Slot: ceil_finish_mat + + +The type of material used to finish a ceiling + +URI: [mixs.vocab:ceil_finish_mat](https://w3id.org/mixs/vocab/ceil_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling finish material | +| **Mappings:** | | MIXS:0000780 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 42 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='stucco', description=None) | + diff --git a/mixs6/ceil_struc.md b/mixs6/ceil_struc.md new file mode 100644 index 00000000..2102334c --- /dev/null +++ b/mixs6/ceil_struc.md @@ -0,0 +1,48 @@ + +# Slot: ceil_struc + + +The construction format of the ceiling + +URI: [mixs.vocab:ceil_struc](https://w3id.org/mixs/vocab/ceil_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling structure | +| **Mappings:** | | MIXS:0000782 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 44 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='concrete', description=None) | + diff --git a/mixs6/ceil_texture.md b/mixs6/ceil_texture.md new file mode 100644 index 00000000..9fe49b7f --- /dev/null +++ b/mixs6/ceil_texture.md @@ -0,0 +1,48 @@ + +# Slot: ceil_texture + + +The feel, appearance, or consistency of a ceiling surface + +URI: [mixs.vocab:ceil_texture](https://w3id.org/mixs/vocab/ceil_texture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling texture | +| **Mappings:** | | MIXS:0000783 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 45 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='popcorn', description=None) | + diff --git a/mixs6/ceil_thermal_mass.md b/mixs6/ceil_thermal_mass.md new file mode 100644 index 00000000..2491d4f4 --- /dev/null +++ b/mixs6/ceil_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: ceil_thermal_mass + + +The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + +URI: [mixs.vocab:ceil_thermal_mass](https://w3id.org/mixs/vocab/ceil_thermal_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling thermal mass | +| **Mappings:** | | MIXS:0000143 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 46 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ceil_type.md b/mixs6/ceil_type.md new file mode 100644 index 00000000..c1b3d071 --- /dev/null +++ b/mixs6/ceil_type.md @@ -0,0 +1,48 @@ + +# Slot: ceil_type + + +The type of ceiling according to the ceiling's appearance or construction + +URI: [mixs.vocab:ceil_type](https://w3id.org/mixs/vocab/ceil_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling type | +| **Mappings:** | | MIXS:0000784 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 47 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='coffered', description=None) | + diff --git a/mixs6/ceil_water_mold.md b/mixs6/ceil_water_mold.md new file mode 100644 index 00000000..575979d1 --- /dev/null +++ b/mixs6/ceil_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: ceil_water_mold + + +Signs of the presence of mold or mildew on the ceiling + +URI: [mixs.vocab:ceil_water_mold](https://w3id.org/mixs/vocab/ceil_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ceiling signs of water/mold | +| **Mappings:** | | MIXS:0000781 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 43 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='presence of mold visible', description=None) | + diff --git a/mixs6/chem_administration.md b/mixs6/chem_administration.md new file mode 100644 index 00000000..db90ce62 --- /dev/null +++ b/mixs6/chem_administration.md @@ -0,0 +1,192 @@ + +# Slot: chem_administration + + +List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + +URI: [mixs.vocab:chem_administration](https://w3id.org/mixs/vocab/chem_administration) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical administration | +| **Mappings:** | | MIXS:0000751 | +| **Comments:** | | Expected value: CHEBI;timestamp | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='agar [CHEBI:2509];2018-05-11T20:00Z', description=None) | + diff --git a/mixs6/chem_mutagen.md b/mixs6/chem_mutagen.md new file mode 100644 index 00000000..6384e2af --- /dev/null +++ b/mixs6/chem_mutagen.md @@ -0,0 +1,48 @@ + +# Slot: chem_mutagen + + +Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + +URI: [mixs.vocab:chem_mutagen](https://w3id.org/mixs/vocab/chem_mutagen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical mutagen | +| **Mappings:** | | MIXS:0000555 | +| **Comments:** | | Expected value: mutagen name;mutagen amount;treatment interval and duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/chem_oxygen_dem.md b/mixs6/chem_oxygen_dem.md new file mode 100644 index 00000000..f2774536 --- /dev/null +++ b/mixs6/chem_oxygen_dem.md @@ -0,0 +1,48 @@ + +# Slot: chem_oxygen_dem + + +A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + +URI: [mixs.vocab:chem_oxygen_dem](https://w3id.org/mixs/vocab/chem_oxygen_dem) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical oxygen demand | +| **Mappings:** | | MIXS:0000656 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/chem_treatment.md b/mixs6/chem_treatment.md new file mode 100644 index 00000000..7138c847 --- /dev/null +++ b/mixs6/chem_treatment.md @@ -0,0 +1,48 @@ + +# Slot: chem_treatment + + +List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + +URI: [mixs.vocab:chem_treatment](https://w3id.org/mixs/vocab/chem_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical treatment | +| **Mappings:** | | MIXS:0001012 | +| **Comments:** | | Expected value: name;name;timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 32 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='ACCENT 1125;DOW;2010-11-17', description=None) | + diff --git a/mixs6/chem_treatment_method.md b/mixs6/chem_treatment_method.md new file mode 100644 index 00000000..00bfcec1 --- /dev/null +++ b/mixs6/chem_treatment_method.md @@ -0,0 +1,48 @@ + +# Slot: chem_treatment_method + + +Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + +URI: [mixs.vocab:chem_treatment_method](https://w3id.org/mixs/vocab/chem_treatment_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chemical treatment method | +| **Mappings:** | | MIXS:0000457 | +| **Comments:** | | Expected value: measurement value;frequency;duration;duration | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 33 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/chimera_check.md b/mixs6/chimera_check.md new file mode 100644 index 00000000..0c91a466 --- /dev/null +++ b/mixs6/chimera_check.md @@ -0,0 +1,56 @@ + +# Slot: chimera_check + + +A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + +URI: [mixs.vocab:chimera_check](https://w3id.org/mixs/vocab/chimera_check) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chimera check | +| **Comments:** | | Expected value: name and version of software, parameters used | +| | | Preferred unit: | +| | | Position: 52.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='uchime;v4.1;default parameters', description=None) | + diff --git a/mixs6/chloride.md b/mixs6/chloride.md new file mode 100644 index 00000000..ed2320ad --- /dev/null +++ b/mixs6/chloride.md @@ -0,0 +1,108 @@ + +# Slot: chloride + + +Concentration of chloride in the sample + +URI: [mixs.vocab:chloride](https://w3id.org/mixs/vocab/chloride) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chloride | +| **Mappings:** | | MIXS:0000429 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 67 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5000 milligram per liter', description=None) | + diff --git a/mixs6/chlorophyll.md b/mixs6/chlorophyll.md new file mode 100644 index 00000000..5358ce60 --- /dev/null +++ b/mixs6/chlorophyll.md @@ -0,0 +1,84 @@ + +# Slot: chlorophyll + + +Concentration of chlorophyll + +URI: [mixs.vocab:chlorophyll](https://w3id.org/mixs/vocab/chlorophyll) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | chlorophyll | +| **Mappings:** | | MIXS:0000177 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter, microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 milligram per cubic meter', description=None) | + diff --git a/mixs6/climate_environment.md b/mixs6/climate_environment.md new file mode 100644 index 00000000..42fa1709 --- /dev/null +++ b/mixs6/climate_environment.md @@ -0,0 +1,48 @@ + +# Slot: climate_environment + + +Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + +URI: [mixs.vocab:climate_environment](https://w3id.org/mixs/vocab/climate_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | climate environment | +| **Mappings:** | | MIXS:0001040 | +| **Comments:** | | Expected value: climate name;treatment interval and duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/collection_date.md b/mixs6/collection_date.md new file mode 100644 index 00000000..f5b45268 --- /dev/null +++ b/mixs6/collection_date.md @@ -0,0 +1,56 @@ + +# Slot: collection_date + + +The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + +URI: [mixs.vocab:collection_date](https://w3id.org/mixs/vocab/collection_date) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | collection date | +| **Comments:** | | Expected value: date and time | +| | | Preferred unit: | +| | | Position: 9.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='2018-05-11T10:00:00+01:00', description=None) | + diff --git a/mixs6/compl_appr.md b/mixs6/compl_appr.md new file mode 100644 index 00000000..9e612caa --- /dev/null +++ b/mixs6/compl_appr.md @@ -0,0 +1,56 @@ + +# Slot: compl_appr + + +The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + +URI: [mixs.vocab:compl_appr](https://w3id.org/mixs/vocab/compl_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness approach | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 69.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)', description=None) | + diff --git a/mixs6/compl_score.md b/mixs6/compl_score.md new file mode 100644 index 00000000..9322bcd3 --- /dev/null +++ b/mixs6/compl_score.md @@ -0,0 +1,56 @@ + +# Slot: compl_score + + +Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + +URI: [mixs.vocab:compl_score](https://w3id.org/mixs/vocab/compl_score) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness score | +| **Comments:** | | Expected value: quality;percent completeness | +| | | Preferred unit: | +| | | Position: 67.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='med;60%', description=None) | + diff --git a/mixs6/compl_software.md b/mixs6/compl_software.md new file mode 100644 index 00000000..834d65d9 --- /dev/null +++ b/mixs6/compl_software.md @@ -0,0 +1,56 @@ + +# Slot: compl_software + + +Tools used for completion estimate, i.e. checkm, anvi'o, busco + +URI: [mixs.vocab:compl_software](https://w3id.org/mixs/vocab/compl_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | completeness software | +| **Comments:** | | Expected value: names and versions of software(s) used | +| | | Preferred unit: | +| | | Position: 68.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='checkm', description=None) | + diff --git a/mixs6/conduc.md b/mixs6/conduc.md new file mode 100644 index 00000000..dfce8e55 --- /dev/null +++ b/mixs6/conduc.md @@ -0,0 +1,48 @@ + +# Slot: conduc + + +Electrical conductivity of water + +URI: [mixs.vocab:conduc](https://w3id.org/mixs/vocab/conduc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | conductivity | +| **Mappings:** | | MIXS:0000692 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milliSiemens per centimeter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='10 milliSiemens per centimeter', description=None) | + diff --git a/mixs6/contam_score.md b/mixs6/contam_score.md new file mode 100644 index 00000000..196500ea --- /dev/null +++ b/mixs6/contam_score.md @@ -0,0 +1,56 @@ + +# Slot: contam_score + + +The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + +URI: [mixs.vocab:contam_score](https://w3id.org/mixs/vocab/contam_score) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination score | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Position: 70.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='1%', description=None) | + diff --git a/mixs6/contam_screen_input.md b/mixs6/contam_screen_input.md new file mode 100644 index 00000000..521a7752 --- /dev/null +++ b/mixs6/contam_screen_input.md @@ -0,0 +1,56 @@ + +# Slot: contam_screen_input + + +The type of sequence data used as input + +URI: [mixs.vocab:contam_screen_input](https://w3id.org/mixs/vocab/contam_screen_input) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination screening input | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 71.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='contigs', description=None) | + diff --git a/mixs6/contam_screen_param.md b/mixs6/contam_screen_param.md new file mode 100644 index 00000000..1cf06869 --- /dev/null +++ b/mixs6/contam_screen_param.md @@ -0,0 +1,56 @@ + +# Slot: contam_screen_param + + +Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + +URI: [mixs.vocab:contam_screen_param](https://w3id.org/mixs/vocab/contam_screen_param) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | contamination screening parameters | +| **Comments:** | | Expected value: enumeration;value or name | +| | | Preferred unit: | +| | | Position: 72.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='kmer', description=None) | + diff --git a/mixs6/cool_syst_id.md b/mixs6/cool_syst_id.md new file mode 100644 index 00000000..ea0df443 --- /dev/null +++ b/mixs6/cool_syst_id.md @@ -0,0 +1,48 @@ + +# Slot: cool_syst_id + + +The cooling system identifier + +URI: [mixs.vocab:cool_syst_id](https://w3id.org/mixs/vocab/cool_syst_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | cooling system identifier | +| **Mappings:** | | MIXS:0000785 | +| **Comments:** | | Expected value: unique identifier | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 48 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12345', description=None) | + diff --git a/mixs6/core_field.md b/mixs6/core_field.md new file mode 100644 index 00000000..14932e0c --- /dev/null +++ b/mixs6/core_field.md @@ -0,0 +1,22 @@ + +# Slot: core_field + + +basic fields + +URI: [mixs.vocab:core_field](https://w3id.org/mixs/vocab/core_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [sample_name](sample_name.md) + +## Used by + diff --git a/mixs6/crop_rotation.md b/mixs6/crop_rotation.md new file mode 100644 index 00000000..7c173c2d --- /dev/null +++ b/mixs6/crop_rotation.md @@ -0,0 +1,48 @@ + +# Slot: crop_rotation + + +Whether or not crop is rotated, and if yes, rotation schedule + +URI: [mixs.vocab:crop_rotation](https://w3id.org/mixs/vocab/crop_rotation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/crop rotation | +| **Mappings:** | | MIXS:0000318 | +| **Comments:** | | Expected value: crop rotation status;schedule | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 6 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='yes;R2/2017-01-01/2018-12-31/P6M', description=None) | + diff --git a/mixs6/cult_root_med.md b/mixs6/cult_root_med.md new file mode 100644 index 00000000..6fccf609 --- /dev/null +++ b/mixs6/cult_root_med.md @@ -0,0 +1,48 @@ + +# Slot: cult_root_med + + +Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + +URI: [mixs.vocab:cult_root_med](https://w3id.org/mixs/vocab/cult_root_med) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | culture rooting medium | +| **Mappings:** | | MIXS:0001041 | +| **Comments:** | | Expected value: name, PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | + diff --git a/mixs6/cur_land_use.md b/mixs6/cur_land_use.md new file mode 100644 index 00000000..eaceee06 --- /dev/null +++ b/mixs6/cur_land_use.md @@ -0,0 +1,48 @@ + +# Slot: cur_land_use + + +Present state of sample site + +URI: [mixs.vocab:cur_land_use](https://w3id.org/mixs/vocab/cur_land_use) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current land use | +| **Mappings:** | | MIXS:0001080 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='conifers', description=None) | + diff --git a/mixs6/cur_vegetation.md b/mixs6/cur_vegetation.md new file mode 100644 index 00000000..75035705 --- /dev/null +++ b/mixs6/cur_vegetation.md @@ -0,0 +1,48 @@ + +# Slot: cur_vegetation + + +Vegetation classification from one or more standard classification systems, or agricultural crop + +URI: [mixs.vocab:cur_vegetation](https://w3id.org/mixs/vocab/cur_vegetation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current vegetation | +| **Mappings:** | | MIXS:0000312 | +| **Comments:** | | Expected value: current vegetation type | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/cur_vegetation_meth.md b/mixs6/cur_vegetation_meth.md new file mode 100644 index 00000000..716eb5c9 --- /dev/null +++ b/mixs6/cur_vegetation_meth.md @@ -0,0 +1,48 @@ + +# Slot: cur_vegetation_meth + + +Reference or method used in vegetation classification + +URI: [mixs.vocab:cur_vegetation_meth](https://w3id.org/mixs/vocab/cur_vegetation_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | current vegetation method | +| **Mappings:** | | MIXS:0000314 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/date_last_rain.md b/mixs6/date_last_rain.md new file mode 100644 index 00000000..80cf783f --- /dev/null +++ b/mixs6/date_last_rain.md @@ -0,0 +1,48 @@ + +# Slot: date_last_rain + + +The date of the last time it rained + +URI: [mixs.vocab:date_last_rain](https://w3id.org/mixs/vocab/date_last_rain) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | date last rain | +| **Mappings:** | | MIXS:0000786 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 49 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | + diff --git a/mixs6/decontam_software.md b/mixs6/decontam_software.md new file mode 100644 index 00000000..de9563f7 --- /dev/null +++ b/mixs6/decontam_software.md @@ -0,0 +1,56 @@ + +# Slot: decontam_software + + +Tool(s) used in contamination screening + +URI: [mixs.vocab:decontam_software](https://w3id.org/mixs/vocab/decontam_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | decontamination software | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 73.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value="anvi'o", description=None) | + diff --git a/mixs6/density.md b/mixs6/density.md new file mode 100644 index 00000000..6cb4096c --- /dev/null +++ b/mixs6/density.md @@ -0,0 +1,96 @@ + +# Slot: density + + +Density of the sample, which is its mass per unit volume (aka volumetric mass density) + +URI: [mixs.vocab:density](https://w3id.org/mixs/vocab/density) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | density | +| **Mappings:** | | MIXS:0000435 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per cubic meter, gram per cubic centimeter | +| | | Occurrence: 1 | +| | | Position: 77 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1000 kilogram per cubic meter', description=None) | + diff --git a/mixs6/depos_env.md b/mixs6/depos_env.md new file mode 100644 index 00000000..ab7fec57 --- /dev/null +++ b/mixs6/depos_env.md @@ -0,0 +1,60 @@ + +# Slot: depos_env + + +Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:depos_env](https://w3id.org/mixs/vocab/depos_env) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depositional environment | +| **Mappings:** | | MIXS:0000992 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 13 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Continental - Alluvial', description=None) | + diff --git a/mixs6/depth.md b/mixs6/depth.md new file mode 100644 index 00000000..e919c58c --- /dev/null +++ b/mixs6/depth.md @@ -0,0 +1,57 @@ + +# Slot: depth + + +Please refer to the definitions of depth in the environmental packages + +URI: [mixs.vocab:depth](https://w3id.org/mixs/vocab/depth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (depth) | +| **Comments:** | | Expected value: - | +| | | Preferred unit: | +| | | Position: 6.0 | +| | | CHECKLIST migs_eu: E | +| | | CHECKLIST migs_ba: E | +| | | CHECKLIST migs_pl: E | +| | | CHECKLIST migs_vi: E | +| | | CHECKLIST migs_org: E | +| | | CHECKLIST me: E | +| | | CHECKLIST mimarks_s: E | +| | | CHECKLIST mimarks_c: E | +| | | CHECKLIST misag: E | +| | | CHECKLIST mimag: E | +| | | CHECKLIST miuvig: E | +| | | This field is used in: 8 packages: host-associated, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/dermatology_disord.md b/mixs6/dermatology_disord.md new file mode 100644 index 00000000..2246abde --- /dev/null +++ b/mixs6/dermatology_disord.md @@ -0,0 +1,48 @@ + +# Slot: dermatology_disord + + +History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + +URI: [mixs.vocab:dermatology_disord](https://w3id.org/mixs/vocab/dermatology_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dermatology disorder | +| **Mappings:** | | MIXS:0000284 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/detec_type.md b/mixs6/detec_type.md new file mode 100644 index 00000000..053b2d99 --- /dev/null +++ b/mixs6/detec_type.md @@ -0,0 +1,56 @@ + +# Slot: detec_type + + +Type of UViG detection + +URI: [mixs.vocab:detec_type](https://w3id.org/mixs/vocab/detec_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | detection type | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 86.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='independent sequence (UViG)', description=None) | + diff --git a/mixs6/dew_point.md b/mixs6/dew_point.md new file mode 100644 index 00000000..e9a43022 --- /dev/null +++ b/mixs6/dew_point.md @@ -0,0 +1,48 @@ + +# Slot: dew_point + + +The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + +URI: [mixs.vocab:dew_point](https://w3id.org/mixs/vocab/dew_point) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dew point | +| **Mappings:** | | MIXS:0000129 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 11 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='22 degree Celsius', description=None) | + diff --git a/mixs6/diet_last_six_month.md b/mixs6/diet_last_six_month.md new file mode 100644 index 00000000..2eb41553 --- /dev/null +++ b/mixs6/diet_last_six_month.md @@ -0,0 +1,48 @@ + +# Slot: diet_last_six_month + + +Specification of major diet changes in the last six months, if yes the change should be specified + +URI: [mixs.vocab:diet_last_six_month](https://w3id.org/mixs/vocab/diet_last_six_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | major diet change in last six months | +| **Mappings:** | | MIXS:0000266 | +| **Comments:** | | Expected value: diet change;current diet | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 21 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;vegetarian diet', description=None) | + diff --git a/mixs6/diether_lipids.md b/mixs6/diether_lipids.md new file mode 100644 index 00000000..139e9095 --- /dev/null +++ b/mixs6/diether_lipids.md @@ -0,0 +1,84 @@ + +# Slot: diether_lipids + + +Concentration of diether lipids; can include multiple types of diether lipids + +URI: [mixs.vocab:diether_lipids](https://w3id.org/mixs/vocab/diether_lipids) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | diether lipids | +| **Mappings:** | | MIXS:0000178 | +| **Comments:** | | Expected value: diether lipid name;measurement value | +| | | Preferred unit: nanogram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.2 nanogram per liter', description=None) | + diff --git a/mixs6/diss_carb_dioxide.md b/mixs6/diss_carb_dioxide.md new file mode 100644 index 00000000..121a2f88 --- /dev/null +++ b/mixs6/diss_carb_dioxide.md @@ -0,0 +1,108 @@ + +# Slot: diss_carb_dioxide + + +Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + +URI: [mixs.vocab:diss_carb_dioxide](https://w3id.org/mixs/vocab/diss_carb_dioxide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved carbon dioxide | +| **Mappings:** | | MIXS:0000436 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 78 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 milligram per liter', description=None) | + diff --git a/mixs6/diss_hydrogen.md b/mixs6/diss_hydrogen.md new file mode 100644 index 00000000..1be01385 --- /dev/null +++ b/mixs6/diss_hydrogen.md @@ -0,0 +1,84 @@ + +# Slot: diss_hydrogen + + +Concentration of dissolved hydrogen + +URI: [mixs.vocab:diss_hydrogen](https://w3id.org/mixs/vocab/diss_hydrogen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved hydrogen | +| **Mappings:** | | MIXS:0000179 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.3 micromole per liter', description=None) | + diff --git a/mixs6/diss_inorg_carb.md b/mixs6/diss_inorg_carb.md new file mode 100644 index 00000000..8191e458 --- /dev/null +++ b/mixs6/diss_inorg_carb.md @@ -0,0 +1,108 @@ + +# Slot: diss_inorg_carb + + +Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + +URI: [mixs.vocab:diss_inorg_carb](https://w3id.org/mixs/vocab/diss_inorg_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic carbon | +| **Mappings:** | | MIXS:0000434 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 73 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2059 micromole per kilogram', description=None) | + diff --git a/mixs6/diss_inorg_nitro.md b/mixs6/diss_inorg_nitro.md new file mode 100644 index 00000000..a3ca8758 --- /dev/null +++ b/mixs6/diss_inorg_nitro.md @@ -0,0 +1,48 @@ + +# Slot: diss_inorg_nitro + + +Concentration of dissolved inorganic nitrogen + +URI: [mixs.vocab:diss_inorg_nitro](https://w3id.org/mixs/vocab/diss_inorg_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic nitrogen | +| **Mappings:** | | MIXS:0000698 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='761 micromole per liter', description=None) | + diff --git a/mixs6/diss_inorg_phosp.md b/mixs6/diss_inorg_phosp.md new file mode 100644 index 00000000..28e7180c --- /dev/null +++ b/mixs6/diss_inorg_phosp.md @@ -0,0 +1,72 @@ + +# Slot: diss_inorg_phosp + + +Concentration of dissolved inorganic phosphorus in the sample + +URI: [mixs.vocab:diss_inorg_phosp](https://w3id.org/mixs/vocab/diss_inorg_phosp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved inorganic phosphorus | +| **Mappings:** | | MIXS:0000106 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 74 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='56.5 micromole per liter', description=None) | + diff --git a/mixs6/diss_iron.md b/mixs6/diss_iron.md new file mode 100644 index 00000000..63a18f80 --- /dev/null +++ b/mixs6/diss_iron.md @@ -0,0 +1,60 @@ + +# Slot: diss_iron + + +Concentration of dissolved iron in the sample + +URI: [mixs.vocab:diss_iron](https://w3id.org/mixs/vocab/diss_iron) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved iron | +| **Mappings:** | | MIXS:0000139 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 65 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/diss_org_carb.md b/mixs6/diss_org_carb.md new file mode 100644 index 00000000..90a0dbb9 --- /dev/null +++ b/mixs6/diss_org_carb.md @@ -0,0 +1,96 @@ + +# Slot: diss_org_carb + + +Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + +URI: [mixs.vocab:diss_org_carb](https://w3id.org/mixs/vocab/diss_org_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved organic carbon | +| **Mappings:** | | MIXS:0000433 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 72 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='197 micromole per liter', description=None) | + diff --git a/mixs6/diss_org_nitro.md b/mixs6/diss_org_nitro.md new file mode 100644 index 00000000..659af407 --- /dev/null +++ b/mixs6/diss_org_nitro.md @@ -0,0 +1,84 @@ + +# Slot: diss_org_nitro + + +Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + +URI: [mixs.vocab:diss_org_nitro](https://w3id.org/mixs/vocab/diss_org_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved organic nitrogen | +| **Mappings:** | | MIXS:0000162 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/diss_oxygen.md b/mixs6/diss_oxygen.md new file mode 100644 index 00000000..5e992c99 --- /dev/null +++ b/mixs6/diss_oxygen.md @@ -0,0 +1,84 @@ + +# Slot: diss_oxygen + + +Concentration of dissolved oxygen + +URI: [mixs.vocab:diss_oxygen](https://w3id.org/mixs/vocab/diss_oxygen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved oxygen | +| **Mappings:** | | MIXS:0000119 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per kilogram, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='175 micromole per kilogram', description=None) | + diff --git a/mixs6/diss_oxygen_fluid.md b/mixs6/diss_oxygen_fluid.md new file mode 100644 index 00000000..bdf9411d --- /dev/null +++ b/mixs6/diss_oxygen_fluid.md @@ -0,0 +1,60 @@ + +# Slot: diss_oxygen_fluid + + +Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + +URI: [mixs.vocab:diss_oxygen_fluid](https://w3id.org/mixs/vocab/diss_oxygen_fluid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dissolved oxygen in fluids | +| **Mappings:** | | MIXS:0000438 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per kilogram, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 79 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/dominant_hand.md b/mixs6/dominant_hand.md new file mode 100644 index 00000000..958915f0 --- /dev/null +++ b/mixs6/dominant_hand.md @@ -0,0 +1,48 @@ + +# Slot: dominant_hand + + +Dominant hand of the subject + +URI: [mixs.vocab:dominant_hand](https://w3id.org/mixs/vocab/dominant_hand) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | dominant hand | +| **Mappings:** | | MIXS:0000944 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='right', description=None) | + diff --git a/mixs6/door_comp_type.md b/mixs6/door_comp_type.md new file mode 100644 index 00000000..de01d432 --- /dev/null +++ b/mixs6/door_comp_type.md @@ -0,0 +1,48 @@ + +# Slot: door_comp_type + + +The composite type of the door + +URI: [mixs.vocab:door_comp_type](https://w3id.org/mixs/vocab/door_comp_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, composite | +| **Mappings:** | | MIXS:0000795 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 59 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='revolving', description=None) | + diff --git a/mixs6/door_cond.md b/mixs6/door_cond.md new file mode 100644 index 00000000..a812eec7 --- /dev/null +++ b/mixs6/door_cond.md @@ -0,0 +1,48 @@ + +# Slot: door_cond + + +The phsical condition of the door + +URI: [mixs.vocab:door_cond](https://w3id.org/mixs/vocab/door_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door condition | +| **Mappings:** | | MIXS:0000788 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 52 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/door_direct.md b/mixs6/door_direct.md new file mode 100644 index 00000000..6a156d0a --- /dev/null +++ b/mixs6/door_direct.md @@ -0,0 +1,48 @@ + +# Slot: door_direct + + +The direction the door opens + +URI: [mixs.vocab:door_direct](https://w3id.org/mixs/vocab/door_direct) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door direction of opening | +| **Mappings:** | | MIXS:0000789 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 53 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='inward', description=None) | + diff --git a/mixs6/door_loc.md b/mixs6/door_loc.md new file mode 100644 index 00000000..fd41886d --- /dev/null +++ b/mixs6/door_loc.md @@ -0,0 +1,48 @@ + +# Slot: door_loc + + +The relative location of the door in the room + +URI: [mixs.vocab:door_loc](https://w3id.org/mixs/vocab/door_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door location | +| **Mappings:** | | MIXS:0000790 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 54 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/door_mat.md b/mixs6/door_mat.md new file mode 100644 index 00000000..307cfb3b --- /dev/null +++ b/mixs6/door_mat.md @@ -0,0 +1,48 @@ + +# Slot: door_mat + + +The material the door is composed of + +URI: [mixs.vocab:door_mat](https://w3id.org/mixs/vocab/door_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door material | +| **Mappings:** | | MIXS:0000791 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 55 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/door_move.md b/mixs6/door_move.md new file mode 100644 index 00000000..62a9737a --- /dev/null +++ b/mixs6/door_move.md @@ -0,0 +1,48 @@ + +# Slot: door_move + + +The type of movement of the door + +URI: [mixs.vocab:door_move](https://w3id.org/mixs/vocab/door_move) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door movement | +| **Mappings:** | | MIXS:0000792 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 56 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='swinging', description=None) | + diff --git a/mixs6/door_size.md b/mixs6/door_size.md new file mode 100644 index 00000000..768d3f3d --- /dev/null +++ b/mixs6/door_size.md @@ -0,0 +1,48 @@ + +# Slot: door_size + + +The size of the door + +URI: [mixs.vocab:door_size](https://w3id.org/mixs/vocab/door_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door area or size | +| **Mappings:** | | MIXS:0000158 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 51 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2.5 square meter', description=None) | + diff --git a/mixs6/door_type.md b/mixs6/door_type.md new file mode 100644 index 00000000..ab9936a1 --- /dev/null +++ b/mixs6/door_type.md @@ -0,0 +1,48 @@ + +# Slot: door_type + + +The type of door material + +URI: [mixs.vocab:door_type](https://w3id.org/mixs/vocab/door_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type | +| **Mappings:** | | MIXS:0000794 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 58 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wooden', description=None) | + diff --git a/mixs6/door_type_metal.md b/mixs6/door_type_metal.md new file mode 100644 index 00000000..e2415020 --- /dev/null +++ b/mixs6/door_type_metal.md @@ -0,0 +1,48 @@ + +# Slot: door_type_metal + + +The type of metal door + +URI: [mixs.vocab:door_type_metal](https://w3id.org/mixs/vocab/door_type_metal) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, metal | +| **Mappings:** | | MIXS:0000796 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 60 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='hollow', description=None) | + diff --git a/mixs6/door_type_wood.md b/mixs6/door_type_wood.md new file mode 100644 index 00000000..ebde396f --- /dev/null +++ b/mixs6/door_type_wood.md @@ -0,0 +1,48 @@ + +# Slot: door_type_wood + + +The type of wood door + +URI: [mixs.vocab:door_type_wood](https://w3id.org/mixs/vocab/door_type_wood) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door type, wood | +| **Mappings:** | | MIXS:0000797 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 61 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='battened', description=None) | + diff --git a/mixs6/door_water_mold.md b/mixs6/door_water_mold.md new file mode 100644 index 00000000..711cf015 --- /dev/null +++ b/mixs6/door_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: door_water_mold + + +Signs of the presence of mold or mildew on a door + +URI: [mixs.vocab:door_water_mold](https://w3id.org/mixs/vocab/door_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | door signs of water/mold | +| **Mappings:** | | MIXS:0000793 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 57 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='presence of mold visible', description=None) | + diff --git a/mixs6/douche.md b/mixs6/douche.md new file mode 100644 index 00000000..b9ddbdca --- /dev/null +++ b/mixs6/douche.md @@ -0,0 +1,48 @@ + +# Slot: douche + + +Date of most recent douche + +URI: [mixs.vocab:douche](https://w3id.org/mixs/vocab/douche) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | douche | +| **Mappings:** | | MIXS:0000967 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 4 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/down_par.md b/mixs6/down_par.md new file mode 100644 index 00000000..bc8727d1 --- /dev/null +++ b/mixs6/down_par.md @@ -0,0 +1,48 @@ + +# Slot: down_par + + +Visible waveband radiance and irradiance measurements in the water column + +URI: [mixs.vocab:down_par](https://w3id.org/mixs/vocab/down_par) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | downward PAR | +| **Mappings:** | | MIXS:0000703 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microEinstein per square meter per second, microEinstein per square centimeter per second | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='28.71 microEinstein per square meter per second', description=None) | + diff --git a/mixs6/drainage_class.md b/mixs6/drainage_class.md new file mode 100644 index 00000000..c809966f --- /dev/null +++ b/mixs6/drainage_class.md @@ -0,0 +1,48 @@ + +# Slot: drainage_class + + +Drainage classification from a standard system such as the USDA system + +URI: [mixs.vocab:drainage_class](https://w3id.org/mixs/vocab/drainage_class) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drainage classification | +| **Mappings:** | | MIXS:0001085 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 34 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='well', description=None) | + diff --git a/mixs6/drawings.md b/mixs6/drawings.md new file mode 100644 index 00000000..dafde8ff --- /dev/null +++ b/mixs6/drawings.md @@ -0,0 +1,48 @@ + +# Slot: drawings + + +The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + +URI: [mixs.vocab:drawings](https://w3id.org/mixs/vocab/drawings) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drawings | +| **Mappings:** | | MIXS:0000798 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 62 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='sketch', description=None) | + diff --git a/mixs6/drug_usage.md b/mixs6/drug_usage.md new file mode 100644 index 00000000..44d51d83 --- /dev/null +++ b/mixs6/drug_usage.md @@ -0,0 +1,48 @@ + +# Slot: drug_usage + + +Any drug used by subject and the frequency of usage; can include multiple drugs used + +URI: [mixs.vocab:drug_usage](https://w3id.org/mixs/vocab/drug_usage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | drug usage | +| **Mappings:** | | MIXS:0000894 | +| **Comments:** | | Expected value: drug name;frequency | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 19 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='Lipitor;2/day', description=None) | + diff --git a/mixs6/efficiency_percent.md b/mixs6/efficiency_percent.md new file mode 100644 index 00000000..a0a83d5e --- /dev/null +++ b/mixs6/efficiency_percent.md @@ -0,0 +1,48 @@ + +# Slot: efficiency_percent + + +Percentage of volatile solids removed from the anaerobic digestor + +URI: [mixs.vocab:efficiency_percent](https://w3id.org/mixs/vocab/efficiency_percent) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | efficiency percent | +| **Mappings:** | | MIXS:0000657 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/elev.md b/mixs6/elev.md new file mode 100644 index 00000000..e76181b9 --- /dev/null +++ b/mixs6/elev.md @@ -0,0 +1,57 @@ + +# Slot: elev + + +Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + +URI: [mixs.vocab:elev](https://w3id.org/mixs/vocab/elev) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | elevation | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Position: 7.0 | +| | | CHECKLIST migs_eu: E | +| | | CHECKLIST migs_ba: E | +| | | CHECKLIST migs_pl: E | +| | | CHECKLIST migs_vi: E | +| | | CHECKLIST migs_org: E | +| | | CHECKLIST me: E | +| | | CHECKLIST mimarks_s: E | +| | | CHECKLIST mimarks_c: E | +| | | CHECKLIST misag: E | +| | | CHECKLIST mimag: E | +| | | CHECKLIST miuvig: E | +| | | This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, water | +| **Examples:** | | Example(value='100 meter', description=None) | + diff --git a/mixs6/elevator.md b/mixs6/elevator.md new file mode 100644 index 00000000..56e00131 --- /dev/null +++ b/mixs6/elevator.md @@ -0,0 +1,48 @@ + +# Slot: elevator + + +The number of elevators within the built structure + +URI: [mixs.vocab:elevator](https://w3id.org/mixs/vocab/elevator) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | elevator count | +| **Mappings:** | | MIXS:0000799 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 63 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/emulsions.md b/mixs6/emulsions.md new file mode 100644 index 00000000..a15278d1 --- /dev/null +++ b/mixs6/emulsions.md @@ -0,0 +1,48 @@ + +# Slot: emulsions + + +Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + +URI: [mixs.vocab:emulsions](https://w3id.org/mixs/vocab/emulsions) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | emulsions | +| **Mappings:** | | MIXS:0000660 | +| **Comments:** | | Expected value: emulsion name;measurement value | +| | | Preferred unit: gram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/encoded_traits.md b/mixs6/encoded_traits.md new file mode 100644 index 00000000..c1cd83aa --- /dev/null +++ b/mixs6/encoded_traits.md @@ -0,0 +1,56 @@ + +# Slot: encoded_traits + + +Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + +URI: [mixs.vocab:encoded_traits](https://w3id.org/mixs/vocab/encoded_traits) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | encoded traits | +| **Comments:** | | Expected value: for plasmid: antibiotic resistance; for phage: converting genes | +| | | Preferred unit: | +| | | Position: 28.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='beta-lactamase class A', description=None) | + diff --git a/mixs6/env_broad_scale.md b/mixs6/env_broad_scale.md new file mode 100644 index 00000000..2b8e28a3 --- /dev/null +++ b/mixs6/env_broad_scale.md @@ -0,0 +1,56 @@ + +# Slot: env_broad_scale + + +In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_broad_scale](https://w3id.org/mixs/vocab/env_broad_scale) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | broad-scale environmental context | +| **Comments:** | | Expected value: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] | +| | | Preferred unit: | +| | | Position: 10.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='forest biome [ENVO:01000174]', description=None) | + diff --git a/mixs6/env_local_scale.md b/mixs6/env_local_scale.md new file mode 100644 index 00000000..081df755 --- /dev/null +++ b/mixs6/env_local_scale.md @@ -0,0 +1,56 @@ + +# Slot: env_local_scale + + +In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_local_scale](https://w3id.org/mixs/vocab/env_local_scale) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | local environmental context | +| **Comments:** | | Expected value: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] | +| | | Preferred unit: | +| | | Position: 11.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='litter layer [ENVO:01000338]', description=None) | + diff --git a/mixs6/env_medium.md b/mixs6/env_medium.md new file mode 100644 index 00000000..195b8eca --- /dev/null +++ b/mixs6/env_medium.md @@ -0,0 +1,56 @@ + +# Slot: env_medium + + +In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + +URI: [mixs.vocab:env_medium](https://w3id.org/mixs/vocab/env_medium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | environmental medium | +| **Comments:** | | Expected value: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] | +| | | Preferred unit: | +| | | Position: 12.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='soil [ENVO:00001998]', description=None) | + diff --git a/mixs6/env_package.md b/mixs6/env_package.md new file mode 100644 index 00000000..a0a5bb4d --- /dev/null +++ b/mixs6/env_package.md @@ -0,0 +1,56 @@ + +# Slot: env_package + + +MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + +URI: [mixs.vocab:env_package](https://w3id.org/mixs/vocab/env_package) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [mixs extension field](mixs_extension_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | environmental package | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 13.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='soil', description=None) | + diff --git a/mixs6/environment_field.md b/mixs6/environment_field.md new file mode 100644 index 00000000..22a2e196 --- /dev/null +++ b/mixs6/environment_field.md @@ -0,0 +1,535 @@ + +# Slot: environment_field + + +field describing environmental aspect of a sample + +URI: [mixs.vocab:environment_field](https://w3id.org/mixs/vocab/environment_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [abs_air_humidity](abs_air_humidity.md) + * [add_recov_method](add_recov_method.md) + * [additional_info](additional_info.md) + * [address](address.md) + * [adj_room](adj_room.md) + * [aero_struc](aero_struc.md) + * [agrochem_addition](agrochem_addition.md) + * [air_temp](air_temp.md) + * [air_temp_regm](air_temp_regm.md) + * [al_sat](al_sat.md) + * [al_sat_meth](al_sat_meth.md) + * [alkalinity](alkalinity.md) + * [alkalinity_method](alkalinity_method.md) + * [alkyl_diethers](alkyl_diethers.md) + * [alt](alt.md) + * [aminopept_act](aminopept_act.md) + * [ammonium](ammonium.md) + * [amniotic_fluid_color](amniotic_fluid_color.md) + * [amount_light](amount_light.md) + * [ances_data](ances_data.md) + * [annual_precpt](annual_precpt.md) + * [annual_temp](annual_temp.md) + * [antibiotic_regm](antibiotic_regm.md) + * [api](api.md) + * [arch_struc](arch_struc.md) + * [aromatics_pc](aromatics_pc.md) + * [asphaltenes_pc](asphaltenes_pc.md) + * [atmospheric_data](atmospheric_data.md) + * [avg_dew_point](avg_dew_point.md) + * [avg_occup](avg_occup.md) + * [avg_temp](avg_temp.md) + * [bac_prod](bac_prod.md) + * [bac_resp](bac_resp.md) + * [bacteria_carb_prod](bacteria_carb_prod.md) + * [barometric_press](barometric_press.md) + * [basin](basin.md) + * [bathroom_count](bathroom_count.md) + * [bedroom_count](bedroom_count.md) + * [benzene](benzene.md) + * [biochem_oxygen_dem](biochem_oxygen_dem.md) + * [biocide](biocide.md) + * [biocide_admin_method](biocide_admin_method.md) + * [biol_stat](biol_stat.md) + * [biomass](biomass.md) + * [biotic_regm](biotic_regm.md) + * [birth_control](birth_control.md) + * [bishomohopanol](bishomohopanol.md) + * [blood_blood_disord](blood_blood_disord.md) + * [bromide](bromide.md) + * [build_docs](build_docs.md) + * [build_occup_type](build_occup_type.md) + * [building_setting](building_setting.md) + * [built_struc_age](built_struc_age.md) + * [built_struc_set](built_struc_set.md) + * [built_struc_type](built_struc_type.md) + * [calcium](calcium.md) + * [carb_dioxide](carb_dioxide.md) + * [carb_monoxide](carb_monoxide.md) + * [carb_nitro_ratio](carb_nitro_ratio.md) + * [ceil_area](ceil_area.md) + * [ceil_cond](ceil_cond.md) + * [ceil_finish_mat](ceil_finish_mat.md) + * [ceil_struc](ceil_struc.md) + * [ceil_texture](ceil_texture.md) + * [ceil_thermal_mass](ceil_thermal_mass.md) + * [ceil_type](ceil_type.md) + * [ceil_water_mold](ceil_water_mold.md) + * [chem_administration](chem_administration.md) + * [chem_mutagen](chem_mutagen.md) + * [chem_oxygen_dem](chem_oxygen_dem.md) + * [chem_treatment](chem_treatment.md) + * [chem_treatment_method](chem_treatment_method.md) + * [chloride](chloride.md) + * [chlorophyll](chlorophyll.md) + * [climate_environment](climate_environment.md) + * [collection_date](collection_date.md) + * [conduc](conduc.md) + * [cool_syst_id](cool_syst_id.md) + * [crop_rotation](crop_rotation.md) + * [cult_root_med](cult_root_med.md) + * [cur_land_use](cur_land_use.md) + * [cur_vegetation](cur_vegetation.md) + * [cur_vegetation_meth](cur_vegetation_meth.md) + * [date_last_rain](date_last_rain.md) + * [density](density.md) + * [depos_env](depos_env.md) + * [depth](depth.md) + * [dermatology_disord](dermatology_disord.md) + * [dew_point](dew_point.md) + * [diet_last_six_month](diet_last_six_month.md) + * [diether_lipids](diether_lipids.md) + * [diss_carb_dioxide](diss_carb_dioxide.md) + * [diss_hydrogen](diss_hydrogen.md) + * [diss_inorg_carb](diss_inorg_carb.md) + * [diss_inorg_nitro](diss_inorg_nitro.md) + * [diss_inorg_phosp](diss_inorg_phosp.md) + * [diss_iron](diss_iron.md) + * [diss_org_carb](diss_org_carb.md) + * [diss_org_nitro](diss_org_nitro.md) + * [diss_oxygen](diss_oxygen.md) + * [diss_oxygen_fluid](diss_oxygen_fluid.md) + * [dominant_hand](dominant_hand.md) + * [door_comp_type](door_comp_type.md) + * [door_cond](door_cond.md) + * [door_direct](door_direct.md) + * [door_loc](door_loc.md) + * [door_mat](door_mat.md) + * [door_move](door_move.md) + * [door_size](door_size.md) + * [door_type](door_type.md) + * [door_type_metal](door_type_metal.md) + * [door_type_wood](door_type_wood.md) + * [door_water_mold](door_water_mold.md) + * [douche](douche.md) + * [down_par](down_par.md) + * [drainage_class](drainage_class.md) + * [drawings](drawings.md) + * [drug_usage](drug_usage.md) + * [efficiency_percent](efficiency_percent.md) + * [elev](elev.md) + * [elevator](elevator.md) + * [emulsions](emulsions.md) + * [env_broad_scale](env_broad_scale.md) + * [env_local_scale](env_local_scale.md) + * [env_medium](env_medium.md) + * [escalator](escalator.md) + * [ethylbenzene](ethylbenzene.md) + * [exp_duct](exp_duct.md) + * [exp_pipe](exp_pipe.md) + * [ext_door](ext_door.md) + * [ext_wall_orient](ext_wall_orient.md) + * [ext_window_orient](ext_window_orient.md) + * [extreme_event](extreme_event.md) + * [extreme_salinity](extreme_salinity.md) + * [fao_class](fao_class.md) + * [fertilizer_regm](fertilizer_regm.md) + * [field](field.md) + * [filter_type](filter_type.md) + * [fire](fire.md) + * [fireplace_type](fireplace_type.md) + * [flooding](flooding.md) + * [floor_age](floor_age.md) + * [floor_area](floor_area.md) + * [floor_cond](floor_cond.md) + * [floor_count](floor_count.md) + * [floor_finish_mat](floor_finish_mat.md) + * [floor_struc](floor_struc.md) + * [floor_thermal_mass](floor_thermal_mass.md) + * [floor_water_mold](floor_water_mold.md) + * [fluor](fluor.md) + * [foetal_health_stat](foetal_health_stat.md) + * [freq_clean](freq_clean.md) + * [freq_cook](freq_cook.md) + * [fungicide_regm](fungicide_regm.md) + * [furniture](furniture.md) + * [gaseous_environment](gaseous_environment.md) + * [gaseous_substances](gaseous_substances.md) + * [gastrointest_disord](gastrointest_disord.md) + * [gender_restroom](gender_restroom.md) + * [genetic_mod](genetic_mod.md) + * [geo_loc_name](geo_loc_name.md) + * [gestation_state](gestation_state.md) + * [glucosidase_act](glucosidase_act.md) + * [gravidity](gravidity.md) + * [gravity](gravity.md) + * [growth_facil](growth_facil.md) + * [growth_habit](growth_habit.md) + * [growth_hormone_regm](growth_hormone_regm.md) + * [gynecologic_disord](gynecologic_disord.md) + * [hall_count](hall_count.md) + * [handidness](handidness.md) + * [hc_produced](hc_produced.md) + * [hcr](hcr.md) + * [hcr_fw_salinity](hcr_fw_salinity.md) + * [hcr_geol_age](hcr_geol_age.md) + * [hcr_pressure](hcr_pressure.md) + * [hcr_temp](hcr_temp.md) + * [heat_cool_type](heat_cool_type.md) + * [heat_deliv_loc](heat_deliv_loc.md) + * [heat_system_deliv_meth](heat_system_deliv_meth.md) + * [heat_system_id](heat_system_id.md) + * [heavy_metals](heavy_metals.md) + * [heavy_metals_meth](heavy_metals_meth.md) + * [height_carper_fiber](height_carper_fiber.md) + * [herbicide_regm](herbicide_regm.md) + * [horizon](horizon.md) + * [horizon_meth](horizon_meth.md) + * [host_age](host_age.md) + * [host_blood_press_diast](host_blood_press_diast.md) + * [host_blood_press_syst](host_blood_press_syst.md) + * [host_body_habitat](host_body_habitat.md) + * [host_body_mass_index](host_body_mass_index.md) + * [host_body_product](host_body_product.md) + * [host_body_site](host_body_site.md) + * [host_body_temp](host_body_temp.md) + * [host_color](host_color.md) + * [host_common_name](host_common_name.md) + * [host_diet](host_diet.md) + * [host_disease_stat](host_disease_stat.md) + * [host_dry_mass](host_dry_mass.md) + * [host_family_relationship](host_family_relationship.md) + * [host_genotype](host_genotype.md) + * [host_growth_cond](host_growth_cond.md) + * [host_height](host_height.md) + * [host_hiv_stat](host_hiv_stat.md) + * [host_infra_specific_name](host_infra_specific_name.md) + * [host_infra_specific_rank](host_infra_specific_rank.md) + * [host_last_meal](host_last_meal.md) + * [host_length](host_length.md) + * [host_life_stage](host_life_stage.md) + * [host_occupation](host_occupation.md) + * [host_phenotype](host_phenotype.md) + * [host_pulse](host_pulse.md) + * [host_sex](host_sex.md) + * [host_shape](host_shape.md) + * [host_subject_id](host_subject_id.md) + * [host_substrate](host_substrate.md) + * [host_taxid](host_taxid.md) + * [host_tot_mass](host_tot_mass.md) + * [host_wet_mass](host_wet_mass.md) + * [hrt](hrt.md) + * [humidity](humidity.md) + * [humidity_regm](humidity_regm.md) + * [hysterectomy](hysterectomy.md) + * [ihmc_ethnicity](ihmc_ethnicity.md) + * [ihmc_medication_code](ihmc_medication_code.md) + * [indoor_space](indoor_space.md) + * [indoor_surf](indoor_surf.md) + * [indust_eff_percent](indust_eff_percent.md) + * [inorg_particles](inorg_particles.md) + * [inside_lux](inside_lux.md) + * [int_wall_cond](int_wall_cond.md) + * [iw_bt_date_well](iw_bt_date_well.md) + * [iwf](iwf.md) + * [last_clean](last_clean.md) + * [lat_lon](lat_lon.md) + * [light_intensity](light_intensity.md) + * [light_regm](light_regm.md) + * [light_type](light_type.md) + * [link_addit_analys](link_addit_analys.md) + * [link_class_info](link_class_info.md) + * [link_climate_info](link_climate_info.md) + * [lithology](lithology.md) + * [liver_disord](liver_disord.md) + * [local_class](local_class.md) + * [local_class_meth](local_class_meth.md) + * [magnesium](magnesium.md) + * [maternal_health_stat](maternal_health_stat.md) + * [max_occup](max_occup.md) + * [mean_frict_vel](mean_frict_vel.md) + * [mean_peak_frict_vel](mean_peak_frict_vel.md) + * [mech_struc](mech_struc.md) + * [mechanical_damage](mechanical_damage.md) + * [medic_hist_perform](medic_hist_perform.md) + * [menarche](menarche.md) + * [menopause](menopause.md) + * [methane](methane.md) + * [microbial_biomass](microbial_biomass.md) + * [microbial_biomass_meth](microbial_biomass_meth.md) + * [mineral_nutr_regm](mineral_nutr_regm.md) + * [misc_param](misc_param.md) + * [n_alkanes](n_alkanes.md) + * [nitrate](nitrate.md) + * [nitrite](nitrite.md) + * [nitro](nitro.md) + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) + * [nose_throat_disord](nose_throat_disord.md) + * [number_pets](number_pets.md) + * [number_plants](number_plants.md) + * [number_resident](number_resident.md) + * [occup_density_samp](occup_density_samp.md) + * [occup_document](occup_document.md) + * [occup_samp](occup_samp.md) + * [org_carb](org_carb.md) + * [org_matter](org_matter.md) + * [org_nitro](org_nitro.md) + * [org_particles](org_particles.md) + * [organism_count](organism_count.md) + * [organism_count_qpcr_info](organism_count_qpcr_info.md) + * [owc_tvdss](owc_tvdss.md) + * [oxy_stat_samp](oxy_stat_samp.md) + * [oxygen](oxygen.md) + * [part_org_carb](part_org_carb.md) + * [part_org_nitro](part_org_nitro.md) + * [particle_class](particle_class.md) + * [permeability](permeability.md) + * [perturbation](perturbation.md) + * [pesticide_regm](pesticide_regm.md) + * [pet_farm_animal](pet_farm_animal.md) + * [petroleum_hydrocarb](petroleum_hydrocarb.md) + * [ph](ph.md) + * [ph_meth](ph_meth.md) + * [ph_regm](ph_regm.md) + * [phaeopigments](phaeopigments.md) + * [phosphate](phosphate.md) + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) + * [photon_flux](photon_flux.md) + * [plant_growth_med](plant_growth_med.md) + * [plant_product](plant_product.md) + * [plant_sex](plant_sex.md) + * [plant_struc](plant_struc.md) + * [pollutants](pollutants.md) + * [pool_dna_extracts](pool_dna_extracts.md) + * [porosity](porosity.md) + * [potassium](potassium.md) + * [pour_point](pour_point.md) + * [pre_treatment](pre_treatment.md) + * [pregnancy](pregnancy.md) + * [pres_animal](pres_animal.md) + * [pressure](pressure.md) + * [previous_land_use](previous_land_use.md) + * [previous_land_use_meth](previous_land_use_meth.md) + * [primary_prod](primary_prod.md) + * [primary_treatment](primary_treatment.md) + * [prod_rate](prod_rate.md) + * [prod_start_date](prod_start_date.md) + * [profile_position](profile_position.md) + * [pulmonary_disord](pulmonary_disord.md) + * [quad_pos](quad_pos.md) + * [radiation_regm](radiation_regm.md) + * [rainfall_regm](rainfall_regm.md) + * [reactor_type](reactor_type.md) + * [redox_potential](redox_potential.md) + * [rel_air_humidity](rel_air_humidity.md) + * [rel_humidity_out](rel_humidity_out.md) + * [rel_samp_loc](rel_samp_loc.md) + * [reservoir](reservoir.md) + * [resins_pc](resins_pc.md) + * [resp_part_matter](resp_part_matter.md) + * [room_air_exch_rate](room_air_exch_rate.md) + * [room_architec_element](room_architec_element.md) + * [room_condt](room_condt.md) + * [room_connected](room_connected.md) + * [room_count](room_count.md) + * [room_dim](room_dim.md) + * [room_door_dist](room_door_dist.md) + * [room_door_share](room_door_share.md) + * [room_hallway](room_hallway.md) + * [room_loc](room_loc.md) + * [room_moist_damage_hist](room_moist_damage_hist.md) + * [room_net_area](room_net_area.md) + * [room_occup](room_occup.md) + * [room_samp_pos](room_samp_pos.md) + * [room_type](room_type.md) + * [room_vol](room_vol.md) + * [room_wall_share](room_wall_share.md) + * [room_window_count](room_window_count.md) + * [root_cond](root_cond.md) + * [root_med_carbon](root_med_carbon.md) + * [root_med_macronutr](root_med_macronutr.md) + * [root_med_micronutr](root_med_micronutr.md) + * [root_med_ph](root_med_ph.md) + * [root_med_regl](root_med_regl.md) + * [root_med_solid](root_med_solid.md) + * [root_med_suppl](root_med_suppl.md) + * [salinity](salinity.md) + * [salinity_meth](salinity_meth.md) + * [salt_regm](salt_regm.md) + * [samp_capt_status](samp_capt_status.md) + * [samp_collection_point](samp_collection_point.md) + * [samp_dis_stage](samp_dis_stage.md) + * [samp_floor](samp_floor.md) + * [samp_loc_corr_rate](samp_loc_corr_rate.md) + * [samp_md](samp_md.md) + * [samp_preserv](samp_preserv.md) + * [samp_room_id](samp_room_id.md) + * [samp_salinity](samp_salinity.md) + * [samp_sort_meth](samp_sort_meth.md) + * [samp_store_dur](samp_store_dur.md) + * [samp_store_loc](samp_store_loc.md) + * [samp_store_temp](samp_store_temp.md) + * [samp_subtype](samp_subtype.md) + * [samp_time_out](samp_time_out.md) + * [samp_transport_cond](samp_transport_cond.md) + * [samp_tvdss](samp_tvdss.md) + * [samp_type](samp_type.md) + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) + * [samp_weather](samp_weather.md) + * [samp_well_name](samp_well_name.md) + * [saturates_pc](saturates_pc.md) + * [season](season.md) + * [season_environment](season_environment.md) + * [season_precpt](season_precpt.md) + * [season_temp](season_temp.md) + * [season_use](season_use.md) + * [secondary_treatment](secondary_treatment.md) + * [sediment_type](sediment_type.md) + * [sewage_type](sewage_type.md) + * [sexual_act](sexual_act.md) + * [shading_device_cond](shading_device_cond.md) + * [shading_device_loc](shading_device_loc.md) + * [shading_device_mat](shading_device_mat.md) + * [shading_device_type](shading_device_type.md) + * [shading_device_water_mold](shading_device_water_mold.md) + * [sieving](sieving.md) + * [silicate](silicate.md) + * [size_frac_low](size_frac_low.md) + * [size_frac_up](size_frac_up.md) + * [slope_aspect](slope_aspect.md) + * [slope_gradient](slope_gradient.md) + * [sludge_retent_time](sludge_retent_time.md) + * [smoker](smoker.md) + * [sodium](sodium.md) + * [soil_type](soil_type.md) + * [soil_type_meth](soil_type_meth.md) + * [solar_irradiance](solar_irradiance.md) + * [soluble_inorg_mat](soluble_inorg_mat.md) + * [soluble_org_mat](soluble_org_mat.md) + * [soluble_react_phosp](soluble_react_phosp.md) + * [space_typ_state](space_typ_state.md) + * [special_diet](special_diet.md) + * [specific](specific.md) + * [specific_humidity](specific_humidity.md) + * [sr_dep_env](sr_dep_env.md) + * [sr_geol_age](sr_geol_age.md) + * [sr_kerog_type](sr_kerog_type.md) + * [sr_lithology](sr_lithology.md) + * [standing_water_regm](standing_water_regm.md) + * [store_cond](store_cond.md) + * [study_complt_stat](study_complt_stat.md) + * [substructure_type](substructure_type.md) + * [sulfate](sulfate.md) + * [sulfate_fw](sulfate_fw.md) + * [sulfide](sulfide.md) + * [surf_air_cont](surf_air_cont.md) + * [surf_humidity](surf_humidity.md) + * [surf_material](surf_material.md) + * [surf_moisture](surf_moisture.md) + * [surf_moisture_ph](surf_moisture_ph.md) + * [surf_temp](surf_temp.md) + * [suspend_part_matter](suspend_part_matter.md) + * [suspend_solids](suspend_solids.md) + * [tan](tan.md) + * [temp](temp.md) + * [temp_out](temp_out.md) + * [tertiary_treatment](tertiary_treatment.md) + * [texture](texture.md) + * [texture_meth](texture_meth.md) + * [tidal_stage](tidal_stage.md) + * [tillage](tillage.md) + * [time_last_toothbrush](time_last_toothbrush.md) + * [time_since_last_wash](time_since_last_wash.md) + * [tiss_cult_growth_med](tiss_cult_growth_med.md) + * [toluene](toluene.md) + * [tot_carb](tot_carb.md) + * [tot_depth_water_col](tot_depth_water_col.md) + * [tot_diss_nitro](tot_diss_nitro.md) + * [tot_inorg_nitro](tot_inorg_nitro.md) + * [tot_iron](tot_iron.md) + * [tot_nitro](tot_nitro.md) + * [tot_nitro_content](tot_nitro_content.md) + * [tot_nitro_content_meth](tot_nitro_content_meth.md) + * [tot_org_c_meth](tot_org_c_meth.md) + * [tot_org_carb](tot_org_carb.md) + * [tot_part_carb](tot_part_carb.md) + * [tot_phosp](tot_phosp.md) + * [tot_phosphate](tot_phosphate.md) + * [tot_sulfur](tot_sulfur.md) + * [train_line](train_line.md) + * [train_stat_loc](train_stat_loc.md) + * [train_stop_loc](train_stop_loc.md) + * [travel_out_six_month](travel_out_six_month.md) + * [turbidity](turbidity.md) + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) + * [twin_sibling](twin_sibling.md) + * [typ_occup_density](typ_occup_density.md) + * [urine_collect_meth](urine_collect_meth.md) + * [urogenit_disord](urogenit_disord.md) + * [urogenit_tract_disor](urogenit_tract_disor.md) + * [ventilation_rate](ventilation_rate.md) + * [ventilation_type](ventilation_type.md) + * [vfa](vfa.md) + * [vfa_fw](vfa_fw.md) + * [vis_media](vis_media.md) + * [viscosity](viscosity.md) + * [volatile_org_comp](volatile_org_comp.md) + * [wall_area](wall_area.md) + * [wall_const_type](wall_const_type.md) + * [wall_finish_mat](wall_finish_mat.md) + * [wall_height](wall_height.md) + * [wall_loc](wall_loc.md) + * [wall_surf_treatment](wall_surf_treatment.md) + * [wall_texture](wall_texture.md) + * [wall_thermal_mass](wall_thermal_mass.md) + * [wall_water_mold](wall_water_mold.md) + * [wastewater_type](wastewater_type.md) + * [water_content](water_content.md) + * [water_content_soil_meth](water_content_soil_meth.md) + * [water_current](water_current.md) + * [water_cut](water_cut.md) + * [water_feat_size](water_feat_size.md) + * [water_feat_type](water_feat_type.md) + * [water_production_rate](water_production_rate.md) + * [water_temp_regm](water_temp_regm.md) + * [watering_regm](watering_regm.md) + * [weekday](weekday.md) + * [weight_loss_3_month](weight_loss_3_month.md) + * [win](win.md) + * [wind_direction](wind_direction.md) + * [wind_speed](wind_speed.md) + * [window_cond](window_cond.md) + * [window_cover](window_cover.md) + * [window_horiz_pos](window_horiz_pos.md) + * [window_loc](window_loc.md) + * [window_mat](window_mat.md) + * [window_open_freq](window_open_freq.md) + * [window_size](window_size.md) + * [window_status](window_status.md) + * [window_type](window_type.md) + * [window_vert_pos](window_vert_pos.md) + * [window_water_mold](window_water_mold.md) + * [xylene](xylene.md) + +## Used by + diff --git a/mixs6/escalator.md b/mixs6/escalator.md new file mode 100644 index 00000000..6986d7cc --- /dev/null +++ b/mixs6/escalator.md @@ -0,0 +1,48 @@ + +# Slot: escalator + + +The number of escalators within the built structure + +URI: [mixs.vocab:escalator](https://w3id.org/mixs/vocab/escalator) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | escalator count | +| **Mappings:** | | MIXS:0000800 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 64 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='4', description=None) | + diff --git a/mixs6/estimated_size.md b/mixs6/estimated_size.md new file mode 100644 index 00000000..fa88fabe --- /dev/null +++ b/mixs6/estimated_size.md @@ -0,0 +1,56 @@ + +# Slot: estimated_size + + +The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + +URI: [mixs.vocab:estimated_size](https://w3id.org/mixs/vocab/estimated_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | estimated size | +| **Comments:** | | Expected value: number of base pairs | +| | | Preferred unit: | +| | | Position: 18.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='300000 bp', description=None) | + diff --git a/mixs6/ethylbenzene.md b/mixs6/ethylbenzene.md new file mode 100644 index 00000000..867b685a --- /dev/null +++ b/mixs6/ethylbenzene.md @@ -0,0 +1,60 @@ + +# Slot: ethylbenzene + + +Concentration of ethylbenzene in the sample + +URI: [mixs.vocab:ethylbenzene](https://w3id.org/mixs/vocab/ethylbenzene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ethylbenzene | +| **Mappings:** | | MIXS:0000155 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 83 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/exp_duct.md b/mixs6/exp_duct.md new file mode 100644 index 00000000..f2536949 --- /dev/null +++ b/mixs6/exp_duct.md @@ -0,0 +1,48 @@ + +# Slot: exp_duct + + +The amount of exposed ductwork in the room + +URI: [mixs.vocab:exp_duct](https://w3id.org/mixs/vocab/exp_duct) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exposed ductwork | +| **Mappings:** | | MIXS:0000144 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 65 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/exp_pipe.md b/mixs6/exp_pipe.md new file mode 100644 index 00000000..bd876343 --- /dev/null +++ b/mixs6/exp_pipe.md @@ -0,0 +1,48 @@ + +# Slot: exp_pipe + + +The number of exposed pipes in the room + +URI: [mixs.vocab:exp_pipe](https://w3id.org/mixs/vocab/exp_pipe) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exposed pipes | +| **Mappings:** | | MIXS:0000220 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 66 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/experimental_factor.md b/mixs6/experimental_factor.md new file mode 100644 index 00000000..584c1049 --- /dev/null +++ b/mixs6/experimental_factor.md @@ -0,0 +1,56 @@ + +# Slot: experimental_factor + + +Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + +URI: [mixs.vocab:experimental_factor](https://w3id.org/mixs/vocab/experimental_factor) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | experimental factor | +| **Comments:** | | Expected value: text or EFO and/or OBI | +| | | Preferred unit: | +| | | Position: 4.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: X | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='time series design [EFO:EFO_0001779]', description=None) | + diff --git a/mixs6/ext_door.md b/mixs6/ext_door.md new file mode 100644 index 00000000..6d75f0d4 --- /dev/null +++ b/mixs6/ext_door.md @@ -0,0 +1,48 @@ + +# Slot: ext_door + + +The number of exterior doors in the built structure + +URI: [mixs.vocab:ext_door](https://w3id.org/mixs/vocab/ext_door) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | exterior door count | +| **Mappings:** | | MIXS:0000170 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 67 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ext_wall_orient.md b/mixs6/ext_wall_orient.md new file mode 100644 index 00000000..9f079fe7 --- /dev/null +++ b/mixs6/ext_wall_orient.md @@ -0,0 +1,48 @@ + +# Slot: ext_wall_orient + + +The orientation of the exterior wall + +URI: [mixs.vocab:ext_wall_orient](https://w3id.org/mixs/vocab/ext_wall_orient) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | orientations of exterior wall | +| **Mappings:** | | MIXS:0000817 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 96 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='northwest', description=None) | + diff --git a/mixs6/ext_window_orient.md b/mixs6/ext_window_orient.md new file mode 100644 index 00000000..f737bd19 --- /dev/null +++ b/mixs6/ext_window_orient.md @@ -0,0 +1,48 @@ + +# Slot: ext_window_orient + + +The compass direction the exterior window of the room is facing + +URI: [mixs.vocab:ext_window_orient](https://w3id.org/mixs/vocab/ext_window_orient) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | orientations of exterior window | +| **Mappings:** | | MIXS:0000818 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 97 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='southwest', description=None) | + diff --git a/mixs6/extrachrom_elements.md b/mixs6/extrachrom_elements.md new file mode 100644 index 00000000..04cba004 --- /dev/null +++ b/mixs6/extrachrom_elements.md @@ -0,0 +1,56 @@ + +# Slot: extrachrom_elements + + +Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + +URI: [mixs.vocab:extrachrom_elements](https://w3id.org/mixs/vocab/extrachrom_elements) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extrachromosomal elements | +| **Comments:** | | Expected value: number of extrachromosmal elements | +| | | Preferred unit: | +| | | Position: 17.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: X | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='5', description=None) | + diff --git a/mixs6/extreme_event.md b/mixs6/extreme_event.md new file mode 100644 index 00000000..568ba318 --- /dev/null +++ b/mixs6/extreme_event.md @@ -0,0 +1,48 @@ + +# Slot: extreme_event + + +Unusual physical events that may have affected microbial populations + +URI: [mixs.vocab:extreme_event](https://w3id.org/mixs/vocab/extreme_event) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/extreme events | +| **Mappings:** | | MIXS:0000320 | +| **Comments:** | | Expected value: date | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 11 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/extreme_salinity.md b/mixs6/extreme_salinity.md new file mode 100644 index 00000000..1c485bb8 --- /dev/null +++ b/mixs6/extreme_salinity.md @@ -0,0 +1,48 @@ + +# Slot: extreme_salinity + + +Measured salinity + +URI: [mixs.vocab:extreme_salinity](https://w3id.org/mixs/vocab/extreme_salinity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/salinity | +| **Mappings:** | | MIXS:0000651 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millisiemens per meter | +| | | Occurrence: 1 | +| | | Position: 46 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fao_class.md b/mixs6/fao_class.md new file mode 100644 index 00000000..b59acaf9 --- /dev/null +++ b/mixs6/fao_class.md @@ -0,0 +1,48 @@ + +# Slot: fao_class + + +Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + +URI: [mixs.vocab:fao_class](https://w3id.org/mixs/vocab/fao_class) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/FAO classification | +| **Mappings:** | | MIXS:0001083 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 26 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='Luvisols', description=None) | + diff --git a/mixs6/feat_pred.md b/mixs6/feat_pred.md new file mode 100644 index 00000000..8f4dea4e --- /dev/null +++ b/mixs6/feat_pred.md @@ -0,0 +1,56 @@ + +# Slot: feat_pred + + +Method used to predict UViGs features such as ORFs, integration site, etc. + +URI: [mixs.vocab:feat_pred](https://w3id.org/mixs/vocab/feat_pred) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | feature prediction | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Preferred unit: | +| | | Position: 59.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='Prodigal;2.6.3;default parameters', description=None) | + diff --git a/mixs6/fertilizer_regm.md b/mixs6/fertilizer_regm.md new file mode 100644 index 00000000..23d253c5 --- /dev/null +++ b/mixs6/fertilizer_regm.md @@ -0,0 +1,48 @@ + +# Slot: fertilizer_regm + + +Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + +URI: [mixs.vocab:fertilizer_regm](https://w3id.org/mixs/vocab/fertilizer_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fertilizer regimen | +| **Mappings:** | | MIXS:0000556 | +| **Comments:** | | Expected value: fertilizer name;fertilizer amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/field.md b/mixs6/field.md new file mode 100644 index 00000000..d7f62d81 --- /dev/null +++ b/mixs6/field.md @@ -0,0 +1,60 @@ + +# Slot: field + + +Name of the hydrocarbon field (e.g. Albacora) + +URI: [mixs.vocab:field](https://w3id.org/mixs/vocab/field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | field name | +| **Mappings:** | | MIXS:0000291 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 4 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/filter_type.md b/mixs6/filter_type.md new file mode 100644 index 00000000..fa2d9e7e --- /dev/null +++ b/mixs6/filter_type.md @@ -0,0 +1,48 @@ + +# Slot: filter_type + + +A device which removes solid particulates or airborne molecular contaminants + +URI: [mixs.vocab:filter_type](https://w3id.org/mixs/vocab/filter_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | filter type | +| **Mappings:** | | MIXS:0000765 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 17 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='HEPA', description=None) | + diff --git a/mixs6/fire.md b/mixs6/fire.md new file mode 100644 index 00000000..92544840 --- /dev/null +++ b/mixs6/fire.md @@ -0,0 +1,48 @@ + +# Slot: fire + + +Historical and/or physical evidence of fire + +URI: [mixs.vocab:fire](https://w3id.org/mixs/vocab/fire) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/fire | +| **Mappings:** | | MIXS:0001086 | +| **Comments:** | | Expected value: date | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 9 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fireplace_type.md b/mixs6/fireplace_type.md new file mode 100644 index 00000000..ee9a91e5 --- /dev/null +++ b/mixs6/fireplace_type.md @@ -0,0 +1,48 @@ + +# Slot: fireplace_type + + +A firebox with chimney + +URI: [mixs.vocab:fireplace_type](https://w3id.org/mixs/vocab/fireplace_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fireplace type | +| **Mappings:** | | MIXS:0000802 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 68 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood burning', description=None) | + diff --git a/mixs6/flooding.md b/mixs6/flooding.md new file mode 100644 index 00000000..04adfbfe --- /dev/null +++ b/mixs6/flooding.md @@ -0,0 +1,48 @@ + +# Slot: flooding + + +Historical and/or physical evidence of flooding + +URI: [mixs.vocab:flooding](https://w3id.org/mixs/vocab/flooding) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/flooding | +| **Mappings:** | | MIXS:0000319 | +| **Comments:** | | Expected value: date | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 10 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_age.md b/mixs6/floor_age.md new file mode 100644 index 00000000..687dedb1 --- /dev/null +++ b/mixs6/floor_age.md @@ -0,0 +1,48 @@ + +# Slot: floor_age + + +The time period since installment of the carpet or flooring + +URI: [mixs.vocab:floor_age](https://w3id.org/mixs/vocab/floor_age) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor age | +| **Mappings:** | | MIXS:0000164 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: years, weeks, days | +| | | Occurrence: 1 | +| | | Position: 69 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_area.md b/mixs6/floor_area.md new file mode 100644 index 00000000..cabf5e05 --- /dev/null +++ b/mixs6/floor_area.md @@ -0,0 +1,48 @@ + +# Slot: floor_area + + +The area of the floor space within the room + +URI: [mixs.vocab:floor_area](https://w3id.org/mixs/vocab/floor_area) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor area | +| **Mappings:** | | MIXS:0000165 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 70 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_cond.md b/mixs6/floor_cond.md new file mode 100644 index 00000000..3ec9d7c0 --- /dev/null +++ b/mixs6/floor_cond.md @@ -0,0 +1,48 @@ + +# Slot: floor_cond + + +The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:floor_cond](https://w3id.org/mixs/vocab/floor_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor condition | +| **Mappings:** | | MIXS:0000803 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 71 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/floor_count.md b/mixs6/floor_count.md new file mode 100644 index 00000000..f41602e3 --- /dev/null +++ b/mixs6/floor_count.md @@ -0,0 +1,48 @@ + +# Slot: floor_count + + +The number of floors in the building, including basements and mechanical penthouse + +URI: [mixs.vocab:floor_count](https://w3id.org/mixs/vocab/floor_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor count | +| **Mappings:** | | MIXS:0000225 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 72 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_finish_mat.md b/mixs6/floor_finish_mat.md new file mode 100644 index 00000000..d903c531 --- /dev/null +++ b/mixs6/floor_finish_mat.md @@ -0,0 +1,48 @@ + +# Slot: floor_finish_mat + + +The floor covering type; the finished surface that is walked on + +URI: [mixs.vocab:floor_finish_mat](https://w3id.org/mixs/vocab/floor_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor finish material | +| **Mappings:** | | MIXS:0000804 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 73 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='carpet', description=None) | + diff --git a/mixs6/floor_struc.md b/mixs6/floor_struc.md new file mode 100644 index 00000000..44101067 --- /dev/null +++ b/mixs6/floor_struc.md @@ -0,0 +1,48 @@ + +# Slot: floor_struc + + +Refers to the structural elements and subfloor upon which the finish flooring is installed + +URI: [mixs.vocab:floor_struc](https://w3id.org/mixs/vocab/floor_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor structure | +| **Mappings:** | | MIXS:0000806 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 75 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='concrete', description=None) | + diff --git a/mixs6/floor_thermal_mass.md b/mixs6/floor_thermal_mass.md new file mode 100644 index 00000000..4951081f --- /dev/null +++ b/mixs6/floor_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: floor_thermal_mass + + +The ability of the floor to provide inertia against temperature fluctuations + +URI: [mixs.vocab:floor_thermal_mass](https://w3id.org/mixs/vocab/floor_thermal_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor thermal mass | +| **Mappings:** | | MIXS:0000166 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 76 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/floor_water_mold.md b/mixs6/floor_water_mold.md new file mode 100644 index 00000000..1a846cf3 --- /dev/null +++ b/mixs6/floor_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: floor_water_mold + + +Signs of the presence of mold or mildew in a room + +URI: [mixs.vocab:floor_water_mold](https://w3id.org/mixs/vocab/floor_water_mold) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | floor signs of water/mold | +| **Mappings:** | | MIXS:0000805 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 74 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='ceiling discoloration', description=None) | + diff --git a/mixs6/fluor.md b/mixs6/fluor.md new file mode 100644 index 00000000..e026726e --- /dev/null +++ b/mixs6/fluor.md @@ -0,0 +1,48 @@ + +# Slot: fluor + + +Raw or converted fluorescence of water + +URI: [mixs.vocab:fluor](https://w3id.org/mixs/vocab/fluor) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fluorescence | +| **Mappings:** | | MIXS:0000704 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram chlorophyll a per cubic meter, volts | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='2.5 volts', description=None) | + diff --git a/mixs6/foetal_health_stat.md b/mixs6/foetal_health_stat.md new file mode 100644 index 00000000..7d841982 --- /dev/null +++ b/mixs6/foetal_health_stat.md @@ -0,0 +1,48 @@ + +# Slot: foetal_health_stat + + +Specification of foetal health status, should also include abortion + +URI: [mixs.vocab:foetal_health_stat](https://w3id.org/mixs/vocab/foetal_health_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/foetal health status | +| **Mappings:** | | MIXS:0000275 | +| **Comments:** | | Expected value: health status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 38 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/freq_clean.md b/mixs6/freq_clean.md new file mode 100644 index 00000000..48ce37dd --- /dev/null +++ b/mixs6/freq_clean.md @@ -0,0 +1,48 @@ + +# Slot: freq_clean + + +The number of times the building is cleaned per week + +URI: [mixs.vocab:freq_clean](https://w3id.org/mixs/vocab/freq_clean) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | frequency of cleaning | +| **Mappings:** | | MIXS:0000226 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 77 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/freq_cook.md b/mixs6/freq_cook.md new file mode 100644 index 00000000..6cb1368c --- /dev/null +++ b/mixs6/freq_cook.md @@ -0,0 +1,48 @@ + +# Slot: freq_cook + + +The number of times a meal is cooked per week + +URI: [mixs.vocab:freq_cook](https://w3id.org/mixs/vocab/freq_cook) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | frequency of cooking | +| **Mappings:** | | MIXS:0000227 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 78 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/fungicide_regm.md b/mixs6/fungicide_regm.md new file mode 100644 index 00000000..f2e2c415 --- /dev/null +++ b/mixs6/fungicide_regm.md @@ -0,0 +1,48 @@ + +# Slot: fungicide_regm + + +Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + +URI: [mixs.vocab:fungicide_regm](https://w3id.org/mixs/vocab/fungicide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | fungicide regimen | +| **Mappings:** | | MIXS:0000557 | +| **Comments:** | | Expected value: fungicide name;fungicide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/furniture.md b/mixs6/furniture.md new file mode 100644 index 00000000..3f89862d --- /dev/null +++ b/mixs6/furniture.md @@ -0,0 +1,48 @@ + +# Slot: furniture + + +The types of furniture present in the sampled room + +URI: [mixs.vocab:furniture](https://w3id.org/mixs/vocab/furniture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | furniture | +| **Mappings:** | | MIXS:0000807 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 79 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='chair', description=None) | + diff --git a/mixs6/gaseous_environment.md b/mixs6/gaseous_environment.md new file mode 100644 index 00000000..64445188 --- /dev/null +++ b/mixs6/gaseous_environment.md @@ -0,0 +1,48 @@ + +# Slot: gaseous_environment + + +Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + +URI: [mixs.vocab:gaseous_environment](https://w3id.org/mixs/vocab/gaseous_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gaseous environment | +| **Mappings:** | | MIXS:0000558 | +| **Comments:** | | Expected value: gaseous compound name;gaseous compound amount;treatment interval and duration | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/gaseous_substances.md b/mixs6/gaseous_substances.md new file mode 100644 index 00000000..ed9cd10a --- /dev/null +++ b/mixs6/gaseous_substances.md @@ -0,0 +1,48 @@ + +# Slot: gaseous_substances + + +Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + +URI: [mixs.vocab:gaseous_substances](https://w3id.org/mixs/vocab/gaseous_substances) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gaseous substances | +| **Mappings:** | | MIXS:0000661 | +| **Comments:** | | Expected value: gaseous substance name;measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/gastrointest_disord.md b/mixs6/gastrointest_disord.md new file mode 100644 index 00000000..7f0fcb3c --- /dev/null +++ b/mixs6/gastrointest_disord.md @@ -0,0 +1,48 @@ + +# Slot: gastrointest_disord + + +History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + +URI: [mixs.vocab:gastrointest_disord](https://w3id.org/mixs/vocab/gastrointest_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gastrointestinal tract disorder | +| **Mappings:** | | MIXS:0000280 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/gender_restroom.md b/mixs6/gender_restroom.md new file mode 100644 index 00000000..80f52ba5 --- /dev/null +++ b/mixs6/gender_restroom.md @@ -0,0 +1,48 @@ + +# Slot: gender_restroom + + +The gender type of the restroom + +URI: [mixs.vocab:gender_restroom](https://w3id.org/mixs/vocab/gender_restroom) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gender of restroom | +| **Mappings:** | | MIXS:0000808 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 80 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='male', description=None) | + diff --git a/mixs6/genetic_mod.md b/mixs6/genetic_mod.md new file mode 100644 index 00000000..dc4a3b2b --- /dev/null +++ b/mixs6/genetic_mod.md @@ -0,0 +1,60 @@ + +# Slot: genetic_mod + + +Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + +URI: [mixs.vocab:genetic_mod](https://w3id.org/mixs/vocab/genetic_mod) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | genetic modification | +| **Mappings:** | | MIXS:0000859 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='aox1A transgenic', description=None) | + diff --git a/mixs6/geo_loc_name.md b/mixs6/geo_loc_name.md new file mode 100644 index 00000000..23fd975f --- /dev/null +++ b/mixs6/geo_loc_name.md @@ -0,0 +1,56 @@ + +# Slot: geo_loc_name + + +The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + +URI: [mixs.vocab:geo_loc_name](https://w3id.org/mixs/vocab/geo_loc_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (country and/or sea,region) | +| **Comments:** | | Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location name | +| | | Preferred unit: | +| | | Position: 8.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='Germany;North Rhine-Westphalia;Eifel National Park', description=None) | + diff --git a/mixs6/gestation_state.md b/mixs6/gestation_state.md new file mode 100644 index 00000000..98e2124a --- /dev/null +++ b/mixs6/gestation_state.md @@ -0,0 +1,48 @@ + +# Slot: gestation_state + + +Specification of the gestation state + +URI: [mixs.vocab:gestation_state](https://w3id.org/mixs/vocab/gestation_state) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/gestation state | +| **Mappings:** | | MIXS:0000272 | +| **Comments:** | | Expected value: gestation state | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 36 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/glucosidase_act.md b/mixs6/glucosidase_act.md new file mode 100644 index 00000000..ae3570aa --- /dev/null +++ b/mixs6/glucosidase_act.md @@ -0,0 +1,72 @@ + +# Slot: glucosidase_act + + +Measurement of glucosidase activity + +URI: [mixs.vocab:glucosidase_act](https://w3id.org/mixs/vocab/glucosidase_act) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | glucosidase activity | +| **Mappings:** | | MIXS:0000137 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mol per liter per hour | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='5 mol per liter per hour', description=None) | + diff --git a/mixs6/gravidity.md b/mixs6/gravidity.md new file mode 100644 index 00000000..ffb13e58 --- /dev/null +++ b/mixs6/gravidity.md @@ -0,0 +1,48 @@ + +# Slot: gravidity + + +Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + +URI: [mixs.vocab:gravidity](https://w3id.org/mixs/vocab/gravidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gravidity | +| **Mappings:** | | MIXS:0000875 | +| **Comments:** | | Expected value: gravidity status;timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 35 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='yes;due date:2018-05-11', description=None) | + diff --git a/mixs6/gravity.md b/mixs6/gravity.md new file mode 100644 index 00000000..3078caa3 --- /dev/null +++ b/mixs6/gravity.md @@ -0,0 +1,48 @@ + +# Slot: gravity + + +Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + +URI: [mixs.vocab:gravity](https://w3id.org/mixs/vocab/gravity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gravity | +| **Mappings:** | | MIXS:0000559 | +| **Comments:** | | Expected value: gravity factor value;treatment interval and duration | +| | | Preferred unit: meter per square second, g | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/growth_facil.md b/mixs6/growth_facil.md new file mode 100644 index 00000000..d8c693d8 --- /dev/null +++ b/mixs6/growth_facil.md @@ -0,0 +1,48 @@ + +# Slot: growth_facil + + +Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + +URI: [mixs.vocab:growth_facil](https://w3id.org/mixs/vocab/growth_facil) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth facility | +| **Mappings:** | | MIXS:0001043 | +| **Comments:** | | Expected value: free text or CO | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='Growth chamber [CO_715:0000189]', description=None) | + diff --git a/mixs6/growth_habit.md b/mixs6/growth_habit.md new file mode 100644 index 00000000..8b276654 --- /dev/null +++ b/mixs6/growth_habit.md @@ -0,0 +1,48 @@ + +# Slot: growth_habit + + +Characteristic shape, appearance or growth form of a plant species + +URI: [mixs.vocab:growth_habit](https://w3id.org/mixs/vocab/growth_habit) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth habit | +| **Mappings:** | | MIXS:0001044 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='spreading', description=None) | + diff --git a/mixs6/growth_hormone_regm.md b/mixs6/growth_hormone_regm.md new file mode 100644 index 00000000..b2d5d302 --- /dev/null +++ b/mixs6/growth_hormone_regm.md @@ -0,0 +1,48 @@ + +# Slot: growth_hormone_regm + + +Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + +URI: [mixs.vocab:growth_hormone_regm](https://w3id.org/mixs/vocab/growth_hormone_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | growth hormone regimen | +| **Mappings:** | | MIXS:0000560 | +| **Comments:** | | Expected value: growth hormone name;growth hormone amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/gynecologic_disord.md b/mixs6/gynecologic_disord.md new file mode 100644 index 00000000..00bf339f --- /dev/null +++ b/mixs6/gynecologic_disord.md @@ -0,0 +1,48 @@ + +# Slot: gynecologic_disord + + +History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + +URI: [mixs.vocab:gynecologic_disord](https://w3id.org/mixs/vocab/gynecologic_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | gynecological disorder | +| **Mappings:** | | MIXS:0000288 | +| **Comments:** | | Expected value: gynecological disorder | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 9 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hall_count.md b/mixs6/hall_count.md new file mode 100644 index 00000000..53889b1e --- /dev/null +++ b/mixs6/hall_count.md @@ -0,0 +1,48 @@ + +# Slot: hall_count + + +The total count of hallways and cooridors in the built structure + +URI: [mixs.vocab:hall_count](https://w3id.org/mixs/vocab/hall_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hallway/corridor count | +| **Mappings:** | | MIXS:0000228 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 81 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/handidness.md b/mixs6/handidness.md new file mode 100644 index 00000000..9147485c --- /dev/null +++ b/mixs6/handidness.md @@ -0,0 +1,48 @@ + +# Slot: handidness + + +The handidness of the individual sampled + +URI: [mixs.vocab:handidness](https://w3id.org/mixs/vocab/handidness) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | handidness | +| **Mappings:** | | MIXS:0000809 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 82 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='right handedness', description=None) | + diff --git a/mixs6/hc_produced.md b/mixs6/hc_produced.md new file mode 100644 index 00000000..dd8a7419 --- /dev/null +++ b/mixs6/hc_produced.md @@ -0,0 +1,60 @@ + +# Slot: hc_produced + + +Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hc_produced](https://w3id.org/mixs/vocab/hc_produced) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon type produced | +| **Mappings:** | | MIXS:0000989 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Gas', description=None) | + diff --git a/mixs6/hcr.md b/mixs6/hcr.md new file mode 100644 index 00000000..1189e26b --- /dev/null +++ b/mixs6/hcr.md @@ -0,0 +1,60 @@ + +# Slot: hcr + + +Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hcr](https://w3id.org/mixs/vocab/hcr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource type | +| **Mappings:** | | MIXS:0000988 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Oil Sand', description=None) | + diff --git a/mixs6/hcr_fw_salinity.md b/mixs6/hcr_fw_salinity.md new file mode 100644 index 00000000..72cfdc8d --- /dev/null +++ b/mixs6/hcr_fw_salinity.md @@ -0,0 +1,60 @@ + +# Slot: hcr_fw_salinity + + +Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + +URI: [mixs.vocab:hcr_fw_salinity](https://w3id.org/mixs/vocab/hcr_fw_salinity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | formation water salinity | +| **Mappings:** | | MIXS:0000406 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 16 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hcr_geol_age.md b/mixs6/hcr_geol_age.md new file mode 100644 index 00000000..ca4e1d5b --- /dev/null +++ b/mixs6/hcr_geol_age.md @@ -0,0 +1,60 @@ + +# Slot: hcr_geol_age + + +Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:hcr_geol_age](https://w3id.org/mixs/vocab/hcr_geol_age) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource geological age | +| **Mappings:** | | MIXS:0000993 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 14 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Silurian', description=None) | + diff --git a/mixs6/hcr_pressure.md b/mixs6/hcr_pressure.md new file mode 100644 index 00000000..cd3e54a5 --- /dev/null +++ b/mixs6/hcr_pressure.md @@ -0,0 +1,60 @@ + +# Slot: hcr_pressure + + +Original pressure of the hydrocarbon resource + +URI: [mixs.vocab:hcr_pressure](https://w3id.org/mixs/vocab/hcr_pressure) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource original pressure | +| **Mappings:** | | MIXS:0000395 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: atmosphere, kilopascal | +| | | Occurrence: 1 | +| | | Position: 8 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/hcr_temp.md b/mixs6/hcr_temp.md new file mode 100644 index 00000000..7ada3e0c --- /dev/null +++ b/mixs6/hcr_temp.md @@ -0,0 +1,60 @@ + +# Slot: hcr_temp + + +Original temperature of the hydrocarbon resource + +URI: [mixs.vocab:hcr_temp](https://w3id.org/mixs/vocab/hcr_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hydrocarbon resource original temperature | +| **Mappings:** | | MIXS:0000393 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 6 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='150-295 degree Celsius', description=None) | + diff --git a/mixs6/health_disease_stat.md b/mixs6/health_disease_stat.md new file mode 100644 index 00000000..99770ae0 --- /dev/null +++ b/mixs6/health_disease_stat.md @@ -0,0 +1,56 @@ + +# Slot: health_disease_stat + + +Health or disease status of specific host at time of collection + +URI: [mixs.vocab:health_disease_stat](https://w3id.org/mixs/vocab/health_disease_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | health or disease status of specific host at time of collection | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 25.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='dead', description=None) | + diff --git a/mixs6/heat_cool_type.md b/mixs6/heat_cool_type.md new file mode 100644 index 00000000..e1fca8e7 --- /dev/null +++ b/mixs6/heat_cool_type.md @@ -0,0 +1,48 @@ + +# Slot: heat_cool_type + + +Methods of conditioning or heating a room or building + +URI: [mixs.vocab:heat_cool_type](https://w3id.org/mixs/vocab/heat_cool_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating and cooling system type | +| **Mappings:** | | MIXS:0000766 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 18 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='heat pump', description=None) | + diff --git a/mixs6/heat_deliv_loc.md b/mixs6/heat_deliv_loc.md new file mode 100644 index 00000000..cad0af42 --- /dev/null +++ b/mixs6/heat_deliv_loc.md @@ -0,0 +1,48 @@ + +# Slot: heat_deliv_loc + + +The location of heat delivery within the room + +URI: [mixs.vocab:heat_deliv_loc](https://w3id.org/mixs/vocab/heat_deliv_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating delivery locations | +| **Mappings:** | | MIXS:0000810 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 83 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/heat_system_deliv_meth.md b/mixs6/heat_system_deliv_meth.md new file mode 100644 index 00000000..66ecfd68 --- /dev/null +++ b/mixs6/heat_system_deliv_meth.md @@ -0,0 +1,48 @@ + +# Slot: heat_system_deliv_meth + + +The method by which the heat is delivered through the system + +URI: [mixs.vocab:heat_system_deliv_meth](https://w3id.org/mixs/vocab/heat_system_deliv_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating system delivery method | +| **Mappings:** | | MIXS:0000812 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 84 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='radiant', description=None) | + diff --git a/mixs6/heat_system_id.md b/mixs6/heat_system_id.md new file mode 100644 index 00000000..8e5e881a --- /dev/null +++ b/mixs6/heat_system_id.md @@ -0,0 +1,48 @@ + +# Slot: heat_system_id + + +The heating system identifier + +URI: [mixs.vocab:heat_system_id](https://w3id.org/mixs/vocab/heat_system_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | heating system identifier | +| **Mappings:** | | MIXS:0000833 | +| **Comments:** | | Expected value: unique identifier | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 85 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/heavy_metals.md b/mixs6/heavy_metals.md new file mode 100644 index 00000000..c97ea7f0 --- /dev/null +++ b/mixs6/heavy_metals.md @@ -0,0 +1,48 @@ + +# Slot: heavy_metals + + +Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + +URI: [mixs.vocab:heavy_metals](https://w3id.org/mixs/vocab/heavy_metals) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/heavy metals | +| **Mappings:** | | MIXS:0000652 | +| **Comments:** | | Expected value: heavy metal name;measurement value | +| | | Preferred unit: microgram per gram | +| | | Occurrence: m | +| | | Position: 48 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/heavy_metals_meth.md b/mixs6/heavy_metals_meth.md new file mode 100644 index 00000000..e95e25d6 --- /dev/null +++ b/mixs6/heavy_metals_meth.md @@ -0,0 +1,48 @@ + +# Slot: heavy_metals_meth + + +Reference or method used in determining heavy metals + +URI: [mixs.vocab:heavy_metals_meth](https://w3id.org/mixs/vocab/heavy_metals_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/heavy metals method | +| **Mappings:** | | MIXS:0000343 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 49 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/height_carper_fiber.md b/mixs6/height_carper_fiber.md new file mode 100644 index 00000000..f724f3f0 --- /dev/null +++ b/mixs6/height_carper_fiber.md @@ -0,0 +1,48 @@ + +# Slot: height_carper_fiber + + +The average carpet fiber height in the indoor environment + +URI: [mixs.vocab:height_carper_fiber](https://w3id.org/mixs/vocab/height_carper_fiber) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | height carpet fiber mat | +| **Mappings:** | | MIXS:0000167 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: centimeter | +| | | Occurrence: 1 | +| | | Position: 86 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/herbicide_regm.md b/mixs6/herbicide_regm.md new file mode 100644 index 00000000..bb63e842 --- /dev/null +++ b/mixs6/herbicide_regm.md @@ -0,0 +1,48 @@ + +# Slot: herbicide_regm + + +Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:herbicide_regm](https://w3id.org/mixs/vocab/herbicide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | herbicide regimen | +| **Mappings:** | | MIXS:0000561 | +| **Comments:** | | Expected value: herbicide name;herbicide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/horizon.md b/mixs6/horizon.md new file mode 100644 index 00000000..d6fb8a92 --- /dev/null +++ b/mixs6/horizon.md @@ -0,0 +1,48 @@ + +# Slot: horizon + + +Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + +URI: [mixs.vocab:horizon](https://w3id.org/mixs/vocab/horizon) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | horizon | +| **Mappings:** | | MIXS:0001082 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 12 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='A horizon', description=None) | + diff --git a/mixs6/horizon_meth.md b/mixs6/horizon_meth.md new file mode 100644 index 00000000..5744514d --- /dev/null +++ b/mixs6/horizon_meth.md @@ -0,0 +1,48 @@ + +# Slot: horizon_meth + + +Reference or method used in determining the horizon + +URI: [mixs.vocab:horizon_meth](https://w3id.org/mixs/vocab/horizon_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | horizon method | +| **Mappings:** | | MIXS:0000321 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 13 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_age.md b/mixs6/host_age.md new file mode 100644 index 00000000..a7b358de --- /dev/null +++ b/mixs6/host_age.md @@ -0,0 +1,120 @@ + +# Slot: host_age + + +Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + +URI: [mixs.vocab:host_age](https://w3id.org/mixs/vocab/host_age) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host age | +| **Mappings:** | | MIXS:0000255 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: year, day, hour | +| | | Occurrence: 1 | +| | | Position: 9 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='10 days', description=None) | + diff --git a/mixs6/host_blood_press_diast.md b/mixs6/host_blood_press_diast.md new file mode 100644 index 00000000..251ca0b4 --- /dev/null +++ b/mixs6/host_blood_press_diast.md @@ -0,0 +1,48 @@ + +# Slot: host_blood_press_diast + + +Resting diastolic blood pressure, measured as mm mercury + +URI: [mixs.vocab:host_blood_press_diast](https://w3id.org/mixs/vocab/host_blood_press_diast) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host blood pressure diastolic | +| **Mappings:** | | MIXS:0000258 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter mercury | +| | | Occurrence: 1 | +| | | Position: 31 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_blood_press_syst.md b/mixs6/host_blood_press_syst.md new file mode 100644 index 00000000..18c249c2 --- /dev/null +++ b/mixs6/host_blood_press_syst.md @@ -0,0 +1,48 @@ + +# Slot: host_blood_press_syst + + +Resting systolic blood pressure, measured as mm mercury + +URI: [mixs.vocab:host_blood_press_syst](https://w3id.org/mixs/vocab/host_blood_press_syst) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host blood pressure systolic | +| **Mappings:** | | MIXS:0000259 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter mercury | +| | | Occurrence: 1 | +| | | Position: 32 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_body_habitat.md b/mixs6/host_body_habitat.md new file mode 100644 index 00000000..3038a403 --- /dev/null +++ b/mixs6/host_body_habitat.md @@ -0,0 +1,48 @@ + +# Slot: host_body_habitat + + +Original body habitat where the sample was obtained from + +URI: [mixs.vocab:host_body_habitat](https://w3id.org/mixs/vocab/host_body_habitat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body habitat | +| **Mappings:** | | MIXS:0000866 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 14 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='nasopharynx', description=None) | + diff --git a/mixs6/host_body_mass_index.md b/mixs6/host_body_mass_index.md new file mode 100644 index 00000000..1a61d559 --- /dev/null +++ b/mixs6/host_body_mass_index.md @@ -0,0 +1,96 @@ + +# Slot: host_body_mass_index + + +Body mass index, calculated as weight/(height)squared + +URI: [mixs.vocab:host_body_mass_index](https://w3id.org/mixs/vocab/host_body_mass_index) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body-mass index | +| **Mappings:** | | MIXS:0000317 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram per square meter | +| | | Occurrence: 1 | +| | | Position: 20 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='22 kilogram per square meter', description=None) | + diff --git a/mixs6/host_body_product.md b/mixs6/host_body_product.md new file mode 100644 index 00000000..d4bf41f7 --- /dev/null +++ b/mixs6/host_body_product.md @@ -0,0 +1,108 @@ + +# Slot: host_body_product + + +Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + +URI: [mixs.vocab:host_body_product](https://w3id.org/mixs/vocab/host_body_product) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body product | +| **Mappings:** | | MIXS:0000888 | +| **Comments:** | | Expected value: FMA or UBERON | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 16 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='Portion of mucus [fma66938]', description=None) | + diff --git a/mixs6/host_body_site.md b/mixs6/host_body_site.md new file mode 100644 index 00000000..5597d18e --- /dev/null +++ b/mixs6/host_body_site.md @@ -0,0 +1,108 @@ + +# Slot: host_body_site + + +Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + +URI: [mixs.vocab:host_body_site](https://w3id.org/mixs/vocab/host_body_site) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body site | +| **Mappings:** | | MIXS:0000867 | +| **Comments:** | | Expected value: FMA or UBERON | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 15 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='gill [UBERON:0002535]', description=None) | + diff --git a/mixs6/host_body_temp.md b/mixs6/host_body_temp.md new file mode 100644 index 00000000..a96e6ad5 --- /dev/null +++ b/mixs6/host_body_temp.md @@ -0,0 +1,108 @@ + +# Slot: host_body_temp + + +Core body temperature of the host when sample was collected + +URI: [mixs.vocab:host_body_temp](https://w3id.org/mixs/vocab/host_body_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host body temperature | +| **Mappings:** | | MIXS:0000274 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 29 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='15 degree Celsius', description=None) | + diff --git a/mixs6/host_color.md b/mixs6/host_color.md new file mode 100644 index 00000000..de0c697c --- /dev/null +++ b/mixs6/host_color.md @@ -0,0 +1,48 @@ + +# Slot: host_color + + +The color of host + +URI: [mixs.vocab:host_color](https://w3id.org/mixs/vocab/host_color) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host color | +| **Mappings:** | | MIXS:0000260 | +| **Comments:** | | Expected value: color | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 33 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/host_common_name.md b/mixs6/host_common_name.md new file mode 100644 index 00000000..34716f20 --- /dev/null +++ b/mixs6/host_common_name.md @@ -0,0 +1,60 @@ + +# Slot: host_common_name + + +Common name of the host, e.g. Human + +URI: [mixs.vocab:host_common_name](https://w3id.org/mixs/vocab/host_common_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host common name | +| **Mappings:** | | MIXS:0000248 | +| **Comments:** | | Expected value: common name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 4 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='mussel', description=None) | + diff --git a/mixs6/host_diet.md b/mixs6/host_diet.md new file mode 100644 index 00000000..8523f285 --- /dev/null +++ b/mixs6/host_diet.md @@ -0,0 +1,108 @@ + +# Slot: host_diet + + +Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + +URI: [mixs.vocab:host_diet](https://w3id.org/mixs/vocab/host_diet) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host diet | +| **Mappings:** | | MIXS:0000869 | +| **Comments:** | | Expected value: diet type | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 20 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='herbivore', description=None) | + diff --git a/mixs6/host_disease_stat.md b/mixs6/host_disease_stat.md new file mode 100644 index 00000000..be1e8340 --- /dev/null +++ b/mixs6/host_disease_stat.md @@ -0,0 +1,120 @@ + +# Slot: host_disease_stat + + +List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + +URI: [mixs.vocab:host_disease_stat](https://w3id.org/mixs/vocab/host_disease_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host disease status | +| **Mappings:** | | MIXS:0000031 | +| **Comments:** | | Expected value: disease name or DO | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 12 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='rabies [DOID:11260]', description=None) | + diff --git a/mixs6/host_dry_mass.md b/mixs6/host_dry_mass.md new file mode 100644 index 00000000..10f1b65e --- /dev/null +++ b/mixs6/host_dry_mass.md @@ -0,0 +1,60 @@ + +# Slot: host_dry_mass + + +Measurement of dry mass + +URI: [mixs.vocab:host_dry_mass](https://w3id.org/mixs/vocab/host_dry_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host dry mass | +| **Mappings:** | | MIXS:0000257 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 30 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='500 gram', description=None) | + diff --git a/mixs6/host_family_relationship.md b/mixs6/host_family_relationship.md new file mode 100644 index 00000000..4e1556db --- /dev/null +++ b/mixs6/host_family_relationship.md @@ -0,0 +1,108 @@ + +# Slot: host_family_relationship + + +Relationships to other hosts in the same study; can include multiple relationships + +URI: [mixs.vocab:host_family_relationship](https://w3id.org/mixs/vocab/host_family_relationship) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host family relationship | +| **Mappings:** | | MIXS:0000872 | +| **Comments:** | | Expected value: relationship type;arbitrary identifier | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 24 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='offspring;Mussel25', description=None) | + diff --git a/mixs6/host_genotype.md b/mixs6/host_genotype.md new file mode 100644 index 00000000..9902da5b --- /dev/null +++ b/mixs6/host_genotype.md @@ -0,0 +1,120 @@ + +# Slot: host_genotype + + +Observed genotype + +URI: [mixs.vocab:host_genotype](https://w3id.org/mixs/vocab/host_genotype) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host genotype | +| **Mappings:** | | MIXS:0000365 | +| **Comments:** | | Expected value: genotype | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 27 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='C57BL/6', description=None) | + diff --git a/mixs6/host_growth_cond.md b/mixs6/host_growth_cond.md new file mode 100644 index 00000000..e3465f99 --- /dev/null +++ b/mixs6/host_growth_cond.md @@ -0,0 +1,48 @@ + +# Slot: host_growth_cond + + +Literature reference giving growth conditions of the host + +URI: [mixs.vocab:host_growth_cond](https://w3id.org/mixs/vocab/host_growth_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host growth conditions | +| **Mappings:** | | MIXS:0000871 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 22 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='https://academic.oup.com/icesjms/article/68/2/349/617247', description=None) | + diff --git a/mixs6/host_height.md b/mixs6/host_height.md new file mode 100644 index 00000000..4c496e2c --- /dev/null +++ b/mixs6/host_height.md @@ -0,0 +1,120 @@ + +# Slot: host_height + + +The height of subject + +URI: [mixs.vocab:host_height](https://w3id.org/mixs/vocab/host_height) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host height | +| **Mappings:** | | MIXS:0000264 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: centimeter, millimeter, meter | +| | | Occurrence: 1 | +| | | Position: 18 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='0.1 meter', description=None) | + diff --git a/mixs6/host_hiv_stat.md b/mixs6/host_hiv_stat.md new file mode 100644 index 00000000..87cbd93a --- /dev/null +++ b/mixs6/host_hiv_stat.md @@ -0,0 +1,48 @@ + +# Slot: host_hiv_stat + + +HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + +URI: [mixs.vocab:host_hiv_stat](https://w3id.org/mixs/vocab/host_hiv_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host HIV status | +| **Mappings:** | | MIXS:0000265 | +| **Comments:** | | Expected value: HIV status;HAART initiation status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 18 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;yes', description=None) | + diff --git a/mixs6/host_infra_specific_name.md b/mixs6/host_infra_specific_name.md new file mode 100644 index 00000000..ea57ca68 --- /dev/null +++ b/mixs6/host_infra_specific_name.md @@ -0,0 +1,60 @@ + +# Slot: host_infra_specific_name + + +Taxonomic information about the host below subspecies level + +URI: [mixs.vocab:host_infra_specific_name](https://w3id.org/mixs/vocab/host_infra_specific_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host infra-specific name | +| **Mappings:** | | MIXS:0000253 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 25 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='borealis', description=None) | + diff --git a/mixs6/host_infra_specific_rank.md b/mixs6/host_infra_specific_rank.md new file mode 100644 index 00000000..1bdd10ff --- /dev/null +++ b/mixs6/host_infra_specific_rank.md @@ -0,0 +1,60 @@ + +# Slot: host_infra_specific_rank + + +Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + +URI: [mixs.vocab:host_infra_specific_rank](https://w3id.org/mixs/vocab/host_infra_specific_rank) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host infra-specific rank | +| **Mappings:** | | MIXS:0000254 | +| **Comments:** | | Expected value: rank | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 26 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='subspecies', description=None) | + diff --git a/mixs6/host_last_meal.md b/mixs6/host_last_meal.md new file mode 100644 index 00000000..19e06ae5 --- /dev/null +++ b/mixs6/host_last_meal.md @@ -0,0 +1,108 @@ + +# Slot: host_last_meal + + +Content of last meal and time since feeding; can include multiple values + +URI: [mixs.vocab:host_last_meal](https://w3id.org/mixs/vocab/host_last_meal) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host last meal | +| **Mappings:** | | MIXS:0000870 | +| **Comments:** | | Expected value: content;duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 21 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='corn feed;P2H', description=None) | + diff --git a/mixs6/host_length.md b/mixs6/host_length.md new file mode 100644 index 00000000..9443bc9b --- /dev/null +++ b/mixs6/host_length.md @@ -0,0 +1,60 @@ + +# Slot: host_length + + +The length of subject + +URI: [mixs.vocab:host_length](https://w3id.org/mixs/vocab/host_length) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host length | +| **Mappings:** | | MIXS:0000256 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: centimeter, millimeter, meter | +| | | Occurrence: 1 | +| | | Position: 19 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='1 meter', description=None) | + diff --git a/mixs6/host_life_stage.md b/mixs6/host_life_stage.md new file mode 100644 index 00000000..63a29a51 --- /dev/null +++ b/mixs6/host_life_stage.md @@ -0,0 +1,60 @@ + +# Slot: host_life_stage + + +Description of life stage of host + +URI: [mixs.vocab:host_life_stage](https://w3id.org/mixs/vocab/host_life_stage) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host life stage | +| **Mappings:** | | MIXS:0000251 | +| **Comments:** | | Expected value: stage | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 10 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='adult', description=None) | + diff --git a/mixs6/host_occupation.md b/mixs6/host_occupation.md new file mode 100644 index 00000000..8122c112 --- /dev/null +++ b/mixs6/host_occupation.md @@ -0,0 +1,96 @@ + +# Slot: host_occupation + + +Most frequent job performed by subject + +URI: [mixs.vocab:host_occupation](https://w3id.org/mixs/vocab/host_occupation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host occupation | +| **Mappings:** | | MIXS:0000896 | +| **Comments:** | | Expected value: IHMC code | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 24 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='veterinary', description=None) | + diff --git a/mixs6/host_phenotype.md b/mixs6/host_phenotype.md new file mode 100644 index 00000000..c013a434 --- /dev/null +++ b/mixs6/host_phenotype.md @@ -0,0 +1,120 @@ + +# Slot: host_phenotype + + +Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + +URI: [mixs.vocab:host_phenotype](https://w3id.org/mixs/vocab/host_phenotype) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host phenotype | +| **Mappings:** | | MIXS:0000874 | +| **Comments:** | | Expected value: PATO or HP | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 28 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='elongated [PATO:0001154]', description=None) | + diff --git a/mixs6/host_pred_appr.md b/mixs6/host_pred_appr.md new file mode 100644 index 00000000..39e5d40d --- /dev/null +++ b/mixs6/host_pred_appr.md @@ -0,0 +1,56 @@ + +# Slot: host_pred_appr + + +Tool or approach used for host prediction + +URI: [mixs.vocab:host_pred_appr](https://w3id.org/mixs/vocab/host_pred_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host prediction approach | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 90.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='CRISPR spacer match', description=None) | + diff --git a/mixs6/host_pred_est_acc.md b/mixs6/host_pred_est_acc.md new file mode 100644 index 00000000..2cce1cba --- /dev/null +++ b/mixs6/host_pred_est_acc.md @@ -0,0 +1,56 @@ + +# Slot: host_pred_est_acc + + +For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + +URI: [mixs.vocab:host_pred_est_acc](https://w3id.org/mixs/vocab/host_pred_est_acc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host prediction estimated accuracy | +| **Comments:** | | Expected value: false discovery rate | +| | | Preferred unit: | +| | | Position: 91.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)', description=None) | + diff --git a/mixs6/host_pulse.md b/mixs6/host_pulse.md new file mode 100644 index 00000000..60291e7f --- /dev/null +++ b/mixs6/host_pulse.md @@ -0,0 +1,96 @@ + +# Slot: host_pulse + + +Resting pulse, measured as beats per minute + +URI: [mixs.vocab:host_pulse](https://w3id.org/mixs/vocab/host_pulse) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host pulse | +| **Mappings:** | | MIXS:0000333 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: beats per minute | +| | | Occurrence: 1 | +| | | Position: 35 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='65 beats per minute', description=None) | + diff --git a/mixs6/host_sex.md b/mixs6/host_sex.md new file mode 100644 index 00000000..47d5df4f --- /dev/null +++ b/mixs6/host_sex.md @@ -0,0 +1,108 @@ + +# Slot: host_sex + + +Physical sex of the host + +URI: [mixs.vocab:host_sex](https://w3id.org/mixs/vocab/host_sex) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host sex | +| **Mappings:** | | MIXS:0000811 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 11 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='female', description=None) | + diff --git a/mixs6/host_shape.md b/mixs6/host_shape.md new file mode 100644 index 00000000..b721bf62 --- /dev/null +++ b/mixs6/host_shape.md @@ -0,0 +1,48 @@ + +# Slot: host_shape + + +Morphological shape of host + +URI: [mixs.vocab:host_shape](https://w3id.org/mixs/vocab/host_shape) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host shape | +| **Mappings:** | | MIXS:0000261 | +| **Comments:** | | Expected value: shape | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 34 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='round', description=None) | + diff --git a/mixs6/host_spec_range.md b/mixs6/host_spec_range.md new file mode 100644 index 00000000..29ba2ee5 --- /dev/null +++ b/mixs6/host_spec_range.md @@ -0,0 +1,56 @@ + +# Slot: host_spec_range + + +The NCBI taxonomy identifier of the specific host if it is known + +URI: [mixs.vocab:host_spec_range](https://w3id.org/mixs/vocab/host_spec_range) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host specificity or range | +| **Comments:** | | Expected value: NCBI taxid | +| | | Preferred unit: | +| | | Position: 24.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='9606', description=None) | + diff --git a/mixs6/host_subject_id.md b/mixs6/host_subject_id.md new file mode 100644 index 00000000..7e30b6ce --- /dev/null +++ b/mixs6/host_subject_id.md @@ -0,0 +1,108 @@ + +# Slot: host_subject_id + + +A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + +URI: [mixs.vocab:host_subject_id](https://w3id.org/mixs/vocab/host_subject_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host subject id | +| **Mappings:** | | MIXS:0000861 | +| **Comments:** | | Expected value: unique identifier | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 8 | +| | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='MPI123', description=None) | + diff --git a/mixs6/host_substrate.md b/mixs6/host_substrate.md new file mode 100644 index 00000000..b68e7f48 --- /dev/null +++ b/mixs6/host_substrate.md @@ -0,0 +1,48 @@ + +# Slot: host_substrate + + +The growth substrate of the host + +URI: [mixs.vocab:host_substrate](https://w3id.org/mixs/vocab/host_substrate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host substrate | +| **Mappings:** | | MIXS:0000252 | +| **Comments:** | | Expected value: substrate name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 23 | +| | | This field is used uniquely in: host-associated | +| **Examples:** | | Example(value='rock', description=None) | + diff --git a/mixs6/host_taxid.md b/mixs6/host_taxid.md new file mode 100644 index 00000000..39c3f412 --- /dev/null +++ b/mixs6/host_taxid.md @@ -0,0 +1,60 @@ + +# Slot: host_taxid + + +NCBI taxon id of the host, e.g. 9606 + +URI: [mixs.vocab:host_taxid](https://w3id.org/mixs/vocab/host_taxid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host taxid | +| **Mappings:** | | MIXS:0000250 | +| **Comments:** | | Expected value: NCBI taxon identifier | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 7 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='7955', description=None) | + diff --git a/mixs6/host_tot_mass.md b/mixs6/host_tot_mass.md new file mode 100644 index 00000000..9ed641da --- /dev/null +++ b/mixs6/host_tot_mass.md @@ -0,0 +1,120 @@ + +# Slot: host_tot_mass + + +Total mass of the host at collection, the unit depends on host + +URI: [mixs.vocab:host_tot_mass](https://w3id.org/mixs/vocab/host_tot_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host total mass | +| **Mappings:** | | MIXS:0000263 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 17 | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='2500 gram', description=None) | + diff --git a/mixs6/host_wet_mass.md b/mixs6/host_wet_mass.md new file mode 100644 index 00000000..fe7a5b64 --- /dev/null +++ b/mixs6/host_wet_mass.md @@ -0,0 +1,48 @@ + +# Slot: host_wet_mass + + +Measurement of wet mass + +URI: [mixs.vocab:host_wet_mass](https://w3id.org/mixs/vocab/host_wet_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | host wet mass | +| **Mappings:** | | MIXS:0000567 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='1500 gram', description=None) | + diff --git a/mixs6/hrt.md b/mixs6/hrt.md new file mode 100644 index 00000000..0821186e --- /dev/null +++ b/mixs6/hrt.md @@ -0,0 +1,48 @@ + +# Slot: hrt + + +Whether subject had hormone replacement theraphy, and if yes start date + +URI: [mixs.vocab:hrt](https://w3id.org/mixs/vocab/hrt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | HRT | +| **Mappings:** | | MIXS:0000969 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 7 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/humidity.md b/mixs6/humidity.md new file mode 100644 index 00000000..ecee61f9 --- /dev/null +++ b/mixs6/humidity.md @@ -0,0 +1,48 @@ + +# Slot: humidity + + +Amount of water vapour in the air, at the time of sampling + +URI: [mixs.vocab:humidity](https://w3id.org/mixs/vocab/humidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | humidity | +| **Mappings:** | | MIXS:0000100 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per cubic meter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='25 gram per cubic meter', description=None) | + diff --git a/mixs6/humidity_regm.md b/mixs6/humidity_regm.md new file mode 100644 index 00000000..8fd9aab5 --- /dev/null +++ b/mixs6/humidity_regm.md @@ -0,0 +1,48 @@ + +# Slot: humidity_regm + + +Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:humidity_regm](https://w3id.org/mixs/vocab/humidity_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | humidity regimen | +| **Mappings:** | | MIXS:0000568 | +| **Comments:** | | Expected value: humidity value;treatment interval and duration | +| | | Preferred unit: gram per cubic meter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/hysterectomy.md b/mixs6/hysterectomy.md new file mode 100644 index 00000000..9a2daa50 --- /dev/null +++ b/mixs6/hysterectomy.md @@ -0,0 +1,48 @@ + +# Slot: hysterectomy + + +Specification of whether hysterectomy was performed + +URI: [mixs.vocab:hysterectomy](https://w3id.org/mixs/vocab/hysterectomy) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | hysterectomy | +| **Mappings:** | | MIXS:0000287 | +| **Comments:** | | Expected value: hysterectomy status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 8 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='no', description=None) | + diff --git a/mixs6/ihmc_ethnicity.md b/mixs6/ihmc_ethnicity.md new file mode 100644 index 00000000..aaf9c335 --- /dev/null +++ b/mixs6/ihmc_ethnicity.md @@ -0,0 +1,96 @@ + +# Slot: ihmc_ethnicity + + +Ethnicity of the subject + +URI: [mixs.vocab:ihmc_ethnicity](https://w3id.org/mixs/vocab/ihmc_ethnicity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | IHMC ethnicity | +| **Mappings:** | | MIXS:0000895 | +| **Comments:** | | Expected value: IHMC code or free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 23 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='caucasian', description=None) | + diff --git a/mixs6/ihmc_medication_code.md b/mixs6/ihmc_medication_code.md new file mode 100644 index 00000000..2bbcf53f --- /dev/null +++ b/mixs6/ihmc_medication_code.md @@ -0,0 +1,96 @@ + +# Slot: ihmc_medication_code + + +Can include multiple medication codes + +URI: [mixs.vocab:ihmc_medication_code](https://w3id.org/mixs/vocab/ihmc_medication_code) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | IHMC medication code | +| **Mappings:** | | MIXS:0000884 | +| **Comments:** | | Expected value: IHMC code | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 5 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='810', description=None) | + diff --git a/mixs6/index.md b/mixs6/index.md new file mode 100644 index 00000000..1dfea2e6 --- /dev/null +++ b/mixs6/index.md @@ -0,0 +1,884 @@ + +# Mixs6 schema + + +MIxS 6 linkml rendering + + +### Classes + + * [Air](Air.md) - air + * [AirMe](AirMe.md) - Combinatorial checklist for air with me + * [AirMigsBa](AirMigsBa.md) - Combinatorial checklist for air with migs_ba + * [AirMigsEu](AirMigsEu.md) - Combinatorial checklist for air with migs_eu + * [AirMigsOrg](AirMigsOrg.md) - Combinatorial checklist for air with migs_org + * [AirMigsPl](AirMigsPl.md) - Combinatorial checklist for air with migs_pl + * [AirMigsVi](AirMigsVi.md) - Combinatorial checklist for air with migs_vi + * [AirMimag](AirMimag.md) - Combinatorial checklist for air with mimag + * [AirMimarksC](AirMimarksC.md) - Combinatorial checklist for air with mimarks_c + * [AirMimarksS](AirMimarksS.md) - Combinatorial checklist for air with mimarks_s + * [AirMisag](AirMisag.md) - Combinatorial checklist for air with misag + * [AirMiuvig](AirMiuvig.md) - Combinatorial checklist for air with miuvig + * [BuiltEnvironment](BuiltEnvironment.md) - built environment + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - Combinatorial checklist for built environment with me + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - Combinatorial checklist for built environment with migs_ba + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - Combinatorial checklist for built environment with migs_eu + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - Combinatorial checklist for built environment with migs_org + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - Combinatorial checklist for built environment with migs_pl + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - Combinatorial checklist for built environment with migs_vi + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - Combinatorial checklist for built environment with mimag + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - Combinatorial checklist for built environment with mimarks_c + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - Combinatorial checklist for built environment with mimarks_s + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - Combinatorial checklist for built environment with misag + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) - Combinatorial checklist for built environment with miuvig + * [Core](Core.md) - core package + * [CoreMe](CoreMe.md) - Combinatorial checklist for core with me + * [CoreMigsBa](CoreMigsBa.md) - Combinatorial checklist for core with migs_ba + * [CoreMigsEu](CoreMigsEu.md) - Combinatorial checklist for core with migs_eu + * [CoreMigsOrg](CoreMigsOrg.md) - Combinatorial checklist for core with migs_org + * [CoreMigsPl](CoreMigsPl.md) - Combinatorial checklist for core with migs_pl + * [CoreMigsVi](CoreMigsVi.md) - Combinatorial checklist for core with migs_vi + * [CoreMimag](CoreMimag.md) - Combinatorial checklist for core with mimag + * [CoreMimarksC](CoreMimarksC.md) - Combinatorial checklist for core with mimarks_c + * [CoreMimarksS](CoreMimarksS.md) - Combinatorial checklist for core with mimarks_s + * [CoreMisag](CoreMisag.md) - Combinatorial checklist for core with misag + * [CoreMiuvig](CoreMiuvig.md) - Combinatorial checklist for core with miuvig + * [Host-associated](Host-associated.md) - host-associated + * [Host-associatedMe](Host-associatedMe.md) - Combinatorial checklist for host-associated with me + * [Host-associatedMigsBa](Host-associatedMigsBa.md) - Combinatorial checklist for host-associated with migs_ba + * [Host-associatedMigsEu](Host-associatedMigsEu.md) - Combinatorial checklist for host-associated with migs_eu + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - Combinatorial checklist for host-associated with migs_org + * [Host-associatedMigsPl](Host-associatedMigsPl.md) - Combinatorial checklist for host-associated with migs_pl + * [Host-associatedMigsVi](Host-associatedMigsVi.md) - Combinatorial checklist for host-associated with migs_vi + * [Host-associatedMimag](Host-associatedMimag.md) - Combinatorial checklist for host-associated with mimag + * [Host-associatedMimarksC](Host-associatedMimarksC.md) - Combinatorial checklist for host-associated with mimarks_c + * [Host-associatedMimarksS](Host-associatedMimarksS.md) - Combinatorial checklist for host-associated with mimarks_s + * [Host-associatedMisag](Host-associatedMisag.md) - Combinatorial checklist for host-associated with misag + * [Host-associatedMiuvig](Host-associatedMiuvig.md) - Combinatorial checklist for host-associated with miuvig + * [Human-associated](Human-associated.md) - human-associated + * [Human-associatedMe](Human-associatedMe.md) - Combinatorial checklist for human-associated with me + * [Human-associatedMigsBa](Human-associatedMigsBa.md) - Combinatorial checklist for human-associated with migs_ba + * [Human-associatedMigsEu](Human-associatedMigsEu.md) - Combinatorial checklist for human-associated with migs_eu + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - Combinatorial checklist for human-associated with migs_org + * [Human-associatedMigsPl](Human-associatedMigsPl.md) - Combinatorial checklist for human-associated with migs_pl + * [Human-associatedMigsVi](Human-associatedMigsVi.md) - Combinatorial checklist for human-associated with migs_vi + * [Human-associatedMimag](Human-associatedMimag.md) - Combinatorial checklist for human-associated with mimag + * [Human-associatedMimarksC](Human-associatedMimarksC.md) - Combinatorial checklist for human-associated with mimarks_c + * [Human-associatedMimarksS](Human-associatedMimarksS.md) - Combinatorial checklist for human-associated with mimarks_s + * [Human-associatedMisag](Human-associatedMisag.md) - Combinatorial checklist for human-associated with misag + * [Human-associatedMiuvig](Human-associatedMiuvig.md) - Combinatorial checklist for human-associated with miuvig + * [Human-gut](Human-gut.md) - human-gut + * [Human-gutMe](Human-gutMe.md) - Combinatorial checklist for human-gut with me + * [Human-gutMigsBa](Human-gutMigsBa.md) - Combinatorial checklist for human-gut with migs_ba + * [Human-gutMigsEu](Human-gutMigsEu.md) - Combinatorial checklist for human-gut with migs_eu + * [Human-gutMigsOrg](Human-gutMigsOrg.md) - Combinatorial checklist for human-gut with migs_org + * [Human-gutMigsPl](Human-gutMigsPl.md) - Combinatorial checklist for human-gut with migs_pl + * [Human-gutMigsVi](Human-gutMigsVi.md) - Combinatorial checklist for human-gut with migs_vi + * [Human-gutMimag](Human-gutMimag.md) - Combinatorial checklist for human-gut with mimag + * [Human-gutMimarksC](Human-gutMimarksC.md) - Combinatorial checklist for human-gut with mimarks_c + * [Human-gutMimarksS](Human-gutMimarksS.md) - Combinatorial checklist for human-gut with mimarks_s + * [Human-gutMisag](Human-gutMisag.md) - Combinatorial checklist for human-gut with misag + * [Human-gutMiuvig](Human-gutMiuvig.md) - Combinatorial checklist for human-gut with miuvig + * [Human-oral](Human-oral.md) - human-oral + * [Human-oralMe](Human-oralMe.md) - Combinatorial checklist for human-oral with me + * [Human-oralMigsBa](Human-oralMigsBa.md) - Combinatorial checklist for human-oral with migs_ba + * [Human-oralMigsEu](Human-oralMigsEu.md) - Combinatorial checklist for human-oral with migs_eu + * [Human-oralMigsOrg](Human-oralMigsOrg.md) - Combinatorial checklist for human-oral with migs_org + * [Human-oralMigsPl](Human-oralMigsPl.md) - Combinatorial checklist for human-oral with migs_pl + * [Human-oralMigsVi](Human-oralMigsVi.md) - Combinatorial checklist for human-oral with migs_vi + * [Human-oralMimag](Human-oralMimag.md) - Combinatorial checklist for human-oral with mimag + * [Human-oralMimarksC](Human-oralMimarksC.md) - Combinatorial checklist for human-oral with mimarks_c + * [Human-oralMimarksS](Human-oralMimarksS.md) - Combinatorial checklist for human-oral with mimarks_s + * [Human-oralMisag](Human-oralMisag.md) - Combinatorial checklist for human-oral with misag + * [Human-oralMiuvig](Human-oralMiuvig.md) - Combinatorial checklist for human-oral with miuvig + * [Human-skin](Human-skin.md) - human-skin + * [Human-skinMe](Human-skinMe.md) - Combinatorial checklist for human-skin with me + * [Human-skinMigsBa](Human-skinMigsBa.md) - Combinatorial checklist for human-skin with migs_ba + * [Human-skinMigsEu](Human-skinMigsEu.md) - Combinatorial checklist for human-skin with migs_eu + * [Human-skinMigsOrg](Human-skinMigsOrg.md) - Combinatorial checklist for human-skin with migs_org + * [Human-skinMigsPl](Human-skinMigsPl.md) - Combinatorial checklist for human-skin with migs_pl + * [Human-skinMigsVi](Human-skinMigsVi.md) - Combinatorial checklist for human-skin with migs_vi + * [Human-skinMimag](Human-skinMimag.md) - Combinatorial checklist for human-skin with mimag + * [Human-skinMimarksC](Human-skinMimarksC.md) - Combinatorial checklist for human-skin with mimarks_c + * [Human-skinMimarksS](Human-skinMimarksS.md) - Combinatorial checklist for human-skin with mimarks_s + * [Human-skinMisag](Human-skinMisag.md) - Combinatorial checklist for human-skin with misag + * [Human-skinMiuvig](Human-skinMiuvig.md) - Combinatorial checklist for human-skin with miuvig + * [Human-vaginal](Human-vaginal.md) - human-vaginal + * [Human-vaginalMe](Human-vaginalMe.md) - Combinatorial checklist for human-vaginal with me + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - Combinatorial checklist for human-vaginal with migs_ba + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - Combinatorial checklist for human-vaginal with migs_eu + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - Combinatorial checklist for human-vaginal with migs_org + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - Combinatorial checklist for human-vaginal with migs_pl + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - Combinatorial checklist for human-vaginal with migs_vi + * [Human-vaginalMimag](Human-vaginalMimag.md) - Combinatorial checklist for human-vaginal with mimag + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - Combinatorial checklist for human-vaginal with mimarks_c + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - Combinatorial checklist for human-vaginal with mimarks_s + * [Human-vaginalMisag](Human-vaginalMisag.md) - Combinatorial checklist for human-vaginal with misag + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) - Combinatorial checklist for human-vaginal with miuvig + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - Combinatorial checklist for hydrocarbon resources-cores with me + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_ba + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_eu + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_org + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_pl + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_vi + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - Combinatorial checklist for hydrocarbon resources-cores with mimag + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_c + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_s + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - Combinatorial checklist for hydrocarbon resources-cores with misag + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) - Combinatorial checklist for hydrocarbon resources-cores with miuvig + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with me + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - Combinatorial checklist for microbial mat_biofilm with me + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - Combinatorial checklist for microbial mat_biofilm with migs_ba + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - Combinatorial checklist for microbial mat_biofilm with migs_eu + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - Combinatorial checklist for microbial mat_biofilm with migs_org + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - Combinatorial checklist for microbial mat_biofilm with migs_pl + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - Combinatorial checklist for microbial mat_biofilm with migs_vi + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - Combinatorial checklist for microbial mat_biofilm with mimag + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_c + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_s + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - Combinatorial checklist for microbial mat_biofilm with misag + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) - Combinatorial checklist for microbial mat_biofilm with miuvig + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - Combinatorial checklist for miscellaneous natural or artificial environment with me + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_org + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimag + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with misag + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) - Combinatorial checklist for miscellaneous natural or artificial environment with miuvig + * [Plant-associated](Plant-associated.md) - plant-associated + * [Plant-associatedMe](Plant-associatedMe.md) - Combinatorial checklist for plant-associated with me + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - Combinatorial checklist for plant-associated with migs_ba + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - Combinatorial checklist for plant-associated with migs_eu + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - Combinatorial checklist for plant-associated with migs_org + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - Combinatorial checklist for plant-associated with migs_pl + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - Combinatorial checklist for plant-associated with migs_vi + * [Plant-associatedMimag](Plant-associatedMimag.md) - Combinatorial checklist for plant-associated with mimag + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - Combinatorial checklist for plant-associated with mimarks_c + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - Combinatorial checklist for plant-associated with mimarks_s + * [Plant-associatedMisag](Plant-associatedMisag.md) - Combinatorial checklist for plant-associated with misag + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) - Combinatorial checklist for plant-associated with miuvig + * [Sediment](Sediment.md) - sediment + * [SedimentMe](SedimentMe.md) - Combinatorial checklist for sediment with me + * [SedimentMigsBa](SedimentMigsBa.md) - Combinatorial checklist for sediment with migs_ba + * [SedimentMigsEu](SedimentMigsEu.md) - Combinatorial checklist for sediment with migs_eu + * [SedimentMigsOrg](SedimentMigsOrg.md) - Combinatorial checklist for sediment with migs_org + * [SedimentMigsPl](SedimentMigsPl.md) - Combinatorial checklist for sediment with migs_pl + * [SedimentMigsVi](SedimentMigsVi.md) - Combinatorial checklist for sediment with migs_vi + * [SedimentMimag](SedimentMimag.md) - Combinatorial checklist for sediment with mimag + * [SedimentMimarksC](SedimentMimarksC.md) - Combinatorial checklist for sediment with mimarks_c + * [SedimentMimarksS](SedimentMimarksS.md) - Combinatorial checklist for sediment with mimarks_s + * [SedimentMisag](SedimentMisag.md) - Combinatorial checklist for sediment with misag + * [SedimentMiuvig](SedimentMiuvig.md) - Combinatorial checklist for sediment with miuvig + * [Soil](Soil.md) - soil + * [SoilMe](SoilMe.md) - Combinatorial checklist for soil with me + * [SoilMigsBa](SoilMigsBa.md) - Combinatorial checklist for soil with migs_ba + * [SoilMigsEu](SoilMigsEu.md) - Combinatorial checklist for soil with migs_eu + * [SoilMigsOrg](SoilMigsOrg.md) - Combinatorial checklist for soil with migs_org + * [SoilMigsPl](SoilMigsPl.md) - Combinatorial checklist for soil with migs_pl + * [SoilMigsVi](SoilMigsVi.md) - Combinatorial checklist for soil with migs_vi + * [SoilMimag](SoilMimag.md) - Combinatorial checklist for soil with mimag + * [SoilMimarksC](SoilMimarksC.md) - Combinatorial checklist for soil with mimarks_c + * [SoilMimarksS](SoilMimarksS.md) - Combinatorial checklist for soil with mimarks_s + * [SoilMisag](SoilMisag.md) - Combinatorial checklist for soil with misag + * [SoilMiuvig](SoilMiuvig.md) - Combinatorial checklist for soil with miuvig + * [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + * [WastewaterSludgeMe](WastewaterSludgeMe.md) - Combinatorial checklist for wastewater_sludge with me + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - Combinatorial checklist for wastewater_sludge with migs_ba + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - Combinatorial checklist for wastewater_sludge with migs_eu + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - Combinatorial checklist for wastewater_sludge with migs_org + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - Combinatorial checklist for wastewater_sludge with migs_pl + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - Combinatorial checklist for wastewater_sludge with migs_vi + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - Combinatorial checklist for wastewater_sludge with mimag + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - Combinatorial checklist for wastewater_sludge with mimarks_c + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - Combinatorial checklist for wastewater_sludge with mimarks_s + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - Combinatorial checklist for wastewater_sludge with misag + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) - Combinatorial checklist for wastewater_sludge with miuvig + * [Water](Water.md) - water + * [WaterMe](WaterMe.md) - Combinatorial checklist for water with me + * [WaterMigsBa](WaterMigsBa.md) - Combinatorial checklist for water with migs_ba + * [WaterMigsEu](WaterMigsEu.md) - Combinatorial checklist for water with migs_eu + * [WaterMigsOrg](WaterMigsOrg.md) - Combinatorial checklist for water with migs_org + * [WaterMigsPl](WaterMigsPl.md) - Combinatorial checklist for water with migs_pl + * [WaterMigsVi](WaterMigsVi.md) - Combinatorial checklist for water with migs_vi + * [WaterMimag](WaterMimag.md) - Combinatorial checklist for water with mimag + * [WaterMimarksC](WaterMimarksC.md) - Combinatorial checklist for water with mimarks_c + * [WaterMimarksS](WaterMimarksS.md) - Combinatorial checklist for water with mimarks_s + * [WaterMisag](WaterMisag.md) - Combinatorial checklist for water with misag + * [WaterMiuvig](WaterMiuvig.md) - Combinatorial checklist for water with miuvig + +### Mixins + + * [Me](Me.md) - me Checklist + * [MigsBa](MigsBa.md) - migs_ba Checklist + * [MigsEu](MigsEu.md) - migs_eu Checklist + * [MigsOrg](MigsOrg.md) - migs_org Checklist + * [MigsPl](MigsPl.md) - migs_pl Checklist + * [MigsVi](MigsVi.md) - migs_vi Checklist + * [Mimag](Mimag.md) - mimag Checklist + * [MimarksC](MimarksC.md) - mimarks_c Checklist + * [MimarksS](MimarksS.md) - mimarks_s Checklist + * [Misag](Misag.md) - misag Checklist + * [Miuvig](Miuvig.md) - miuvig Checklist + +### Slots + + * [core field](core_field.md) - basic fields + * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * [environment field](environment_field.md) - field describing environmental aspect of a sample + * [abs_air_humidity](abs_air_humidity.md) - Actual mass of water vapor - mh20 - present in the air water vapor mixture + * [add_recov_method](add_recov_method.md) - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * [additional_info](additional_info.md) - Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * [address](address.md) - The street name and building number where the sampling occurred. + * [adj_room](adj_room.md) - List of rooms (room number, room name) immediately adjacent to the sampling room + * [aero_struc](aero_struc.md) - Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * [agrochem_addition](agrochem_addition.md) - Addition of fertilizers, pesticides, etc. - amount and time of applications + * [air_temp](air_temp.md) - Temperature of the air at the time of sampling + * [air_temp_regm](air_temp_regm.md) - Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * [al_sat](al_sat.md) - Aluminum saturation (esp. For tropical soils) + * [al_sat_meth](al_sat_meth.md) - Reference or method used in determining Al saturation + * [alkalinity](alkalinity.md) - Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * [alkalinity_method](alkalinity_method.md) - Method used for alkalinity measurement + * [alkyl_diethers](alkyl_diethers.md) - Concentration of alkyl diethers + * [alt](alt.md) - Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * [aminopept_act](aminopept_act.md) - Measurement of aminopeptidase activity + * [ammonium](ammonium.md) - Concentration of ammonium in the sample + * [amniotic_fluid_color](amniotic_fluid_color.md) - Specification of the color of the amniotic fluid sample + * [amount_light](amount_light.md) - The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * [ances_data](ances_data.md) - Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * [annual_precpt](annual_precpt.md) - The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * [annual_temp](annual_temp.md) - Mean annual temperature + * [antibiotic_regm](antibiotic_regm.md) - Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * [api](api.md) - API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * [arch_struc](arch_struc.md) - An architectural structure is a human-made, free-standing, immobile outdoor construction + * [aromatics_pc](aromatics_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [asphaltenes_pc](asphaltenes_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [atmospheric_data](atmospheric_data.md) - Measurement of atmospheric data; can include multiple data + * [avg_dew_point](avg_dew_point.md) - The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * [avg_occup](avg_occup.md) - Daily average occupancy of room + * [avg_temp](avg_temp.md) - The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * [bac_prod](bac_prod.md) - Bacterial production in the water column measured by isotope uptake + * [bac_resp](bac_resp.md) - Measurement of bacterial respiration in the water column + * [bacteria_carb_prod](bacteria_carb_prod.md) - Measurement of bacterial carbon production + * [barometric_press](barometric_press.md) - Force per unit area exerted against a surface by the weight of air above that surface + * [basin](basin.md) - Name of the basin (e.g. Campos) + * [bathroom_count](bathroom_count.md) - The number of bathrooms in the building + * [bedroom_count](bedroom_count.md) - The number of bedrooms in the building + * [benzene](benzene.md) - Concentration of benzene in the sample + * [biochem_oxygen_dem](biochem_oxygen_dem.md) - Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * [biocide](biocide.md) - List of biocides (commercial name of product and supplier) and date of administration + * [biocide_admin_method](biocide_admin_method.md) - Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * [biol_stat](biol_stat.md) - The level of genome modification + * [biomass](biomass.md) - Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * [biotic_regm](biotic_regm.md) - Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * [birth_control](birth_control.md) - Specification of birth control medication used + * [bishomohopanol](bishomohopanol.md) - Concentration of bishomohopanol + * [blood_blood_disord](blood_blood_disord.md) - History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * [bromide](bromide.md) - Concentration of bromide + * [build_docs](build_docs.md) - The building design, construction and operation documents + * [build_occup_type](build_occup_type.md) - The primary function for which a building or discrete part of a building is intended to be used + * [building_setting](building_setting.md) - A location (geography) where a building is set + * [built_struc_age](built_struc_age.md) - The age of the built structure since construction + * [built_struc_set](built_struc_set.md) - The characterization of the location of the built structure as high or low human density + * [built_struc_type](built_struc_type.md) - A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * [calcium](calcium.md) - Concentration of calcium in the sample + * [carb_dioxide](carb_dioxide.md) - Carbon dioxide (gas) amount or concentration at the time of sampling + * [carb_monoxide](carb_monoxide.md) - Carbon monoxide (gas) amount or concentration at the time of sampling + * [carb_nitro_ratio](carb_nitro_ratio.md) - Ratio of amount or concentrations of carbon to nitrogen + * [ceil_area](ceil_area.md) - The area of the ceiling space within the room + * [ceil_cond](ceil_cond.md) - The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [ceil_finish_mat](ceil_finish_mat.md) - The type of material used to finish a ceiling + * [ceil_struc](ceil_struc.md) - The construction format of the ceiling + * [ceil_texture](ceil_texture.md) - The feel, appearance, or consistency of a ceiling surface + * [ceil_thermal_mass](ceil_thermal_mass.md) - The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * [ceil_type](ceil_type.md) - The type of ceiling according to the ceiling's appearance or construction + * [ceil_water_mold](ceil_water_mold.md) - Signs of the presence of mold or mildew on the ceiling + * [chem_administration](chem_administration.md) - List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * [chem_mutagen](chem_mutagen.md) - Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * [chem_oxygen_dem](chem_oxygen_dem.md) - A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * [chem_treatment](chem_treatment.md) - List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * [chem_treatment_method](chem_treatment_method.md) - Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * [chloride](chloride.md) - Concentration of chloride in the sample + * [chlorophyll](chlorophyll.md) - Concentration of chlorophyll + * [climate_environment](climate_environment.md) - Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * [collection_date](collection_date.md) - The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * [conduc](conduc.md) - Electrical conductivity of water + * [cool_syst_id](cool_syst_id.md) - The cooling system identifier + * [crop_rotation](crop_rotation.md) - Whether or not crop is rotated, and if yes, rotation schedule + * [cult_root_med](cult_root_med.md) - Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * [cur_land_use](cur_land_use.md) - Present state of sample site + * [cur_vegetation](cur_vegetation.md) - Vegetation classification from one or more standard classification systems, or agricultural crop + * [cur_vegetation_meth](cur_vegetation_meth.md) - Reference or method used in vegetation classification + * [date_last_rain](date_last_rain.md) - The date of the last time it rained + * [density](density.md) - Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * [depos_env](depos_env.md) - Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * [depth](depth.md) - Please refer to the definitions of depth in the environmental packages + * [dermatology_disord](dermatology_disord.md) - History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * [dew_point](dew_point.md) - The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * [diet_last_six_month](diet_last_six_month.md) - Specification of major diet changes in the last six months, if yes the change should be specified + * [diether_lipids](diether_lipids.md) - Concentration of diether lipids; can include multiple types of diether lipids + * [diss_carb_dioxide](diss_carb_dioxide.md) - Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * [diss_hydrogen](diss_hydrogen.md) - Concentration of dissolved hydrogen + * [diss_inorg_carb](diss_inorg_carb.md) - Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * [diss_inorg_nitro](diss_inorg_nitro.md) - Concentration of dissolved inorganic nitrogen + * [diss_inorg_phosp](diss_inorg_phosp.md) - Concentration of dissolved inorganic phosphorus in the sample + * [diss_iron](diss_iron.md) - Concentration of dissolved iron in the sample + * [diss_org_carb](diss_org_carb.md) - Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * [diss_org_nitro](diss_org_nitro.md) - Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * [diss_oxygen](diss_oxygen.md) - Concentration of dissolved oxygen + * [diss_oxygen_fluid](diss_oxygen_fluid.md) - Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * [dominant_hand](dominant_hand.md) - Dominant hand of the subject + * [door_comp_type](door_comp_type.md) - The composite type of the door + * [door_cond](door_cond.md) - The phsical condition of the door + * [door_direct](door_direct.md) - The direction the door opens + * [door_loc](door_loc.md) - The relative location of the door in the room + * [door_mat](door_mat.md) - The material the door is composed of + * [door_move](door_move.md) - The type of movement of the door + * [door_size](door_size.md) - The size of the door + * [door_type](door_type.md) - The type of door material + * [door_type_metal](door_type_metal.md) - The type of metal door + * [door_type_wood](door_type_wood.md) - The type of wood door + * [door_water_mold](door_water_mold.md) - Signs of the presence of mold or mildew on a door + * [douche](douche.md) - Date of most recent douche + * [down_par](down_par.md) - Visible waveband radiance and irradiance measurements in the water column + * [drainage_class](drainage_class.md) - Drainage classification from a standard system such as the USDA system + * [drawings](drawings.md) - The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * [drug_usage](drug_usage.md) - Any drug used by subject and the frequency of usage; can include multiple drugs used + * [efficiency_percent](efficiency_percent.md) - Percentage of volatile solids removed from the anaerobic digestor + * [elev](elev.md) - Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * [elevator](elevator.md) - The number of elevators within the built structure + * [emulsions](emulsions.md) - Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * [env_broad_scale](env_broad_scale.md) - In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [env_local_scale](env_local_scale.md) - In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [env_medium](env_medium.md) - In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [escalator](escalator.md) - The number of escalators within the built structure + * [ethylbenzene](ethylbenzene.md) - Concentration of ethylbenzene in the sample + * [exp_duct](exp_duct.md) - The amount of exposed ductwork in the room + * [exp_pipe](exp_pipe.md) - The number of exposed pipes in the room + * [ext_door](ext_door.md) - The number of exterior doors in the built structure + * [ext_wall_orient](ext_wall_orient.md) - The orientation of the exterior wall + * [ext_window_orient](ext_window_orient.md) - The compass direction the exterior window of the room is facing + * [extreme_event](extreme_event.md) - Unusual physical events that may have affected microbial populations + * [extreme_salinity](extreme_salinity.md) - Measured salinity + * [fao_class](fao_class.md) - Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * [fertilizer_regm](fertilizer_regm.md) - Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * [field](field.md) - Name of the hydrocarbon field (e.g. Albacora) + * [filter_type](filter_type.md) - A device which removes solid particulates or airborne molecular contaminants + * [fire](fire.md) - Historical and/or physical evidence of fire + * [fireplace_type](fireplace_type.md) - A firebox with chimney + * [flooding](flooding.md) - Historical and/or physical evidence of flooding + * [floor_age](floor_age.md) - The time period since installment of the carpet or flooring + * [floor_area](floor_area.md) - The area of the floor space within the room + * [floor_cond](floor_cond.md) - The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [floor_count](floor_count.md) - The number of floors in the building, including basements and mechanical penthouse + * [floor_finish_mat](floor_finish_mat.md) - The floor covering type; the finished surface that is walked on + * [floor_struc](floor_struc.md) - Refers to the structural elements and subfloor upon which the finish flooring is installed + * [floor_thermal_mass](floor_thermal_mass.md) - The ability of the floor to provide inertia against temperature fluctuations + * [floor_water_mold](floor_water_mold.md) - Signs of the presence of mold or mildew in a room + * [fluor](fluor.md) - Raw or converted fluorescence of water + * [foetal_health_stat](foetal_health_stat.md) - Specification of foetal health status, should also include abortion + * [freq_clean](freq_clean.md) - The number of times the building is cleaned per week + * [freq_cook](freq_cook.md) - The number of times a meal is cooked per week + * [fungicide_regm](fungicide_regm.md) - Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * [furniture](furniture.md) - The types of furniture present in the sampled room + * [gaseous_environment](gaseous_environment.md) - Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * [gaseous_substances](gaseous_substances.md) - Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * [gastrointest_disord](gastrointest_disord.md) - History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * [gender_restroom](gender_restroom.md) - The gender type of the restroom + * [genetic_mod](genetic_mod.md) - Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * [geo_loc_name](geo_loc_name.md) - The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * [gestation_state](gestation_state.md) - Specification of the gestation state + * [glucosidase_act](glucosidase_act.md) - Measurement of glucosidase activity + * [gravidity](gravidity.md) - Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * [gravity](gravity.md) - Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * [growth_facil](growth_facil.md) - Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * [growth_habit](growth_habit.md) - Characteristic shape, appearance or growth form of a plant species + * [growth_hormone_regm](growth_hormone_regm.md) - Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * [gynecologic_disord](gynecologic_disord.md) - History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * [hall_count](hall_count.md) - The total count of hallways and cooridors in the built structure + * [handidness](handidness.md) - The handidness of the individual sampled + * [hc_produced](hc_produced.md) - Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * [hcr](hcr.md) - Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * [hcr_fw_salinity](hcr_fw_salinity.md) - Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * [hcr_geol_age](hcr_geol_age.md) - Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * [hcr_pressure](hcr_pressure.md) - Original pressure of the hydrocarbon resource + * [hcr_temp](hcr_temp.md) - Original temperature of the hydrocarbon resource + * [heat_cool_type](heat_cool_type.md) - Methods of conditioning or heating a room or building + * [heat_deliv_loc](heat_deliv_loc.md) - The location of heat delivery within the room + * [heat_system_deliv_meth](heat_system_deliv_meth.md) - The method by which the heat is delivered through the system + * [heat_system_id](heat_system_id.md) - The heating system identifier + * [heavy_metals](heavy_metals.md) - Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * [heavy_metals_meth](heavy_metals_meth.md) - Reference or method used in determining heavy metals + * [height_carper_fiber](height_carper_fiber.md) - The average carpet fiber height in the indoor environment + * [herbicide_regm](herbicide_regm.md) - Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [horizon](horizon.md) - Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * [horizon_meth](horizon_meth.md) - Reference or method used in determining the horizon + * [host_age](host_age.md) - Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * [host_blood_press_diast](host_blood_press_diast.md) - Resting diastolic blood pressure, measured as mm mercury + * [host_blood_press_syst](host_blood_press_syst.md) - Resting systolic blood pressure, measured as mm mercury + * [host_body_habitat](host_body_habitat.md) - Original body habitat where the sample was obtained from + * [host_body_mass_index](host_body_mass_index.md) - Body mass index, calculated as weight/(height)squared + * [host_body_product](host_body_product.md) - Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * [host_body_site](host_body_site.md) - Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * [host_body_temp](host_body_temp.md) - Core body temperature of the host when sample was collected + * [host_color](host_color.md) - The color of host + * [host_common_name](host_common_name.md) - Common name of the host, e.g. Human + * [host_diet](host_diet.md) - Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * [host_disease_stat](host_disease_stat.md) - List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * [host_dry_mass](host_dry_mass.md) - Measurement of dry mass + * [host_family_relationship](host_family_relationship.md) - Relationships to other hosts in the same study; can include multiple relationships + * [host_genotype](host_genotype.md) - Observed genotype + * [host_growth_cond](host_growth_cond.md) - Literature reference giving growth conditions of the host + * [host_height](host_height.md) - The height of subject + * [host_hiv_stat](host_hiv_stat.md) - HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * [host_infra_specific_name](host_infra_specific_name.md) - Taxonomic information about the host below subspecies level + * [host_infra_specific_rank](host_infra_specific_rank.md) - Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * [host_last_meal](host_last_meal.md) - Content of last meal and time since feeding; can include multiple values + * [host_length](host_length.md) - The length of subject + * [host_life_stage](host_life_stage.md) - Description of life stage of host + * [host_occupation](host_occupation.md) - Most frequent job performed by subject + * [host_phenotype](host_phenotype.md) - Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * [host_pulse](host_pulse.md) - Resting pulse, measured as beats per minute + * [host_sex](host_sex.md) - Physical sex of the host + * [host_shape](host_shape.md) - Morphological shape of host + * [host_subject_id](host_subject_id.md) - A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * [host_substrate](host_substrate.md) - The growth substrate of the host + * [host_taxid](host_taxid.md) - NCBI taxon id of the host, e.g. 9606 + * [host_tot_mass](host_tot_mass.md) - Total mass of the host at collection, the unit depends on host + * [host_wet_mass](host_wet_mass.md) - Measurement of wet mass + * [hrt](hrt.md) - Whether subject had hormone replacement theraphy, and if yes start date + * [humidity](humidity.md) - Amount of water vapour in the air, at the time of sampling + * [humidity_regm](humidity_regm.md) - Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [hysterectomy](hysterectomy.md) - Specification of whether hysterectomy was performed + * [ihmc_ethnicity](ihmc_ethnicity.md) - Ethnicity of the subject + * [ihmc_medication_code](ihmc_medication_code.md) - Can include multiple medication codes + * [indoor_space](indoor_space.md) - A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * [indoor_surf](indoor_surf.md) - Type of indoor surface + * [indust_eff_percent](indust_eff_percent.md) - Percentage of industrial effluents received by wastewater treatment plant + * [inorg_particles](inorg_particles.md) - Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * [inside_lux](inside_lux.md) - The recorded value at sampling time (power density) + * [int_wall_cond](int_wall_cond.md) - The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * [iw_bt_date_well](iw_bt_date_well.md) - Injection water breakthrough date per well following a secondary and/or tertiary recovery + * [iwf](iwf.md) - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * [last_clean](last_clean.md) - The last time the floor was cleaned (swept, mopped, vacuumed) + * [lat_lon](lat_lon.md) - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * [light_intensity](light_intensity.md) - Measurement of light intensity + * [light_regm](light_regm.md) - Information about treatment(s) involving exposure to light, including both light intensity and quality. + * [light_type](light_type.md) - Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * [link_addit_analys](link_addit_analys.md) - Link to additional analysis results performed on the sample + * [link_class_info](link_class_info.md) - Link to digitized soil maps or other soil classification information + * [link_climate_info](link_climate_info.md) - Link to climate resource + * [lithology](lithology.md) - Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * [liver_disord](liver_disord.md) - History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * [local_class](local_class.md) - Soil classification based on local soil classification system + * [local_class_meth](local_class_meth.md) - Reference or method used in determining the local soil classification + * [magnesium](magnesium.md) - Concentration of magnesium in the sample + * [maternal_health_stat](maternal_health_stat.md) - Specification of the maternal health status + * [max_occup](max_occup.md) - The maximum amount of people allowed in the indoor environment + * [mean_frict_vel](mean_frict_vel.md) - Measurement of mean friction velocity + * [mean_peak_frict_vel](mean_peak_frict_vel.md) - Measurement of mean peak friction velocity + * [mech_struc](mech_struc.md) - mechanical structure: a moving structure + * [mechanical_damage](mechanical_damage.md) - Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * [medic_hist_perform](medic_hist_perform.md) - Whether full medical history was collected + * [menarche](menarche.md) - Date of most recent menstruation + * [menopause](menopause.md) - Date of onset of menopause + * [methane](methane.md) - Methane (gas) amount or concentration at the time of sampling + * [microbial_biomass](microbial_biomass.md) - The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * [microbial_biomass_meth](microbial_biomass_meth.md) - Reference or method used in determining microbial biomass + * [mineral_nutr_regm](mineral_nutr_regm.md) - Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * [misc_param](misc_param.md) - Any other measurement performed or parameter collected, that is not listed here + * [n_alkanes](n_alkanes.md) - Concentration of n-alkanes; can include multiple n-alkanes + * [nitrate](nitrate.md) - Concentration of nitrate in the sample + * [nitrite](nitrite.md) - Concentration of nitrite in the sample + * [nitro](nitro.md) - Concentration of nitrogen (total) + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) - Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) - History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * [nose_throat_disord](nose_throat_disord.md) - History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * [number_pets](number_pets.md) - The number of pets residing in the sampled space + * [number_plants](number_plants.md) - The number of plant(s) in the sampling space + * [number_resident](number_resident.md) - The number of individuals currently occupying in the sampling location + * [occup_density_samp](occup_density_samp.md) - Average number of occupants at time of sampling per square footage + * [occup_document](occup_document.md) - The type of documentation of occupancy + * [occup_samp](occup_samp.md) - Number of occupants present at time of sample within the given space + * [org_carb](org_carb.md) - Concentration of organic carbon + * [org_matter](org_matter.md) - Concentration of organic matter + * [org_nitro](org_nitro.md) - Concentration of organic nitrogen + * [org_particles](org_particles.md) - Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * [organism_count](organism_count.md) - Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * [organism_count_qpcr_info](organism_count_qpcr_info.md) - If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * [owc_tvdss](owc_tvdss.md) - Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * [oxy_stat_samp](oxy_stat_samp.md) - Oxygenation status of sample + * [oxygen](oxygen.md) - Oxygen (gas) amount or concentration at the time of sampling + * [part_org_carb](part_org_carb.md) - Concentration of particulate organic carbon + * [part_org_nitro](part_org_nitro.md) - Concentration of particulate organic nitrogen + * [particle_class](particle_class.md) - Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * [permeability](permeability.md) - Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * [perturbation](perturbation.md) - Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * [pesticide_regm](pesticide_regm.md) - Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * [pet_farm_animal](pet_farm_animal.md) - Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * [petroleum_hydrocarb](petroleum_hydrocarb.md) - Concentration of petroleum hydrocarbon + * [ph](ph.md) - Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * [ph_meth](ph_meth.md) - Reference or method used in determining ph + * [ph_regm](ph_regm.md) - Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * [phaeopigments](phaeopigments.md) - Concentration of phaeopigments; can include multiple phaeopigments + * [phosphate](phosphate.md) - Concentration of phosphate + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) - Concentration of phospholipid fatty acids; can include multiple values + * [photon_flux](photon_flux.md) - Measurement of photon flux + * [plant_growth_med](plant_growth_med.md) - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * [plant_product](plant_product.md) - Substance produced by the plant, where the sample was obtained from + * [plant_sex](plant_sex.md) - Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * [plant_struc](plant_struc.md) - Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * [pollutants](pollutants.md) - Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * [pool_dna_extracts](pool_dna_extracts.md) - Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * [porosity](porosity.md) - Porosity of deposited sediment is volume of voids divided by the total volume of sample + * [potassium](potassium.md) - Concentration of potassium in the sample + * [pour_point](pour_point.md) - Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * [pre_treatment](pre_treatment.md) - The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * [pregnancy](pregnancy.md) - Date due of pregnancy + * [pres_animal](pres_animal.md) - The number and type of animals present in the sampling space + * [pressure](pressure.md) - Pressure to which the sample is subject to, in atmospheres + * [previous_land_use](previous_land_use.md) - Previous land use and dates + * [previous_land_use_meth](previous_land_use_meth.md) - Reference or method used in determining previous land use and dates + * [primary_prod](primary_prod.md) - Measurement of primary production, generally measured as isotope uptake + * [primary_treatment](primary_treatment.md) - The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * [prod_rate](prod_rate.md) - Oil and/or gas production rates per well (e.g. 524 m3 / day) + * [prod_start_date](prod_start_date.md) - Date of field's first production + * [profile_position](profile_position.md) - Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * [pulmonary_disord](pulmonary_disord.md) - History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * [quad_pos](quad_pos.md) - The quadrant position of the sampling room within the building + * [radiation_regm](radiation_regm.md) - Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * [rainfall_regm](rainfall_regm.md) - Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [reactor_type](reactor_type.md) - Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * [redox_potential](redox_potential.md) - Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * [rel_air_humidity](rel_air_humidity.md) - Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * [rel_humidity_out](rel_humidity_out.md) - The recorded outside relative humidity value at the time of sampling + * [rel_samp_loc](rel_samp_loc.md) - The sampling location within the train car + * [reservoir](reservoir.md) - Name of the reservoir (e.g. Carapebus) + * [resins_pc](resins_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [resp_part_matter](resp_part_matter.md) - Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * [room_air_exch_rate](room_air_exch_rate.md) - The rate at which outside air replaces indoor air in a given space + * [room_architec_element](room_architec_element.md) - The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * [room_condt](room_condt.md) - The condition of the room at the time of sampling + * [room_connected](room_connected.md) - List of rooms connected to the sampling room by a doorway + * [room_count](room_count.md) - The total count of rooms in the built structure including all room types + * [room_dim](room_dim.md) - The length, width and height of sampling room + * [room_door_dist](room_door_dist.md) - Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * [room_door_share](room_door_share.md) - List of room(s) (room number, room name) sharing a door with the sampling room + * [room_hallway](room_hallway.md) - List of room(s) (room number, room name) located in the same hallway as sampling room + * [room_loc](room_loc.md) - The position of the room within the building + * [room_moist_damage_hist](room_moist_damage_hist.md) - The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * [room_net_area](room_net_area.md) - The net floor area of sampling room. Net area excludes wall thicknesses + * [room_occup](room_occup.md) - Count of room occupancy at time of sampling + * [room_samp_pos](room_samp_pos.md) - The horizontal sampling position in the room relative to architectural elements + * [room_type](room_type.md) - The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * [room_vol](room_vol.md) - Volume of sampling room + * [room_wall_share](room_wall_share.md) - List of room(s) (room number, room name) sharing a wall with the sampling room + * [room_window_count](room_window_count.md) - Number of windows in the room + * [root_cond](root_cond.md) - Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * [root_med_carbon](root_med_carbon.md) - Source of organic carbon in the culture rooting medium; e.g. sucrose. + * [root_med_macronutr](root_med_macronutr.md) - Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * [root_med_micronutr](root_med_micronutr.md) - Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * [root_med_ph](root_med_ph.md) - pH measurement of the culture rooting medium; e.g. 5.5. + * [root_med_regl](root_med_regl.md) - Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * [root_med_solid](root_med_solid.md) - Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * [root_med_suppl](root_med_suppl.md) - Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * [salinity](salinity.md) - Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * [salinity_meth](salinity_meth.md) - Reference or method used in determining salinity + * [salt_regm](salt_regm.md) - Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * [samp_capt_status](samp_capt_status.md) - Reason for the sample + * [samp_collection_point](samp_collection_point.md) - Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * [samp_dis_stage](samp_dis_stage.md) - Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * [samp_floor](samp_floor.md) - The floor of the building, where the sampling room is located + * [samp_loc_corr_rate](samp_loc_corr_rate.md) - Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * [samp_md](samp_md.md) - In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * [samp_preserv](samp_preserv.md) - Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * [samp_room_id](samp_room_id.md) - Sampling room number. This ID should be consistent with the designations on the building floor plans + * [samp_salinity](samp_salinity.md) - Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * [samp_sort_meth](samp_sort_meth.md) - Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * [samp_store_dur](samp_store_dur.md) - Duration for which the sample was stored + * [samp_store_loc](samp_store_loc.md) - Location at which sample was stored, usually name of a specific freezer/room + * [samp_store_temp](samp_store_temp.md) - Temperature at which sample was stored, e.g. -80 degree Celsius + * [samp_subtype](samp_subtype.md) - Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * [samp_time_out](samp_time_out.md) - The recent and long term history of outside sampling + * [samp_transport_cond](samp_transport_cond.md) - Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * [samp_tvdss](samp_tvdss.md) - Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * [samp_type](samp_type.md) - Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) - Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * [samp_weather](samp_weather.md) - The weather on the sampling day + * [samp_well_name](samp_well_name.md) - Name of the well (e.g. BXA1123) where sample was taken + * [saturates_pc](saturates_pc.md) - Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * [season](season.md) - The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * [season_environment](season_environment.md) - Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * [season_precpt](season_precpt.md) - The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * [season_temp](season_temp.md) - Mean seasonal temperature + * [season_use](season_use.md) - The seasons the space is occupied + * [secondary_treatment](secondary_treatment.md) - The process for substantially degrading the biological content of the sewage + * [sediment_type](sediment_type.md) - Information about the sediment type based on major constituents + * [sewage_type](sewage_type.md) - Type of wastewater treatment plant as municipial or industrial + * [sexual_act](sexual_act.md) - Current sexual partner and frequency of sex + * [shading_device_cond](shading_device_cond.md) - The physical condition of the shading device at the time of sampling + * [shading_device_loc](shading_device_loc.md) - The location of the shading device in relation to the built structure + * [shading_device_mat](shading_device_mat.md) - The material the shading device is composed of + * [shading_device_type](shading_device_type.md) - The type of shading device + * [shading_device_water_mold](shading_device_water_mold.md) - Signs of the presence of mold or mildew on the shading device + * [sieving](sieving.md) - Collection design of pooled samples and/or sieve size and amount of sample sieved + * [silicate](silicate.md) - Concentration of silicate + * [size_frac_low](size_frac_low.md) - Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * [size_frac_up](size_frac_up.md) - Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * [slope_aspect](slope_aspect.md) - The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * [slope_gradient](slope_gradient.md) - Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * [sludge_retent_time](sludge_retent_time.md) - The time activated sludge remains in reactor + * [smoker](smoker.md) - Specification of smoking status + * [sodium](sodium.md) - Sodium concentration in the sample + * [soil_type](soil_type.md) - Soil series name or other lower-level classification + * [soil_type_meth](soil_type_meth.md) - Reference or method used in determining soil series name or other lower-level classification + * [solar_irradiance](solar_irradiance.md) - The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * [soluble_inorg_mat](soluble_inorg_mat.md) - Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * [soluble_org_mat](soluble_org_mat.md) - Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * [soluble_react_phosp](soluble_react_phosp.md) - Concentration of soluble reactive phosphorus + * [space_typ_state](space_typ_state.md) - Customary or normal state of the space + * [special_diet](special_diet.md) - Specification of special diet; can include multiple special diets + * [specific](specific.md) - The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * [specific_humidity](specific_humidity.md) - The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * [sr_dep_env](sr_dep_env.md) - Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * [sr_geol_age](sr_geol_age.md) - Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * [sr_kerog_type](sr_kerog_type.md) - Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * [sr_lithology](sr_lithology.md) - Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * [standing_water_regm](standing_water_regm.md) - Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [store_cond](store_cond.md) - Explain how and for how long the soil sample was stored before DNA extraction + * [study_complt_stat](study_complt_stat.md) - Specification of study completion status, if no the reason should be specified + * [substructure_type](substructure_type.md) - The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * [sulfate](sulfate.md) - Concentration of sulfate in the sample + * [sulfate_fw](sulfate_fw.md) - Original sulfate concentration in the hydrocarbon resource + * [sulfide](sulfide.md) - Concentration of sulfide in the sample + * [surf_air_cont](surf_air_cont.md) - Contaminant identified on surface + * [surf_humidity](surf_humidity.md) - Surfaces: water activity as a function of air and material moisture + * [surf_material](surf_material.md) - Surface materials at the point of sampling + * [surf_moisture](surf_moisture.md) - Water held on a surface + * [surf_moisture_ph](surf_moisture_ph.md) - ph measurement of surface + * [surf_temp](surf_temp.md) - Temperature of the surface at the time of sampling + * [suspend_part_matter](suspend_part_matter.md) - Concentration of suspended particulate matter + * [suspend_solids](suspend_solids.md) - Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * [tan](tan.md) - Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * [temp](temp.md) - Temperature of the sample at the time of sampling + * [temp_out](temp_out.md) - The recorded temperature value at sampling time outside + * [tertiary_treatment](tertiary_treatment.md) - The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * [texture](texture.md) - The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * [texture_meth](texture_meth.md) - Reference or method used in determining soil texture + * [tidal_stage](tidal_stage.md) - Stage of tide + * [tillage](tillage.md) - Note method(s) used for tilling + * [time_last_toothbrush](time_last_toothbrush.md) - Specification of the time since last toothbrushing + * [time_since_last_wash](time_since_last_wash.md) - Specification of the time since last wash + * [tiss_cult_growth_med](tiss_cult_growth_med.md) - Description of plant tissue culture growth media used + * [toluene](toluene.md) - Concentration of toluene in the sample + * [tot_carb](tot_carb.md) - Total carbon content + * [tot_depth_water_col](tot_depth_water_col.md) - Measurement of total depth of water column + * [tot_diss_nitro](tot_diss_nitro.md) - Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * [tot_inorg_nitro](tot_inorg_nitro.md) - Total inorganic nitrogen content + * [tot_iron](tot_iron.md) - Concentration of total iron in the sample + * [tot_nitro](tot_nitro.md) - Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * [tot_nitro_content](tot_nitro_content.md) - Total nitrogen content of the sample + * [tot_nitro_content_meth](tot_nitro_content_meth.md) - Reference or method used in determining the total nitrogen + * [tot_org_c_meth](tot_org_c_meth.md) - Reference or method used in determining total organic carbon + * [tot_org_carb](tot_org_carb.md) - Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * [tot_part_carb](tot_part_carb.md) - Total particulate carbon content + * [tot_phosp](tot_phosp.md) - Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * [tot_phosphate](tot_phosphate.md) - Total amount or concentration of phosphate + * [tot_sulfur](tot_sulfur.md) - Concentration of total sulfur in the sample + * [train_line](train_line.md) - The subway line name + * [train_stat_loc](train_stat_loc.md) - The train station collection location + * [train_stop_loc](train_stop_loc.md) - The train stop collection location + * [travel_out_six_month](travel_out_six_month.md) - Specification of the countries travelled in the last six months; can include multiple travels + * [turbidity](turbidity.md) - Measure of the amount of cloudiness or haziness in water caused by individual particles + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * [twin_sibling](twin_sibling.md) - Specification of twin sibling presence + * [typ_occup_density](typ_occup_density.md) - Customary or normal density of occupants + * [urine_collect_meth](urine_collect_meth.md) - Specification of urine collection method + * [urogenit_disord](urogenit_disord.md) - History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * [urogenit_tract_disor](urogenit_tract_disor.md) - History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * [ventilation_rate](ventilation_rate.md) - Ventilation rate of the system in the sampled premises + * [ventilation_type](ventilation_type.md) - Ventilation system used in the sampled premises + * [vfa](vfa.md) - Concentration of Volatile Fatty Acids in the sample + * [vfa_fw](vfa_fw.md) - Original volatile fatty acid concentration in the hydrocarbon resource + * [vis_media](vis_media.md) - The building visual media + * [viscosity](viscosity.md) - A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * [volatile_org_comp](volatile_org_comp.md) - Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * [wall_area](wall_area.md) - The total area of the sampled room's walls + * [wall_const_type](wall_const_type.md) - The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * [wall_finish_mat](wall_finish_mat.md) - The material utilized to finish the outer most layer of the wall + * [wall_height](wall_height.md) - The average height of the walls in the sampled room + * [wall_loc](wall_loc.md) - The relative location of the wall within the room + * [wall_surf_treatment](wall_surf_treatment.md) - The surface treatment of interior wall + * [wall_texture](wall_texture.md) - The feel, appearance, or consistency of a wall surface + * [wall_thermal_mass](wall_thermal_mass.md) - The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * [wall_water_mold](wall_water_mold.md) - Signs of the presence of mold or mildew on a wall + * [wastewater_type](wastewater_type.md) - The origin of wastewater such as human waste, rainfall, storm drains, etc. + * [water_content](water_content.md) - Water content measurement + * [water_content_soil_meth](water_content_soil_meth.md) - Reference or method used in determining the water content of soil + * [water_current](water_current.md) - Measurement of magnitude and direction of flow within a fluid + * [water_cut](water_cut.md) - Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * [water_feat_size](water_feat_size.md) - The size of the water feature + * [water_feat_type](water_feat_type.md) - The type of water feature present within the building being sampled + * [water_production_rate](water_production_rate.md) - Water production rates per well (e.g. 987 m3 / day) + * [water_temp_regm](water_temp_regm.md) - Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [watering_regm](watering_regm.md) - Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * [weekday](weekday.md) - The day of the week when sampling occurred + * [weight_loss_3_month](weight_loss_3_month.md) - Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * [win](win.md) - A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * [wind_direction](wind_direction.md) - Wind direction is the direction from which a wind originates + * [wind_speed](wind_speed.md) - Speed of wind measured at the time of sampling + * [window_cond](window_cond.md) - The physical condition of the window at the time of sampling + * [window_cover](window_cover.md) - The type of window covering + * [window_horiz_pos](window_horiz_pos.md) - The horizontal position of the window on the wall + * [window_loc](window_loc.md) - The relative location of the window within the room + * [window_mat](window_mat.md) - The type of material used to finish a window + * [window_open_freq](window_open_freq.md) - The number of times windows are opened per week + * [window_size](window_size.md) - The window's length and width + * [window_status](window_status.md) - Defines whether the windows were open or closed during environmental testing + * [window_type](window_type.md) - The type of windows + * [window_vert_pos](window_vert_pos.md) - The vertical position of the window on the wall + * [window_water_mold](window_water_mold.md) - Signs of the presence of mold or mildew on the window. + * [xylene](xylene.md) - Concentration of xylene in the sample + * [investigation field](investigation_field.md) - field describing aspect of the investigation/study to which the sample belongs + * [experimental_factor](experimental_factor.md) - Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [investigation_type](investigation_type.md) - Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * [project_name](project_name.md) - Name of the project within which the sequencing was organized + * [submitted_to_insdc](submitted_to_insdc.md) - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * [mixs extension field](mixs_extension_field.md) + * [env_package](env_package.md) - MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + * [biotic_relationship](biotic_relationship.md) - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * [encoded_traits](encoded_traits.md) - Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * [estimated_size](estimated_size.md) - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * [extrachrom_elements](extrachrom_elements.md) - Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * [health_disease_stat](health_disease_stat.md) - Health or disease status of specific host at time of collection + * [host_spec_range](host_spec_range.md) - The NCBI taxonomy identifier of the specific host if it is known + * [isol_growth_condt](isol_growth_condt.md) - Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * [num_replicons](num_replicons.md) - Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * [pathogenicity](pathogenicity.md) - To what is the entity pathogenic + * [ploidy](ploidy.md) - The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * [propagation](propagation.md) - This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * [ref_biomaterial](ref_biomaterial.md) - Primary publication if isolated before genome publication; otherwise, primary genome report + * [rel_to_oxygen](rel_to_oxygen.md) - Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * [samp_collect_device](samp_collect_device.md) - The method or device employed for collecting the sample + * [samp_mat_process](samp_mat_process.md) - Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [samp_size](samp_size.md) - Amount or size of sample (volume, mass or area) that was collected + * [size_frac](size_frac.md) - Filtering pore size used in sample preparation + * [source_mat_id](source_mat_id.md) - A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * [source_uvig](source_uvig.md) - Type of dataset from which the UViG was obtained + * [specific_host](specific_host.md) - If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * [subspecf_gen_lin](subspecf_gen_lin.md) - This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * [trophic_level](trophic_level.md) - Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * [virus_enrich_appr](virus_enrich_appr.md) - List of approaches used to enrich the sample for viruses, if any + * [sequencing field](sequencing_field.md) + * [adapters](adapters.md) - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * [annot](annot.md) - Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * [assembly_name](assembly_name.md) - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * [assembly_qual](assembly_qual.md) - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * [assembly_software](assembly_software.md) - Tool(s) used for assembly, including version number and parameters + * [bin_param](bin_param.md) - The parameters that have been applied during the extraction of genomes from metagenomic datasets + * [bin_software](bin_software.md) - Tool(s) used for the extraction of genomes from metagenomic datasets + * [chimera_check](chimera_check.md) - A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * [compl_appr](compl_appr.md) - The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * [compl_score](compl_score.md) - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * [compl_software](compl_software.md) - Tools used for completion estimate, i.e. checkm, anvi'o, busco + * [contam_score](contam_score.md) - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * [contam_screen_input](contam_screen_input.md) - The type of sequence data used as input + * [contam_screen_param](contam_screen_param.md) - Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * [decontam_software](decontam_software.md) - Tool(s) used in contamination screening + * [detec_type](detec_type.md) - Type of UViG detection + * [feat_pred](feat_pred.md) - Method used to predict UViGs features such as ORFs, integration site, etc. + * [host_pred_appr](host_pred_appr.md) - Tool or approach used for host prediction + * [host_pred_est_acc](host_pred_est_acc.md) - For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * [lib_layout](lib_layout.md) - Specify whether to expect single, paired, or other configuration of reads + * [lib_reads_seqd](lib_reads_seqd.md) - Total number of clones sequenced from the library + * [lib_screen](lib_screen.md) - Specific enrichment or screening methods applied before and/or after creating libraries + * [lib_size](lib_size.md) - Total number of clones in the library prepared for the project + * [lib_vector](lib_vector.md) - Cloning vector type(s) used in construction of libraries + * [mag_cov_software](mag_cov_software.md) - Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * [mid](mid.md) - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * [nucl_acid_amp](nucl_acid_amp.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * [nucl_acid_ext](nucl_acid_ext.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * [number_contig](number_contig.md) - Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * [pcr_cond](pcr_cond.md) - Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * [pcr_primers](pcr_primers.md) - PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * [pred_genome_struc](pred_genome_struc.md) - Expected structure of the viral genome + * [pred_genome_type](pred_genome_type.md) - Type of genome predicted for the UViG + * [reassembly_bin](reassembly_bin.md) - Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * [ref_db](ref_db.md) - List of database(s) used for ORF annotation, along with version number and reference to website or publication + * [seq_meth](seq_meth.md) - Sequencing method used; e.g. Sanger, ABI-solid + * [seq_quality_check](seq_quality_check.md) - Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * [sim_search_meth](sim_search_meth.md) - Tool used to compare ORFs with database, along with version and cutoffs used + * [single_cell_lysis_appr](single_cell_lysis_appr.md) - Method used to free DNA from interior of the cell(s) or particle(s) + * [single_cell_lysis_prot](single_cell_lysis_prot.md) - Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * [sop](sop.md) - Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * [sort_tech](sort_tech.md) - Method used to sort/isolate cells or particles of interest + * [target_gene](target_gene.md) - Targeted gene or locus name for marker gene studies + * [target_subfragment](target_subfragment.md) - Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * [tax_class](tax_class.md) - Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * [tax_ident](tax_ident.md) - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * [trna_ext_software](trna_ext_software.md) - Tools used for tRNA identification + * [trnas](trnas.md) - The total number of tRNAs identified from the SAG or MAG + * [url](url.md) + * [vir_ident_software](vir_ident_software.md) - Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * [votu_class_appr](votu_class_appr.md) - Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * [votu_db](votu_db.md) - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * [votu_seq_comp_appr](votu_seq_comp_appr.md) - Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * [wga_amp_appr](wga_amp_appr.md) - Method used to amplify genomic DNA in preparation for sequencing + * [wga_amp_kit](wga_amp_kit.md) - Kit used to amplify genomic DNA in preparation for sequencing + * [x_16s_recover](x_16s_recover.md) - Can a 16S gene be recovered from the submitted SAG or MAG? + * [x_16s_recover_software](x_16s_recover_software.md) - Tools used for 16S rRNA gene extraction + +### Types + + +#### Built in + + * **Bool** + * **Decimal** + * **ElementIdentifier** + * **NCName** + * **NodeIdentifier** + * **URI** + * **URIorCURIE** + * **XSDDate** + * **XSDDateTime** + * **XSDTime** + * **float** + * **int** + * **str** + +#### Defined + + * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value + * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar + * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time + * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification + * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification + * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification + * [Integer](types/Integer.md) (**int**) - An integer + * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE + * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. + * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. + * [String](types/String.md) (**str**) - A character string + * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day + * [Uri](types/Uri.md) (**URI**) - a complete URI + * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/mixs6/indoor_space.md b/mixs6/indoor_space.md new file mode 100644 index 00000000..91553d87 --- /dev/null +++ b/mixs6/indoor_space.md @@ -0,0 +1,48 @@ + +# Slot: indoor_space + + +A distinguishable space within a structure, the purpose for which discrete areas of a building is used + +URI: [mixs.vocab:indoor_space](https://w3id.org/mixs/vocab/indoor_space) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | indoor space | +| **Mappings:** | | MIXS:0000763 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 15 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='foyer', description=None) | + diff --git a/mixs6/indoor_surf.md b/mixs6/indoor_surf.md new file mode 100644 index 00000000..73241b96 --- /dev/null +++ b/mixs6/indoor_surf.md @@ -0,0 +1,48 @@ + +# Slot: indoor_surf + + +Type of indoor surface + +URI: [mixs.vocab:indoor_surf](https://w3id.org/mixs/vocab/indoor_surf) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | indoor surface | +| **Mappings:** | | MIXS:0000764 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 16 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wall', description=None) | + diff --git a/mixs6/indust_eff_percent.md b/mixs6/indust_eff_percent.md new file mode 100644 index 00000000..7529dc36 --- /dev/null +++ b/mixs6/indust_eff_percent.md @@ -0,0 +1,48 @@ + +# Slot: indust_eff_percent + + +Percentage of industrial effluents received by wastewater treatment plant + +URI: [mixs.vocab:indust_eff_percent](https://w3id.org/mixs/vocab/indust_eff_percent) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | industrial effluent percent | +| **Mappings:** | | MIXS:0000662 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/inorg_particles.md b/mixs6/inorg_particles.md new file mode 100644 index 00000000..df735cfc --- /dev/null +++ b/mixs6/inorg_particles.md @@ -0,0 +1,48 @@ + +# Slot: inorg_particles + + +Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + +URI: [mixs.vocab:inorg_particles](https://w3id.org/mixs/vocab/inorg_particles) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | inorganic particles | +| **Mappings:** | | MIXS:0000664 | +| **Comments:** | | Expected value: inorganic particle name;measurement value | +| | | Preferred unit: mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/inside_lux.md b/mixs6/inside_lux.md new file mode 100644 index 00000000..b6b723ca --- /dev/null +++ b/mixs6/inside_lux.md @@ -0,0 +1,48 @@ + +# Slot: inside_lux + + +The recorded value at sampling time (power density) + +URI: [mixs.vocab:inside_lux](https://w3id.org/mixs/vocab/inside_lux) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | inside lux light | +| **Mappings:** | | MIXS:0000168 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilowatt per square metre | +| | | Occurrence: 1 | +| | | Position: 87 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/int_wall_cond.md b/mixs6/int_wall_cond.md new file mode 100644 index 00000000..ddda6ae5 --- /dev/null +++ b/mixs6/int_wall_cond.md @@ -0,0 +1,48 @@ + +# Slot: int_wall_cond + + +The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + +URI: [mixs.vocab:int_wall_cond](https://w3id.org/mixs/vocab/int_wall_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | interior wall condition | +| **Mappings:** | | MIXS:0000813 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 88 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='damaged', description=None) | + diff --git a/mixs6/investigation_field.md b/mixs6/investigation_field.md new file mode 100644 index 00000000..f8e785ee --- /dev/null +++ b/mixs6/investigation_field.md @@ -0,0 +1,25 @@ + +# Slot: investigation_field + + +field describing aspect of the investigation/study to which the sample belongs + +URI: [mixs.vocab:investigation_field](https://w3id.org/mixs/vocab/investigation_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [experimental_factor](experimental_factor.md) + * [investigation_type](investigation_type.md) + * [project_name](project_name.md) + * [submitted_to_insdc](submitted_to_insdc.md) + +## Used by + diff --git a/mixs6/investigation_type.md b/mixs6/investigation_type.md new file mode 100644 index 00000000..10dd698e --- /dev/null +++ b/mixs6/investigation_type.md @@ -0,0 +1,56 @@ + +# Slot: investigation_type + + +Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + +URI: [mixs.vocab:investigation_type](https://w3id.org/mixs/vocab/investigation_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | investigation type | +| **Comments:** | | Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genomes | +| | | Preferred unit: | +| | | Position: 2.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='metagenome', description=None) | + diff --git a/mixs6/isol_growth_condt.md b/mixs6/isol_growth_condt.md new file mode 100644 index 00000000..914b5acf --- /dev/null +++ b/mixs6/isol_growth_condt.md @@ -0,0 +1,56 @@ + +# Slot: isol_growth_condt + + +Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + +URI: [mixs.vocab:isol_growth_condt](https://w3id.org/mixs/vocab/isol_growth_condt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | isolation and growth condition | +| **Comments:** | | Expected value: PMID,DOI or URL | +| | | Preferred unit: | +| | | Position: 30.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='doi: 10.1016/j.syapm.2018.01.009', description=None) | + diff --git a/mixs6/iw_bt_date_well.md b/mixs6/iw_bt_date_well.md new file mode 100644 index 00000000..8b7ad3a3 --- /dev/null +++ b/mixs6/iw_bt_date_well.md @@ -0,0 +1,48 @@ + +# Slot: iw_bt_date_well + + +Injection water breakthrough date per well following a secondary and/or tertiary recovery + +URI: [mixs.vocab:iw_bt_date_well](https://w3id.org/mixs/vocab/iw_bt_date_well) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | injection water breakthrough date of specific well | +| **Mappings:** | | MIXS:0001010 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 29 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/iwf.md b/mixs6/iwf.md new file mode 100644 index 00000000..f2478681 --- /dev/null +++ b/mixs6/iwf.md @@ -0,0 +1,48 @@ + +# Slot: iwf + + +Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + +URI: [mixs.vocab:iwf](https://w3id.org/mixs/vocab/iwf) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | injection water fraction | +| **Mappings:** | | MIXS:0000455 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 27 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/last_clean.md b/mixs6/last_clean.md new file mode 100644 index 00000000..92a9ea09 --- /dev/null +++ b/mixs6/last_clean.md @@ -0,0 +1,48 @@ + +# Slot: last_clean + + +The last time the floor was cleaned (swept, mopped, vacuumed) + +URI: [mixs.vocab:last_clean](https://w3id.org/mixs/vocab/last_clean) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | last time swept/mopped/vacuumed | +| **Mappings:** | | MIXS:0000814 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 89 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | + diff --git a/mixs6/lat_lon.md b/mixs6/lat_lon.md new file mode 100644 index 00000000..0089620d --- /dev/null +++ b/mixs6/lat_lon.md @@ -0,0 +1,56 @@ + +# Slot: lat_lon + + +The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + +URI: [mixs.vocab:lat_lon](https://w3id.org/mixs/vocab/lat_lon) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | geographic location (latitude and longitude) | +| **Comments:** | | Expected value: decimal degrees | +| | | Preferred unit: | +| | | Position: 5.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='50.586825 6.408977', description=None) | + diff --git a/mixs6/lib_layout.md b/mixs6/lib_layout.md new file mode 100644 index 00000000..12613448 --- /dev/null +++ b/mixs6/lib_layout.md @@ -0,0 +1,56 @@ + +# Slot: lib_layout + + +Specify whether to expect single, paired, or other configuration of reads + +URI: [mixs.vocab:lib_layout](https://w3id.org/mixs/vocab/lib_layout) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library layout | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 41.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='paired', description=None) | + diff --git a/mixs6/lib_reads_seqd.md b/mixs6/lib_reads_seqd.md new file mode 100644 index 00000000..521c38f7 --- /dev/null +++ b/mixs6/lib_reads_seqd.md @@ -0,0 +1,56 @@ + +# Slot: lib_reads_seqd + + +Total number of clones sequenced from the library + +URI: [mixs.vocab:lib_reads_seqd](https://w3id.org/mixs/vocab/lib_reads_seqd) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library reads sequenced | +| **Comments:** | | Expected value: number of reads sequenced | +| | | Preferred unit: | +| | | Position: 40.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='20', description=None) | + diff --git a/mixs6/lib_screen.md b/mixs6/lib_screen.md new file mode 100644 index 00000000..0d4d7286 --- /dev/null +++ b/mixs6/lib_screen.md @@ -0,0 +1,56 @@ + +# Slot: lib_screen + + +Specific enrichment or screening methods applied before and/or after creating libraries + +URI: [mixs.vocab:lib_screen](https://w3id.org/mixs/vocab/lib_screen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library screening strategy | +| **Comments:** | | Expected value: screening strategy name | +| | | Preferred unit: | +| | | Position: 43.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='enriched, screened, normalized', description=None) | + diff --git a/mixs6/lib_size.md b/mixs6/lib_size.md new file mode 100644 index 00000000..b0f81a53 --- /dev/null +++ b/mixs6/lib_size.md @@ -0,0 +1,56 @@ + +# Slot: lib_size + + +Total number of clones in the library prepared for the project + +URI: [mixs.vocab:lib_size](https://w3id.org/mixs/vocab/lib_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library size | +| **Comments:** | | Expected value: number of clones | +| | | Preferred unit: | +| | | Position: 39.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='50', description=None) | + diff --git a/mixs6/lib_vector.md b/mixs6/lib_vector.md new file mode 100644 index 00000000..558e3f57 --- /dev/null +++ b/mixs6/lib_vector.md @@ -0,0 +1,56 @@ + +# Slot: lib_vector + + +Cloning vector type(s) used in construction of libraries + +URI: [mixs.vocab:lib_vector](https://w3id.org/mixs/vocab/lib_vector) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | library vector | +| **Comments:** | | Expected value: vector | +| | | Preferred unit: | +| | | Position: 42.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='Bacteriophage P1', description=None) | + diff --git a/mixs6/light_intensity.md b/mixs6/light_intensity.md new file mode 100644 index 00000000..47fcd68c --- /dev/null +++ b/mixs6/light_intensity.md @@ -0,0 +1,48 @@ + +# Slot: light_intensity + + +Measurement of light intensity + +URI: [mixs.vocab:light_intensity](https://w3id.org/mixs/vocab/light_intensity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light intensity | +| **Mappings:** | | MIXS:0000706 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: lux | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.3 lux', description=None) | + diff --git a/mixs6/light_regm.md b/mixs6/light_regm.md new file mode 100644 index 00000000..9a084aef --- /dev/null +++ b/mixs6/light_regm.md @@ -0,0 +1,48 @@ + +# Slot: light_regm + + +Information about treatment(s) involving exposure to light, including both light intensity and quality. + +URI: [mixs.vocab:light_regm](https://w3id.org/mixs/vocab/light_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light regimen | +| **Mappings:** | | MIXS:0000569 | +| **Comments:** | | Expected value: exposure type;light intensity;light quality | +| | | Preferred unit: lux; micrometer, nanometer, angstrom | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='incandescant light;10 lux;450 nanometer', description=None) | + diff --git a/mixs6/light_type.md b/mixs6/light_type.md new file mode 100644 index 00000000..04c31f5b --- /dev/null +++ b/mixs6/light_type.md @@ -0,0 +1,48 @@ + +# Slot: light_type + + +Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + +URI: [mixs.vocab:light_type](https://w3id.org/mixs/vocab/light_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | light type | +| **Mappings:** | | MIXS:0000769 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 21 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='desk lamp', description=None) | + diff --git a/mixs6/link_addit_analys.md b/mixs6/link_addit_analys.md new file mode 100644 index 00000000..d88fc2d5 --- /dev/null +++ b/mixs6/link_addit_analys.md @@ -0,0 +1,48 @@ + +# Slot: link_addit_analys + + +Link to additional analysis results performed on the sample + +URI: [mixs.vocab:link_addit_analys](https://w3id.org/mixs/vocab/link_addit_analys) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | links to additional analysis | +| **Mappings:** | | MIXS:0000340 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 45 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/link_class_info.md b/mixs6/link_class_info.md new file mode 100644 index 00000000..a27979a9 --- /dev/null +++ b/mixs6/link_class_info.md @@ -0,0 +1,48 @@ + +# Slot: link_class_info + + +Link to digitized soil maps or other soil classification information + +URI: [mixs.vocab:link_class_info](https://w3id.org/mixs/vocab/link_class_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | link to classification information | +| **Mappings:** | | MIXS:0000329 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 25 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/link_climate_info.md b/mixs6/link_climate_info.md new file mode 100644 index 00000000..f3cd1658 --- /dev/null +++ b/mixs6/link_climate_info.md @@ -0,0 +1,48 @@ + +# Slot: link_climate_info + + +Link to climate resource + +URI: [mixs.vocab:link_climate_info](https://w3id.org/mixs/vocab/link_climate_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | link to climate information | +| **Mappings:** | | MIXS:0000328 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 20 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/lithology.md b/mixs6/lithology.md new file mode 100644 index 00000000..cabf4b36 --- /dev/null +++ b/mixs6/lithology.md @@ -0,0 +1,60 @@ + +# Slot: lithology + + +Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:lithology](https://w3id.org/mixs/vocab/lithology) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lithology | +| **Mappings:** | | MIXS:0000990 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 12 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='Volcanic', description=None) | + diff --git a/mixs6/liver_disord.md b/mixs6/liver_disord.md new file mode 100644 index 00000000..a5fd1a33 --- /dev/null +++ b/mixs6/liver_disord.md @@ -0,0 +1,48 @@ + +# Slot: liver_disord + + +History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + +URI: [mixs.vocab:liver_disord](https://w3id.org/mixs/vocab/liver_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | liver disorder | +| **Mappings:** | | MIXS:0000282 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 2 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/local_class.md b/mixs6/local_class.md new file mode 100644 index 00000000..d10023b1 --- /dev/null +++ b/mixs6/local_class.md @@ -0,0 +1,48 @@ + +# Slot: local_class + + +Soil classification based on local soil classification system + +URI: [mixs.vocab:local_class](https://w3id.org/mixs/vocab/local_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/local classification | +| **Mappings:** | | MIXS:0000330 | +| **Comments:** | | Expected value: local classification name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 27 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/local_class_meth.md b/mixs6/local_class_meth.md new file mode 100644 index 00000000..7660e2a0 --- /dev/null +++ b/mixs6/local_class_meth.md @@ -0,0 +1,48 @@ + +# Slot: local_class_meth + + +Reference or method used in determining the local soil classification + +URI: [mixs.vocab:local_class_meth](https://w3id.org/mixs/vocab/local_class_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil_taxonomic/local classification method | +| **Mappings:** | | MIXS:0000331 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 28 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/mag_cov_software.md b/mixs6/mag_cov_software.md new file mode 100644 index 00000000..62fbb265 --- /dev/null +++ b/mixs6/mag_cov_software.md @@ -0,0 +1,56 @@ + +# Slot: mag_cov_software + + +Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + +URI: [mixs.vocab:mag_cov_software](https://w3id.org/mixs/vocab/mag_cov_software) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MAG coverage software | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 82.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='bbmap', description=None) | + diff --git a/mixs6/magnesium.md b/mixs6/magnesium.md new file mode 100644 index 00000000..c211f549 --- /dev/null +++ b/mixs6/magnesium.md @@ -0,0 +1,96 @@ + +# Slot: magnesium + + +Concentration of magnesium in the sample + +URI: [mixs.vocab:magnesium](https://w3id.org/mixs/vocab/magnesium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | magnesium | +| **Mappings:** | | MIXS:0000431 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: mole per liter, milligram per liter, parts per million, micromole per kilogram | +| | | Occurrence: 1 | +| | | Position: 69 | +| | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='52.8 micromole per kilogram', description=None) | + diff --git a/mixs6/maternal_health_stat.md b/mixs6/maternal_health_stat.md new file mode 100644 index 00000000..67bfa001 --- /dev/null +++ b/mixs6/maternal_health_stat.md @@ -0,0 +1,48 @@ + +# Slot: maternal_health_stat + + +Specification of the maternal health status + +URI: [mixs.vocab:maternal_health_stat](https://w3id.org/mixs/vocab/maternal_health_stat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amniotic fluid/maternal health status | +| **Mappings:** | | MIXS:0000273 | +| **Comments:** | | Expected value: health status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 37 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/max_occup.md b/mixs6/max_occup.md new file mode 100644 index 00000000..1c5bdefa --- /dev/null +++ b/mixs6/max_occup.md @@ -0,0 +1,48 @@ + +# Slot: max_occup + + +The maximum amount of people allowed in the indoor environment + +URI: [mixs.vocab:max_occup](https://w3id.org/mixs/vocab/max_occup) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | maximum occupancy | +| **Mappings:** | | MIXS:0000229 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 90 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/mean_frict_vel.md b/mixs6/mean_frict_vel.md new file mode 100644 index 00000000..6f47a556 --- /dev/null +++ b/mixs6/mean_frict_vel.md @@ -0,0 +1,72 @@ + +# Slot: mean_frict_vel + + +Measurement of mean friction velocity + +URI: [mixs.vocab:mean_frict_vel](https://w3id.org/mixs/vocab/mean_frict_vel) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean friction velocity | +| **Mappings:** | | MIXS:0000498 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.5 meter per second', description=None) | + diff --git a/mixs6/mean_peak_frict_vel.md b/mixs6/mean_peak_frict_vel.md new file mode 100644 index 00000000..914d11f0 --- /dev/null +++ b/mixs6/mean_peak_frict_vel.md @@ -0,0 +1,72 @@ + +# Slot: mean_peak_frict_vel + + +Measurement of mean peak friction velocity + +URI: [mixs.vocab:mean_peak_frict_vel](https://w3id.org/mixs/vocab/mean_peak_frict_vel) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean peak friction velocity | +| **Mappings:** | | MIXS:0000502 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='1 meter per second', description=None) | + diff --git a/mixs6/mech_struc.md b/mixs6/mech_struc.md new file mode 100644 index 00000000..2159bf36 --- /dev/null +++ b/mixs6/mech_struc.md @@ -0,0 +1,48 @@ + +# Slot: mech_struc + + +mechanical structure: a moving structure + +URI: [mixs.vocab:mech_struc](https://w3id.org/mixs/vocab/mech_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mechanical structure | +| **Mappings:** | | MIXS:0000815 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 91 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='elevator', description=None) | + diff --git a/mixs6/mechanical_damage.md b/mixs6/mechanical_damage.md new file mode 100644 index 00000000..7ee649fb --- /dev/null +++ b/mixs6/mechanical_damage.md @@ -0,0 +1,48 @@ + +# Slot: mechanical_damage + + +Information about any mechanical damage exerted on the plant; can include multiple damages and sites + +URI: [mixs.vocab:mechanical_damage](https://w3id.org/mixs/vocab/mechanical_damage) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mechanical damage | +| **Mappings:** | | MIXS:0001052 | +| **Comments:** | | Expected value: damage type;body site | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='pruning;bark', description=None) | + diff --git a/mixs6/medic_hist_perform.md b/mixs6/medic_hist_perform.md new file mode 100644 index 00000000..199fa03b --- /dev/null +++ b/mixs6/medic_hist_perform.md @@ -0,0 +1,96 @@ + +# Slot: medic_hist_perform + + +Whether full medical history was collected + +URI: [mixs.vocab:medic_hist_perform](https://w3id.org/mixs/vocab/medic_hist_perform) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | medical history performed | +| **Mappings:** | | MIXS:0000897 | +| **Comments:** | | Expected value: true or false | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 28 | +| | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | +| **Examples:** | | Example(value='TRUE', description=None) | + diff --git a/mixs6/menarche.md b/mixs6/menarche.md new file mode 100644 index 00000000..9cce0db6 --- /dev/null +++ b/mixs6/menarche.md @@ -0,0 +1,48 @@ + +# Slot: menarche + + +Date of most recent menstruation + +URI: [mixs.vocab:menarche](https://w3id.org/mixs/vocab/menarche) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | menarche | +| **Mappings:** | | MIXS:0000965 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/menopause.md b/mixs6/menopause.md new file mode 100644 index 00000000..a91bfd9c --- /dev/null +++ b/mixs6/menopause.md @@ -0,0 +1,48 @@ + +# Slot: menopause + + +Date of onset of menopause + +URI: [mixs.vocab:menopause](https://w3id.org/mixs/vocab/menopause) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | menopause | +| **Mappings:** | | MIXS:0000968 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 6 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/methane.md b/mixs6/methane.md new file mode 100644 index 00000000..29e7431c --- /dev/null +++ b/mixs6/methane.md @@ -0,0 +1,72 @@ + +# Slot: methane + + +Methane (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:methane](https://w3id.org/mixs/vocab/methane) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | methane | +| **Mappings:** | | MIXS:0000101 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, parts per billion, parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: air, microbial mat_biofilm, sediment | +| **Examples:** | | Example(value='1800 parts per billion', description=None) | + diff --git a/mixs6/microbial_biomass.md b/mixs6/microbial_biomass.md new file mode 100644 index 00000000..a694ed9c --- /dev/null +++ b/mixs6/microbial_biomass.md @@ -0,0 +1,48 @@ + +# Slot: microbial_biomass + + +The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + +URI: [mixs.vocab:microbial_biomass](https://w3id.org/mixs/vocab/microbial_biomass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | microbial biomass | +| **Mappings:** | | MIXS:0000650 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: ton, kilogram, gram per kilogram soil | +| | | Occurrence: 1 | +| | | Position: 43 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/microbial_biomass_meth.md b/mixs6/microbial_biomass_meth.md new file mode 100644 index 00000000..8f5be4c2 --- /dev/null +++ b/mixs6/microbial_biomass_meth.md @@ -0,0 +1,48 @@ + +# Slot: microbial_biomass_meth + + +Reference or method used in determining microbial biomass + +URI: [mixs.vocab:microbial_biomass_meth](https://w3id.org/mixs/vocab/microbial_biomass_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | microbial biomass method | +| **Mappings:** | | MIXS:0000339 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 44 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/mid.md b/mixs6/mid.md new file mode 100644 index 00000000..ee45b56c --- /dev/null +++ b/mixs6/mid.md @@ -0,0 +1,56 @@ + +# Slot: mid + + +Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + +URI: [mixs.vocab:mid](https://w3id.org/mixs/vocab/mid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | multiplex identifiers | +| **Comments:** | | Expected value: multiplex identifier sequence | +| | | Preferred unit: | +| | | Position: 47.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='GTGAATAT', description=None) | + diff --git a/mixs6/mineral_nutr_regm.md b/mixs6/mineral_nutr_regm.md new file mode 100644 index 00000000..74fe7773 --- /dev/null +++ b/mixs6/mineral_nutr_regm.md @@ -0,0 +1,48 @@ + +# Slot: mineral_nutr_regm + + +Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + +URI: [mixs.vocab:mineral_nutr_regm](https://w3id.org/mixs/vocab/mineral_nutr_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mineral nutrient regimen | +| **Mappings:** | | MIXS:0000570 | +| **Comments:** | | Expected value: mineral nutrient name;mineral nutrient amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/misc_param.md b/mixs6/misc_param.md new file mode 100644 index 00000000..03a18be2 --- /dev/null +++ b/mixs6/misc_param.md @@ -0,0 +1,228 @@ + +# Slot: misc_param + + +Any other measurement performed or parameter collected, that is not listed here + +URI: [mixs.vocab:misc_param](https://w3id.org/mixs/vocab/misc_param) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | miscellaneous parameter | +| **Mappings:** | | MIXS:0000752 | +| **Comments:** | | Expected value: parameter name;measurement value | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='Bicarbonate ion concentration;2075 micromole per kilogram', description=None) | + diff --git a/mixs6/mixs_extension_field.md b/mixs6/mixs_extension_field.md new file mode 100644 index 00000000..d64e407f --- /dev/null +++ b/mixs6/mixs_extension_field.md @@ -0,0 +1,22 @@ + +# Slot: mixs_extension_field + + + + +URI: [mixs.vocab:mixs_extension_field](https://w3id.org/mixs/vocab/mixs_extension_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [env_package](env_package.md) + +## Used by + diff --git a/mixs6/n_alkanes.md b/mixs6/n_alkanes.md new file mode 100644 index 00000000..fe45fdb9 --- /dev/null +++ b/mixs6/n_alkanes.md @@ -0,0 +1,72 @@ + +# Slot: n_alkanes + + +Concentration of n-alkanes; can include multiple n-alkanes + +URI: [mixs.vocab:n_alkanes](https://w3id.org/mixs/vocab/n_alkanes) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | n-alkanes | +| **Mappings:** | | MIXS:0000503 | +| **Comments:** | | Expected value: n-alkane name;measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='n-hexadecane;100 milligram per liter', description=None) | + diff --git a/mixs6/nitrate.md b/mixs6/nitrate.md new file mode 100644 index 00000000..c29e1a50 --- /dev/null +++ b/mixs6/nitrate.md @@ -0,0 +1,120 @@ + +# Slot: nitrate + + +Concentration of nitrate in the sample + +URI: [mixs.vocab:nitrate](https://w3id.org/mixs/vocab/nitrate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrate | +| **Mappings:** | | MIXS:0000425 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 61 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='65 micromole per liter', description=None) | + diff --git a/mixs6/nitrite.md b/mixs6/nitrite.md new file mode 100644 index 00000000..fab7a30d --- /dev/null +++ b/mixs6/nitrite.md @@ -0,0 +1,108 @@ + +# Slot: nitrite + + +Concentration of nitrite in the sample + +URI: [mixs.vocab:nitrite](https://w3id.org/mixs/vocab/nitrite) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrite | +| **Mappings:** | | MIXS:0000426 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 62 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.5 micromole per liter', description=None) | + diff --git a/mixs6/nitro.md b/mixs6/nitro.md new file mode 100644 index 00000000..e6f70aea --- /dev/null +++ b/mixs6/nitro.md @@ -0,0 +1,84 @@ + +# Slot: nitro + + +Concentration of nitrogen (total) + +URI: [mixs.vocab:nitro](https://w3id.org/mixs/vocab/nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nitrogen | +| **Mappings:** | | MIXS:0000504 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='4.2 micromole per liter', description=None) | + diff --git a/mixs6/non_mineral_nutr_regm.md b/mixs6/non_mineral_nutr_regm.md new file mode 100644 index 00000000..b703354c --- /dev/null +++ b/mixs6/non_mineral_nutr_regm.md @@ -0,0 +1,48 @@ + +# Slot: non_mineral_nutr_regm + + +Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + +URI: [mixs.vocab:non_mineral_nutr_regm](https://w3id.org/mixs/vocab/non_mineral_nutr_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | non-mineral nutrient regimen | +| **Mappings:** | | MIXS:0000571 | +| **Comments:** | | Expected value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/nose_mouth_teeth_throat_disord.md b/mixs6/nose_mouth_teeth_throat_disord.md new file mode 100644 index 00000000..f489788f --- /dev/null +++ b/mixs6/nose_mouth_teeth_throat_disord.md @@ -0,0 +1,48 @@ + +# Slot: nose_mouth_teeth_throat_disord + + +History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + +URI: [mixs.vocab:nose_mouth_teeth_throat_disord](https://w3id.org/mixs/vocab/nose_mouth_teeth_throat_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nose/mouth/teeth/throat disorder | +| **Mappings:** | | MIXS:0000283 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: human-oral | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/nose_throat_disord.md b/mixs6/nose_throat_disord.md new file mode 100644 index 00000000..8f34c848 --- /dev/null +++ b/mixs6/nose_throat_disord.md @@ -0,0 +1,48 @@ + +# Slot: nose_throat_disord + + +History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + +URI: [mixs.vocab:nose_throat_disord](https://w3id.org/mixs/vocab/nose_throat_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lung/nose-throat disorder | +| **Mappings:** | | MIXS:0000270 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 31 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/nucl_acid_amp.md b/mixs6/nucl_acid_amp.md new file mode 100644 index 00000000..5f739c15 --- /dev/null +++ b/mixs6/nucl_acid_amp.md @@ -0,0 +1,56 @@ + +# Slot: nucl_acid_amp + + +A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + +URI: [mixs.vocab:nucl_acid_amp](https://w3id.org/mixs/vocab/nucl_acid_amp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nucleic acid amplification | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Preferred unit: | +| | | Position: 38.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='https://phylogenomics.me/protocols/16s-pcr-protocol/', description=None) | + diff --git a/mixs6/nucl_acid_ext.md b/mixs6/nucl_acid_ext.md new file mode 100644 index 00000000..4c7237fd --- /dev/null +++ b/mixs6/nucl_acid_ext.md @@ -0,0 +1,56 @@ + +# Slot: nucl_acid_ext + + +A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + +URI: [mixs.vocab:nucl_acid_ext](https://w3id.org/mixs/vocab/nucl_acid_ext) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | nucleic acid extraction | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Preferred unit: | +| | | Position: 37.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf', description=None) | + diff --git a/mixs6/nucleic_acid_sequence_source_field.md b/mixs6/nucleic_acid_sequence_source_field.md new file mode 100644 index 00000000..72cb32c1 --- /dev/null +++ b/mixs6/nucleic_acid_sequence_source_field.md @@ -0,0 +1,44 @@ + +# Slot: nucleic_acid_sequence_source_field + + + + +URI: [mixs.vocab:nucleic_acid_sequence_source_field](https://w3id.org/mixs/vocab/nucleic_acid_sequence_source_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [biotic_relationship](biotic_relationship.md) + * [encoded_traits](encoded_traits.md) + * [estimated_size](estimated_size.md) + * [extrachrom_elements](extrachrom_elements.md) + * [health_disease_stat](health_disease_stat.md) + * [host_spec_range](host_spec_range.md) + * [isol_growth_condt](isol_growth_condt.md) + * [num_replicons](num_replicons.md) + * [pathogenicity](pathogenicity.md) + * [ploidy](ploidy.md) + * [propagation](propagation.md) + * [ref_biomaterial](ref_biomaterial.md) + * [rel_to_oxygen](rel_to_oxygen.md) + * [samp_collect_device](samp_collect_device.md) + * [samp_mat_process](samp_mat_process.md) + * [samp_size](samp_size.md) + * [size_frac](size_frac.md) + * [source_mat_id](source_mat_id.md) + * [source_uvig](source_uvig.md) + * [specific_host](specific_host.md) + * [subspecf_gen_lin](subspecf_gen_lin.md) + * [trophic_level](trophic_level.md) + * [virus_enrich_appr](virus_enrich_appr.md) + +## Used by + diff --git a/mixs6/num_replicons.md b/mixs6/num_replicons.md new file mode 100644 index 00000000..240dff21 --- /dev/null +++ b/mixs6/num_replicons.md @@ -0,0 +1,56 @@ + +# Slot: num_replicons + + +Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + +URI: [mixs.vocab:num_replicons](https://w3id.org/mixs/vocab/num_replicons) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of replicons | +| **Comments:** | | Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments | +| | | Preferred unit: | +| | | Position: 16.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='2', description=None) | + diff --git a/mixs6/number_contig.md b/mixs6/number_contig.md new file mode 100644 index 00000000..c141d738 --- /dev/null +++ b/mixs6/number_contig.md @@ -0,0 +1,56 @@ + +# Slot: number_contig + + +Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + +URI: [mixs.vocab:number_contig](https://w3id.org/mixs/vocab/number_contig) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of contigs | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Position: 58.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='40', description=None) | + diff --git a/mixs6/number_pets.md b/mixs6/number_pets.md new file mode 100644 index 00000000..c4df6476 --- /dev/null +++ b/mixs6/number_pets.md @@ -0,0 +1,48 @@ + +# Slot: number_pets + + +The number of pets residing in the sampled space + +URI: [mixs.vocab:number_pets](https://w3id.org/mixs/vocab/number_pets) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of pets | +| **Mappings:** | | MIXS:0000231 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 93 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/number_plants.md b/mixs6/number_plants.md new file mode 100644 index 00000000..9700fafa --- /dev/null +++ b/mixs6/number_plants.md @@ -0,0 +1,48 @@ + +# Slot: number_plants + + +The number of plant(s) in the sampling space + +URI: [mixs.vocab:number_plants](https://w3id.org/mixs/vocab/number_plants) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of houseplants | +| **Mappings:** | | MIXS:0000230 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 92 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/number_resident.md b/mixs6/number_resident.md new file mode 100644 index 00000000..91b2876e --- /dev/null +++ b/mixs6/number_resident.md @@ -0,0 +1,48 @@ + +# Slot: number_resident + + +The number of individuals currently occupying in the sampling location + +URI: [mixs.vocab:number_resident](https://w3id.org/mixs/vocab/number_resident) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of residents | +| **Mappings:** | | MIXS:0000232 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 94 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/occup_density_samp.md b/mixs6/occup_density_samp.md new file mode 100644 index 00000000..f6deb0b9 --- /dev/null +++ b/mixs6/occup_density_samp.md @@ -0,0 +1,48 @@ + +# Slot: occup_density_samp + + +Average number of occupants at time of sampling per square footage + +URI: [mixs.vocab:occup_density_samp](https://w3id.org/mixs/vocab/occup_density_samp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupant density at sampling | +| **Mappings:** | | MIXS:0000217 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 26 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/occup_document.md b/mixs6/occup_document.md new file mode 100644 index 00000000..40548460 --- /dev/null +++ b/mixs6/occup_document.md @@ -0,0 +1,48 @@ + +# Slot: occup_document + + +The type of documentation of occupancy + +URI: [mixs.vocab:occup_document](https://w3id.org/mixs/vocab/occup_document) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupancy documentation | +| **Mappings:** | | MIXS:0000816 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 95 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='estimate', description=None) | + diff --git a/mixs6/occup_samp.md b/mixs6/occup_samp.md new file mode 100644 index 00000000..a1743786 --- /dev/null +++ b/mixs6/occup_samp.md @@ -0,0 +1,48 @@ + +# Slot: occup_samp + + +Number of occupants present at time of sample within the given space + +URI: [mixs.vocab:occup_samp](https://w3id.org/mixs/vocab/occup_samp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | occupancy at sampling | +| **Mappings:** | | MIXS:0000772 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 25 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='10', description=None) | + diff --git a/mixs6/org_carb.md b/mixs6/org_carb.md new file mode 100644 index 00000000..bf68047e --- /dev/null +++ b/mixs6/org_carb.md @@ -0,0 +1,84 @@ + +# Slot: org_carb + + +Concentration of organic carbon + +URI: [mixs.vocab:org_carb](https://w3id.org/mixs/vocab/org_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic carbon | +| **Mappings:** | | MIXS:0000508 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.5 microgram per liter', description=None) | + diff --git a/mixs6/org_matter.md b/mixs6/org_matter.md new file mode 100644 index 00000000..131b55fd --- /dev/null +++ b/mixs6/org_matter.md @@ -0,0 +1,84 @@ + +# Slot: org_matter + + +Concentration of organic matter + +URI: [mixs.vocab:org_matter](https://w3id.org/mixs/vocab/org_matter) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic matter | +| **Mappings:** | | MIXS:0000204 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='1.75 milligram per cubic meter', description=None) | + diff --git a/mixs6/org_nitro.md b/mixs6/org_nitro.md new file mode 100644 index 00000000..654dd377 --- /dev/null +++ b/mixs6/org_nitro.md @@ -0,0 +1,84 @@ + +# Slot: org_nitro + + +Concentration of organic nitrogen + +URI: [mixs.vocab:org_nitro](https://w3id.org/mixs/vocab/org_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic nitrogen | +| **Mappings:** | | MIXS:0000205 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='4 micromole per liter', description=None) | + diff --git a/mixs6/org_particles.md b/mixs6/org_particles.md new file mode 100644 index 00000000..8be37984 --- /dev/null +++ b/mixs6/org_particles.md @@ -0,0 +1,48 @@ + +# Slot: org_particles + + +Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + +URI: [mixs.vocab:org_particles](https://w3id.org/mixs/vocab/org_particles) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organic particles | +| **Mappings:** | | MIXS:0000665 | +| **Comments:** | | Expected value: particle name;measurement value | +| | | Preferred unit: gram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/organism_count.md b/mixs6/organism_count.md new file mode 100644 index 00000000..50cdcbfb --- /dev/null +++ b/mixs6/organism_count.md @@ -0,0 +1,228 @@ + +# Slot: organism_count + + +Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + +URI: [mixs.vocab:organism_count](https://w3id.org/mixs/vocab/organism_count) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organism count | +| **Mappings:** | | MIXS:0000103 | +| **Comments:** | | Expected value: organism name;measurement value;enumeration | +| | | Preferred unit: number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 16 packages: air, built environment, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='total prokaryotes;3.5e7 cells per milliliter;qPCR', description=None) | + diff --git a/mixs6/organism_count_qpcr_info.md b/mixs6/organism_count_qpcr_info.md new file mode 100644 index 00000000..3969c83d --- /dev/null +++ b/mixs6/organism_count_qpcr_info.md @@ -0,0 +1,60 @@ + +# Slot: organism_count_qpcr_info + + +If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + +URI: [mixs.vocab:organism_count_qpcr_info](https://w3id.org/mixs/vocab/organism_count_qpcr_info) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | organism count qPCR information | +| **Mappings:** | | MIXS:0000099 | +| **Comments:** | | Expected value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles | +| | | Preferred unit: number of cells per gram (or ml or cm^2) | +| | | Occurrence: 1 | +| | | Position: 53 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/owc_tvdss.md b/mixs6/owc_tvdss.md new file mode 100644 index 00000000..bb0c5628 --- /dev/null +++ b/mixs6/owc_tvdss.md @@ -0,0 +1,48 @@ + +# Slot: owc_tvdss + + +Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + +URI: [mixs.vocab:owc_tvdss](https://w3id.org/mixs/vocab/owc_tvdss) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oil water contact depth | +| **Mappings:** | | MIXS:0000405 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 15 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/oxy_stat_samp.md b/mixs6/oxy_stat_samp.md new file mode 100644 index 00000000..e4d6aa26 --- /dev/null +++ b/mixs6/oxy_stat_samp.md @@ -0,0 +1,216 @@ + +# Slot: oxy_stat_samp + + +Oxygenation status of sample + +URI: [mixs.vocab:oxy_stat_samp](https://w3id.org/mixs/vocab/oxy_stat_samp) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oxygenation status of sample | +| **Mappings:** | | MIXS:0000753 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='aerobic', description=None) | + diff --git a/mixs6/oxygen.md b/mixs6/oxygen.md new file mode 100644 index 00000000..aff04179 --- /dev/null +++ b/mixs6/oxygen.md @@ -0,0 +1,48 @@ + +# Slot: oxygen + + +Oxygen (gas) amount or concentration at the time of sampling + +URI: [mixs.vocab:oxygen](https://w3id.org/mixs/vocab/oxygen) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | oxygen | +| **Mappings:** | | MIXS:0000104 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='600 parts per million', description=None) | + diff --git a/mixs6/part_org_carb.md b/mixs6/part_org_carb.md new file mode 100644 index 00000000..17801662 --- /dev/null +++ b/mixs6/part_org_carb.md @@ -0,0 +1,72 @@ + +# Slot: part_org_carb + + +Concentration of particulate organic carbon + +URI: [mixs.vocab:part_org_carb](https://w3id.org/mixs/vocab/part_org_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particulate organic carbon | +| **Mappings:** | | MIXS:0000515 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='1.92 micromole per liter', description=None) | + diff --git a/mixs6/part_org_nitro.md b/mixs6/part_org_nitro.md new file mode 100644 index 00000000..15fa76c5 --- /dev/null +++ b/mixs6/part_org_nitro.md @@ -0,0 +1,48 @@ + +# Slot: part_org_nitro + + +Concentration of particulate organic nitrogen + +URI: [mixs.vocab:part_org_nitro](https://w3id.org/mixs/vocab/part_org_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particulate organic nitrogen | +| **Mappings:** | | MIXS:0000719 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.3 micromole per liter', description=None) | + diff --git a/mixs6/particle_class.md b/mixs6/particle_class.md new file mode 100644 index 00000000..3192bef6 --- /dev/null +++ b/mixs6/particle_class.md @@ -0,0 +1,48 @@ + +# Slot: particle_class + + +Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + +URI: [mixs.vocab:particle_class](https://w3id.org/mixs/vocab/particle_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | particle classification | +| **Mappings:** | | MIXS:0000206 | +| **Comments:** | | Expected value: particle name;measurement value | +| | | Preferred unit: micrometer | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pathogenicity.md b/mixs6/pathogenicity.md new file mode 100644 index 00000000..8661f343 --- /dev/null +++ b/mixs6/pathogenicity.md @@ -0,0 +1,56 @@ + +# Slot: pathogenicity + + +To what is the entity pathogenic + +URI: [mixs.vocab:pathogenicity](https://w3id.org/mixs/vocab/pathogenicity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | known pathogenicity | +| **Comments:** | | Expected value: names of organisms that the entity is pathogenic to | +| | | Preferred unit: | +| | | Position: 21.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='human, animal, plant, fungi, bacteria', description=None) | + diff --git a/mixs6/pcr_cond.md b/mixs6/pcr_cond.md new file mode 100644 index 00000000..eb55d623 --- /dev/null +++ b/mixs6/pcr_cond.md @@ -0,0 +1,56 @@ + +# Slot: pcr_cond + + +Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + +URI: [mixs.vocab:pcr_cond](https://w3id.org/mixs/vocab/pcr_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pcr conditions | +| **Comments:** | | Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles | +| | | Preferred unit: | +| | | Position: 49.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35', description=None) | + diff --git a/mixs6/pcr_primers.md b/mixs6/pcr_primers.md new file mode 100644 index 00000000..1ca7877c --- /dev/null +++ b/mixs6/pcr_primers.md @@ -0,0 +1,56 @@ + +# Slot: pcr_primers + + +PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + +URI: [mixs.vocab:pcr_primers](https://w3id.org/mixs/vocab/pcr_primers) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pcr primers | +| **Comments:** | | Expected value: FWD: forward primer sequence;REV:reverse primer sequence | +| | | Preferred unit: | +| | | Position: 46.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT', description=None) | + diff --git a/mixs6/permeability.md b/mixs6/permeability.md new file mode 100644 index 00000000..590c17c2 --- /dev/null +++ b/mixs6/permeability.md @@ -0,0 +1,48 @@ + +# Slot: permeability + + +Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + +URI: [mixs.vocab:permeability](https://w3id.org/mixs/vocab/permeability) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | permeability | +| **Mappings:** | | MIXS:0000404 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: mD | +| | | Occurrence: 1 | +| | | Position: 10 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/perturbation.md b/mixs6/perturbation.md new file mode 100644 index 00000000..b53feaf9 --- /dev/null +++ b/mixs6/perturbation.md @@ -0,0 +1,192 @@ + +# Slot: perturbation + + +Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + +URI: [mixs.vocab:perturbation](https://w3id.org/mixs/vocab/perturbation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | perturbation | +| **Mappings:** | | MIXS:0000754 | +| **Comments:** | | Expected value: perturbation type name;perturbation interval and duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M', description=None) | + diff --git a/mixs6/pesticide_regm.md b/mixs6/pesticide_regm.md new file mode 100644 index 00000000..05c8b2e4 --- /dev/null +++ b/mixs6/pesticide_regm.md @@ -0,0 +1,48 @@ + +# Slot: pesticide_regm + + +Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + +URI: [mixs.vocab:pesticide_regm](https://w3id.org/mixs/vocab/pesticide_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pesticide regimen | +| **Mappings:** | | MIXS:0000573 | +| **Comments:** | | Expected value: pesticide name;pesticide amount;treatment interval and duration | +| | | Preferred unit: gram, mole per liter, milligram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/pet_farm_animal.md b/mixs6/pet_farm_animal.md new file mode 100644 index 00000000..90f7bfd0 --- /dev/null +++ b/mixs6/pet_farm_animal.md @@ -0,0 +1,48 @@ + +# Slot: pet_farm_animal + + +Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + +URI: [mixs.vocab:pet_farm_animal](https://w3id.org/mixs/vocab/pet_farm_animal) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | presence of pets or farm animals | +| **Mappings:** | | MIXS:0000267 | +| **Comments:** | | Expected value: presence status;type of animal or pet | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 25 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes; 5 cats', description=None) | + diff --git a/mixs6/petroleum_hydrocarb.md b/mixs6/petroleum_hydrocarb.md new file mode 100644 index 00000000..6bd7441f --- /dev/null +++ b/mixs6/petroleum_hydrocarb.md @@ -0,0 +1,72 @@ + +# Slot: petroleum_hydrocarb + + +Concentration of petroleum hydrocarbon + +URI: [mixs.vocab:petroleum_hydrocarb](https://w3id.org/mixs/vocab/petroleum_hydrocarb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | petroleum hydrocarbon | +| **Mappings:** | | MIXS:0000516 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/ph.md b/mixs6/ph.md new file mode 100644 index 00000000..2bf00497 --- /dev/null +++ b/mixs6/ph.md @@ -0,0 +1,132 @@ + +# Slot: ph + + +Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + +URI: [mixs.vocab:ph](https://w3id.org/mixs/vocab/ph) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH | +| **Mappings:** | | MIXS:0001001 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 54 | +| | | This field is used in: 8 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='7.2', description=None) | + diff --git a/mixs6/ph_meth.md b/mixs6/ph_meth.md new file mode 100644 index 00000000..54d63510 --- /dev/null +++ b/mixs6/ph_meth.md @@ -0,0 +1,48 @@ + +# Slot: ph_meth + + +Reference or method used in determining ph + +URI: [mixs.vocab:ph_meth](https://w3id.org/mixs/vocab/ph_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH method | +| **Mappings:** | | MIXS:0001106 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 38 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ph_regm.md b/mixs6/ph_regm.md new file mode 100644 index 00000000..828e21cb --- /dev/null +++ b/mixs6/ph_regm.md @@ -0,0 +1,48 @@ + +# Slot: ph_regm + + +Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + +URI: [mixs.vocab:ph_regm](https://w3id.org/mixs/vocab/ph_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pH regimen | +| **Mappings:** | | MIXS:0001056 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/phaeopigments.md b/mixs6/phaeopigments.md new file mode 100644 index 00000000..868a5581 --- /dev/null +++ b/mixs6/phaeopigments.md @@ -0,0 +1,72 @@ + +# Slot: phaeopigments + + +Concentration of phaeopigments; can include multiple phaeopigments + +URI: [mixs.vocab:phaeopigments](https://w3id.org/mixs/vocab/phaeopigments) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phaeopigments | +| **Mappings:** | | MIXS:0000180 | +| **Comments:** | | Expected value: phaeopigment name;measurement value | +| | | Preferred unit: milligram per cubic meter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='2.5 milligram per cubic meter', description=None) | + diff --git a/mixs6/phosphate.md b/mixs6/phosphate.md new file mode 100644 index 00000000..6b593edb --- /dev/null +++ b/mixs6/phosphate.md @@ -0,0 +1,96 @@ + +# Slot: phosphate + + +Concentration of phosphate + +URI: [mixs.vocab:phosphate](https://w3id.org/mixs/vocab/phosphate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phosphate | +| **Mappings:** | | MIXS:0000505 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 5 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='0.7 micromole per liter', description=None) | + diff --git a/mixs6/phosplipid_fatt_acid.md b/mixs6/phosplipid_fatt_acid.md new file mode 100644 index 00000000..9843e722 --- /dev/null +++ b/mixs6/phosplipid_fatt_acid.md @@ -0,0 +1,84 @@ + +# Slot: phosplipid_fatt_acid + + +Concentration of phospholipid fatty acids; can include multiple values + +URI: [mixs.vocab:phosplipid_fatt_acid](https://w3id.org/mixs/vocab/phosplipid_fatt_acid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | phospholipid fatty acid | +| **Mappings:** | | MIXS:0000181 | +| **Comments:** | | Expected value: phospholipid fatty acid name;measurement value | +| | | Preferred unit: mole per gram, mole per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2.98 milligram per liter', description=None) | + diff --git a/mixs6/photon_flux.md b/mixs6/photon_flux.md new file mode 100644 index 00000000..4077b70d --- /dev/null +++ b/mixs6/photon_flux.md @@ -0,0 +1,48 @@ + +# Slot: photon_flux + + +Measurement of photon flux + +URI: [mixs.vocab:photon_flux](https://w3id.org/mixs/vocab/photon_flux) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | photon flux | +| **Mappings:** | | MIXS:0000725 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: number of photons per second per unit area | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='3.926 micromole photons per second per square meter', description=None) | + diff --git a/mixs6/plant_growth_med.md b/mixs6/plant_growth_med.md new file mode 100644 index 00000000..958733c5 --- /dev/null +++ b/mixs6/plant_growth_med.md @@ -0,0 +1,48 @@ + +# Slot: plant_growth_med + + +Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + +URI: [mixs.vocab:plant_growth_med](https://w3id.org/mixs/vocab/plant_growth_med) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant growth medium | +| **Mappings:** | | MIXS:0001057 | +| **Comments:** | | Expected value: EO or enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='hydroponic plant culture media [EO:0007067]', description=None) | + diff --git a/mixs6/plant_product.md b/mixs6/plant_product.md new file mode 100644 index 00000000..625a85bf --- /dev/null +++ b/mixs6/plant_product.md @@ -0,0 +1,48 @@ + +# Slot: plant_product + + +Substance produced by the plant, where the sample was obtained from + +URI: [mixs.vocab:plant_product](https://w3id.org/mixs/vocab/plant_product) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant product | +| **Mappings:** | | MIXS:0001058 | +| **Comments:** | | Expected value: product name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='xylem sap [PO:0025539]', description=None) | + diff --git a/mixs6/plant_sex.md b/mixs6/plant_sex.md new file mode 100644 index 00000000..b49c67a4 --- /dev/null +++ b/mixs6/plant_sex.md @@ -0,0 +1,48 @@ + +# Slot: plant_sex + + +Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + +URI: [mixs.vocab:plant_sex](https://w3id.org/mixs/vocab/plant_sex) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant sex | +| **Mappings:** | | MIXS:0001059 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='Hermaphroditic', description=None) | + diff --git a/mixs6/plant_struc.md b/mixs6/plant_struc.md new file mode 100644 index 00000000..13195696 --- /dev/null +++ b/mixs6/plant_struc.md @@ -0,0 +1,48 @@ + +# Slot: plant_struc + + +Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + +URI: [mixs.vocab:plant_struc](https://w3id.org/mixs/vocab/plant_struc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | plant structure | +| **Mappings:** | | MIXS:0001060 | +| **Comments:** | | Expected value: PO | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='epidermis [PO:0005679]', description=None) | + diff --git a/mixs6/ploidy.md b/mixs6/ploidy.md new file mode 100644 index 00000000..f1594aa1 --- /dev/null +++ b/mixs6/ploidy.md @@ -0,0 +1,56 @@ + +# Slot: ploidy + + +The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + +URI: [mixs.vocab:ploidy](https://w3id.org/mixs/vocab/ploidy) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ploidy | +| **Comments:** | | Expected value: PATO | +| | | Preferred unit: | +| | | Position: 15.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='allopolyploidy [PATO:0001379]', description=None) | + diff --git a/mixs6/pollutants.md b/mixs6/pollutants.md new file mode 100644 index 00000000..cda94787 --- /dev/null +++ b/mixs6/pollutants.md @@ -0,0 +1,48 @@ + +# Slot: pollutants + + +Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + +URI: [mixs.vocab:pollutants](https://w3id.org/mixs/vocab/pollutants) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pollutants | +| **Mappings:** | | MIXS:0000107 | +| **Comments:** | | Expected value: pollutant name;measurement value | +| | | Preferred unit: gram, mole per liter, milligram per liter, microgram per cubic meter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='lead;0.15 microgram per cubic meter', description=None) | + diff --git a/mixs6/pool_dna_extracts.md b/mixs6/pool_dna_extracts.md new file mode 100644 index 00000000..271b6e7d --- /dev/null +++ b/mixs6/pool_dna_extracts.md @@ -0,0 +1,48 @@ + +# Slot: pool_dna_extracts + + +Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + +URI: [mixs.vocab:pool_dna_extracts](https://w3id.org/mixs/vocab/pool_dna_extracts) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pooling of DNA extracts (if done) | +| **Mappings:** | | MIXS:0000325 | +| **Comments:** | | Expected value: pooling status;number of pooled extracts | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 18 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='yes;5', description=None) | + diff --git a/mixs6/porosity.md b/mixs6/porosity.md new file mode 100644 index 00000000..894d5057 --- /dev/null +++ b/mixs6/porosity.md @@ -0,0 +1,60 @@ + +# Slot: porosity + + +Porosity of deposited sediment is volume of voids divided by the total volume of sample + +URI: [mixs.vocab:porosity](https://w3id.org/mixs/vocab/porosity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | porosity | +| **Mappings:** | | MIXS:0000211 | +| **Comments:** | | Expected value: measurement value or range | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 11 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/potassium.md b/mixs6/potassium.md new file mode 100644 index 00000000..bae598aa --- /dev/null +++ b/mixs6/potassium.md @@ -0,0 +1,108 @@ + +# Slot: potassium + + +Concentration of potassium in the sample + +URI: [mixs.vocab:potassium](https://w3id.org/mixs/vocab/potassium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | potassium | +| **Mappings:** | | MIXS:0000430 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 68 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='463 milligram per liter', description=None) | + diff --git a/mixs6/pour_point.md b/mixs6/pour_point.md new file mode 100644 index 00000000..c25634ce --- /dev/null +++ b/mixs6/pour_point.md @@ -0,0 +1,60 @@ + +# Slot: pour_point + + +Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + +URI: [mixs.vocab:pour_point](https://w3id.org/mixs/vocab/pour_point) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pour point | +| **Mappings:** | | MIXS:0000127 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 88 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pre_treatment.md b/mixs6/pre_treatment.md new file mode 100644 index 00000000..22e5b57a --- /dev/null +++ b/mixs6/pre_treatment.md @@ -0,0 +1,48 @@ + +# Slot: pre_treatment + + +The process of pre-treatment removes materials that can be easily collected from the raw wastewater + +URI: [mixs.vocab:pre_treatment](https://w3id.org/mixs/vocab/pre_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pre-treatment | +| **Mappings:** | | MIXS:0000348 | +| **Comments:** | | Expected value: pre-treatment type | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/pred_genome_struc.md b/mixs6/pred_genome_struc.md new file mode 100644 index 00000000..45d11946 --- /dev/null +++ b/mixs6/pred_genome_struc.md @@ -0,0 +1,56 @@ + +# Slot: pred_genome_struc + + +Expected structure of the viral genome + +URI: [mixs.vocab:pred_genome_struc](https://w3id.org/mixs/vocab/pred_genome_struc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | predicted genome structure | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 85.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='non-segmented', description=None) | + diff --git a/mixs6/pred_genome_type.md b/mixs6/pred_genome_type.md new file mode 100644 index 00000000..5af23f27 --- /dev/null +++ b/mixs6/pred_genome_type.md @@ -0,0 +1,56 @@ + +# Slot: pred_genome_type + + +Type of genome predicted for the UViG + +URI: [mixs.vocab:pred_genome_type](https://w3id.org/mixs/vocab/pred_genome_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | predicted genome type | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 84.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='dsDNA', description=None) | + diff --git a/mixs6/pregnancy.md b/mixs6/pregnancy.md new file mode 100644 index 00000000..1ae70257 --- /dev/null +++ b/mixs6/pregnancy.md @@ -0,0 +1,48 @@ + +# Slot: pregnancy + + +Date due of pregnancy + +URI: [mixs.vocab:pregnancy](https://w3id.org/mixs/vocab/pregnancy) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pregnancy | +| **Mappings:** | | MIXS:0000966 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/pres_animal.md b/mixs6/pres_animal.md new file mode 100644 index 00000000..3fb3fff5 --- /dev/null +++ b/mixs6/pres_animal.md @@ -0,0 +1,48 @@ + +# Slot: pres_animal + + +The number and type of animals present in the sampling space + +URI: [mixs.vocab:pres_animal](https://w3id.org/mixs/vocab/pres_animal) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | presence of pets, animals, or insects | +| **Mappings:** | | MIXS:0000819 | +| **Comments:** | | Expected value: enumeration;count | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 99 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='cat;5', description=None) | + diff --git a/mixs6/pressure.md b/mixs6/pressure.md new file mode 100644 index 00000000..ec66800a --- /dev/null +++ b/mixs6/pressure.md @@ -0,0 +1,108 @@ + +# Slot: pressure + + +Pressure to which the sample is subject to, in atmospheres + +URI: [mixs.vocab:pressure](https://w3id.org/mixs/vocab/pressure) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | pressure | +| **Mappings:** | | MIXS:0000412 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: atmosphere | +| | | Occurrence: 1 | +| | | Position: 41 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='50 atmosphere', description=None) | + diff --git a/mixs6/previous_land_use.md b/mixs6/previous_land_use.md new file mode 100644 index 00000000..d8ba829b --- /dev/null +++ b/mixs6/previous_land_use.md @@ -0,0 +1,48 @@ + +# Slot: previous_land_use + + +Previous land use and dates + +URI: [mixs.vocab:previous_land_use](https://w3id.org/mixs/vocab/previous_land_use) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/previous land use | +| **Mappings:** | | MIXS:0000315 | +| **Comments:** | | Expected value: land use name;date | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 4 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/previous_land_use_meth.md b/mixs6/previous_land_use_meth.md new file mode 100644 index 00000000..7b0fa348 --- /dev/null +++ b/mixs6/previous_land_use_meth.md @@ -0,0 +1,48 @@ + +# Slot: previous_land_use_meth + + +Reference or method used in determining previous land use and dates + +URI: [mixs.vocab:previous_land_use_meth](https://w3id.org/mixs/vocab/previous_land_use_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/previous land use method | +| **Mappings:** | | MIXS:0000316 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 5 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/primary_prod.md b/mixs6/primary_prod.md new file mode 100644 index 00000000..01855825 --- /dev/null +++ b/mixs6/primary_prod.md @@ -0,0 +1,48 @@ + +# Slot: primary_prod + + +Measurement of primary production, generally measured as isotope uptake + +URI: [mixs.vocab:primary_prod](https://w3id.org/mixs/vocab/primary_prod) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | primary production | +| **Mappings:** | | MIXS:0000728 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per cubic meter per day, gram per square meter per day | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='100 milligram per cubic meter per day', description=None) | + diff --git a/mixs6/primary_treatment.md b/mixs6/primary_treatment.md new file mode 100644 index 00000000..fd505f46 --- /dev/null +++ b/mixs6/primary_treatment.md @@ -0,0 +1,48 @@ + +# Slot: primary_treatment + + +The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + +URI: [mixs.vocab:primary_treatment](https://w3id.org/mixs/vocab/primary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | primary treatment | +| **Mappings:** | | MIXS:0000349 | +| **Comments:** | | Expected value: primary treatment type | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/prod_rate.md b/mixs6/prod_rate.md new file mode 100644 index 00000000..18ca9191 --- /dev/null +++ b/mixs6/prod_rate.md @@ -0,0 +1,48 @@ + +# Slot: prod_rate + + +Oil and/or gas production rates per well (e.g. 524 m3 / day) + +URI: [mixs.vocab:prod_rate](https://w3id.org/mixs/vocab/prod_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | production rate | +| **Mappings:** | | MIXS:0000452 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 24 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/prod_start_date.md b/mixs6/prod_start_date.md new file mode 100644 index 00000000..ca0c9434 --- /dev/null +++ b/mixs6/prod_start_date.md @@ -0,0 +1,48 @@ + +# Slot: prod_start_date + + +Date of field's first production + +URI: [mixs.vocab:prod_start_date](https://w3id.org/mixs/vocab/prod_start_date) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | production start date | +| **Mappings:** | | MIXS:0001008 | +| **Comments:** | | Expected value: timestamp | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 23 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='2018-05-11', description=None) | + diff --git a/mixs6/profile_position.md b/mixs6/profile_position.md new file mode 100644 index 00000000..4af8338c --- /dev/null +++ b/mixs6/profile_position.md @@ -0,0 +1,48 @@ + +# Slot: profile_position + + +Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + +URI: [mixs.vocab:profile_position](https://w3id.org/mixs/vocab/profile_position) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | profile position | +| **Mappings:** | | MIXS:0001084 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 33 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='summit', description=None) | + diff --git a/mixs6/project_name.md b/mixs6/project_name.md new file mode 100644 index 00000000..0df86d42 --- /dev/null +++ b/mixs6/project_name.md @@ -0,0 +1,56 @@ + +# Slot: project_name + + +Name of the project within which the sequencing was organized + +URI: [mixs.vocab:project_name](https://w3id.org/mixs/vocab/project_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | project name | +| **Comments:** | | Expected value: | +| | | Preferred unit: | +| | | Position: 3.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='Forest soil metagenome', description=None) | + diff --git a/mixs6/propagation.md b/mixs6/propagation.md new file mode 100644 index 00000000..1a4b8ca0 --- /dev/null +++ b/mixs6/propagation.md @@ -0,0 +1,56 @@ + +# Slot: propagation + + +This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + +URI: [mixs.vocab:propagation](https://w3id.org/mixs/vocab/propagation) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | propagation | +| **Comments:** | | Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual | +| | | Preferred unit: | +| | | Position: 27.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='lytic', description=None) | + diff --git a/mixs6/pulmonary_disord.md b/mixs6/pulmonary_disord.md new file mode 100644 index 00000000..7c59f603 --- /dev/null +++ b/mixs6/pulmonary_disord.md @@ -0,0 +1,48 @@ + +# Slot: pulmonary_disord + + +History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + +URI: [mixs.vocab:pulmonary_disord](https://w3id.org/mixs/vocab/pulmonary_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | lung/pulmonary disorder | +| **Mappings:** | | MIXS:0000269 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 30 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/quad_pos.md b/mixs6/quad_pos.md new file mode 100644 index 00000000..0453166d --- /dev/null +++ b/mixs6/quad_pos.md @@ -0,0 +1,48 @@ + +# Slot: quad_pos + + +The quadrant position of the sampling room within the building + +URI: [mixs.vocab:quad_pos](https://w3id.org/mixs/vocab/quad_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | quadrant position | +| **Mappings:** | | MIXS:0000820 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 100 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='West side', description=None) | + diff --git a/mixs6/radiation_regm.md b/mixs6/radiation_regm.md new file mode 100644 index 00000000..a8188981 --- /dev/null +++ b/mixs6/radiation_regm.md @@ -0,0 +1,48 @@ + +# Slot: radiation_regm + + +Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + +URI: [mixs.vocab:radiation_regm](https://w3id.org/mixs/vocab/radiation_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | radiation regimen | +| **Mappings:** | | MIXS:0000575 | +| **Comments:** | | Expected value: radiation type name;radiation amount;treatment interval and duration | +| | | Preferred unit: rad, gray | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/rainfall_regm.md b/mixs6/rainfall_regm.md new file mode 100644 index 00000000..0d96d066 --- /dev/null +++ b/mixs6/rainfall_regm.md @@ -0,0 +1,48 @@ + +# Slot: rainfall_regm + + +Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:rainfall_regm](https://w3id.org/mixs/vocab/rainfall_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rainfall regimen | +| **Mappings:** | | MIXS:0000576 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: millimeter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/reactor_type.md b/mixs6/reactor_type.md new file mode 100644 index 00000000..bc4d59f8 --- /dev/null +++ b/mixs6/reactor_type.md @@ -0,0 +1,48 @@ + +# Slot: reactor_type + + +Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + +URI: [mixs.vocab:reactor_type](https://w3id.org/mixs/vocab/reactor_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reactor type | +| **Mappings:** | | MIXS:0000350 | +| **Comments:** | | Expected value: reactor type name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/reassembly_bin.md b/mixs6/reassembly_bin.md new file mode 100644 index 00000000..e12ede21 --- /dev/null +++ b/mixs6/reassembly_bin.md @@ -0,0 +1,56 @@ + +# Slot: reassembly_bin + + +Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + +URI: [mixs.vocab:reassembly_bin](https://w3id.org/mixs/vocab/reassembly_bin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reassembly post binning | +| **Comments:** | | Expected value: boolean | +| | | Preferred unit: | +| | | Position: 81.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='no', description=None) | + diff --git a/mixs6/redox_potential.md b/mixs6/redox_potential.md new file mode 100644 index 00000000..db022351 --- /dev/null +++ b/mixs6/redox_potential.md @@ -0,0 +1,72 @@ + +# Slot: redox_potential + + +Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + +URI: [mixs.vocab:redox_potential](https://w3id.org/mixs/vocab/redox_potential) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | redox potential | +| **Mappings:** | | MIXS:0000182 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millivolt | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='300 millivolt', description=None) | + diff --git a/mixs6/ref_biomaterial.md b/mixs6/ref_biomaterial.md new file mode 100644 index 00000000..eb708476 --- /dev/null +++ b/mixs6/ref_biomaterial.md @@ -0,0 +1,56 @@ + +# Slot: ref_biomaterial + + +Primary publication if isolated before genome publication; otherwise, primary genome report + +URI: [mixs.vocab:ref_biomaterial](https://w3id.org/mixs/vocab/ref_biomaterial) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reference for biomaterial | +| **Comments:** | | Expected value: PMID, DOI or URL | +| | | Preferred unit: | +| | | Position: 19.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='doi:10.1016/j.syapm.2018.01.009', description=None) | + diff --git a/mixs6/ref_db.md b/mixs6/ref_db.md new file mode 100644 index 00000000..d1450d49 --- /dev/null +++ b/mixs6/ref_db.md @@ -0,0 +1,56 @@ + +# Slot: ref_db + + +List of database(s) used for ORF annotation, along with version number and reference to website or publication + +URI: [mixs.vocab:ref_db](https://w3id.org/mixs/vocab/ref_db) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reference database(s) | +| **Comments:** | | Expected value: names, versions, and references of databases | +| | | Preferred unit: | +| | | Position: 60.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975', description=None) | + diff --git a/mixs6/rel_air_humidity.md b/mixs6/rel_air_humidity.md new file mode 100644 index 00000000..9ebd00a6 --- /dev/null +++ b/mixs6/rel_air_humidity.md @@ -0,0 +1,48 @@ + +# Slot: rel_air_humidity + + +Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + +URI: [mixs.vocab:rel_air_humidity](https://w3id.org/mixs/vocab/rel_air_humidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relative air humidity | +| **Mappings:** | | MIXS:0000121 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 3 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='80%', description=None) | + diff --git a/mixs6/rel_humidity_out.md b/mixs6/rel_humidity_out.md new file mode 100644 index 00000000..50e8665d --- /dev/null +++ b/mixs6/rel_humidity_out.md @@ -0,0 +1,48 @@ + +# Slot: rel_humidity_out + + +The recorded outside relative humidity value at the time of sampling + +URI: [mixs.vocab:rel_humidity_out](https://w3id.org/mixs/vocab/rel_humidity_out) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | outside relative humidity | +| **Mappings:** | | MIXS:0000188 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram of air, kilogram of air | +| | | Occurrence: 1 | +| | | Position: 98 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='12 per kilogram of air', description=None) | + diff --git a/mixs6/rel_samp_loc.md b/mixs6/rel_samp_loc.md new file mode 100644 index 00000000..ee0b20b7 --- /dev/null +++ b/mixs6/rel_samp_loc.md @@ -0,0 +1,48 @@ + +# Slot: rel_samp_loc + + +The sampling location within the train car + +URI: [mixs.vocab:rel_samp_loc](https://w3id.org/mixs/vocab/rel_samp_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relative sampling location | +| **Mappings:** | | MIXS:0000821 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 101 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='center of car', description=None) | + diff --git a/mixs6/rel_to_oxygen.md b/mixs6/rel_to_oxygen.md new file mode 100644 index 00000000..0eb4968e --- /dev/null +++ b/mixs6/rel_to_oxygen.md @@ -0,0 +1,56 @@ + +# Slot: rel_to_oxygen + + +Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + +URI: [mixs.vocab:rel_to_oxygen](https://w3id.org/mixs/vocab/rel_to_oxygen) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relationship to oxygen | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 29.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: X | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='aerobe', description=None) | + diff --git a/mixs6/reservoir.md b/mixs6/reservoir.md new file mode 100644 index 00000000..4a283f36 --- /dev/null +++ b/mixs6/reservoir.md @@ -0,0 +1,60 @@ + +# Slot: reservoir + + +Name of the reservoir (e.g. Carapebus) + +URI: [mixs.vocab:reservoir](https://w3id.org/mixs/vocab/reservoir) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | reservoir name | +| **Mappings:** | | MIXS:0000303 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 5 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/resins_pc.md b/mixs6/resins_pc.md new file mode 100644 index 00000000..04b1a07a --- /dev/null +++ b/mixs6/resins_pc.md @@ -0,0 +1,60 @@ + +# Slot: resins_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:resins_pc](https://w3id.org/mixs/vocab/resins_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | resins wt% | +| **Mappings:** | | MIXS:0000134 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 91 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/resp_part_matter.md b/mixs6/resp_part_matter.md new file mode 100644 index 00000000..93161b5a --- /dev/null +++ b/mixs6/resp_part_matter.md @@ -0,0 +1,48 @@ + +# Slot: resp_part_matter + + +Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + +URI: [mixs.vocab:resp_part_matter](https://w3id.org/mixs/vocab/resp_part_matter) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | respirable particulate matter | +| **Mappings:** | | MIXS:0000108 | +| **Comments:** | | Expected value: particulate matter name;measurement value | +| | | Preferred unit: microgram per cubic meter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='PM2.5;10 microgram per cubic meter', description=None) | + diff --git a/mixs6/room_air_exch_rate.md b/mixs6/room_air_exch_rate.md new file mode 100644 index 00000000..9aea04d2 --- /dev/null +++ b/mixs6/room_air_exch_rate.md @@ -0,0 +1,48 @@ + +# Slot: room_air_exch_rate + + +The rate at which outside air replaces indoor air in a given space + +URI: [mixs.vocab:room_air_exch_rate](https://w3id.org/mixs/vocab/room_air_exch_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room air exchange rate | +| **Mappings:** | | MIXS:0000169 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: liter per hour | +| | | Occurrence: 1 | +| | | Position: 102 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_architec_element.md b/mixs6/room_architec_element.md new file mode 100644 index 00000000..dfa6caf5 --- /dev/null +++ b/mixs6/room_architec_element.md @@ -0,0 +1,48 @@ + +# Slot: room_architec_element + + +The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + +URI: [mixs.vocab:room_architec_element](https://w3id.org/mixs/vocab/room_architec_element) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room architectural elements | +| **Mappings:** | | MIXS:0000233 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 103 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_condt.md b/mixs6/room_condt.md new file mode 100644 index 00000000..cfff06fb --- /dev/null +++ b/mixs6/room_condt.md @@ -0,0 +1,48 @@ + +# Slot: room_condt + + +The condition of the room at the time of sampling + +URI: [mixs.vocab:room_condt](https://w3id.org/mixs/vocab/room_condt) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room condition | +| **Mappings:** | | MIXS:0000822 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 104 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/room_connected.md b/mixs6/room_connected.md new file mode 100644 index 00000000..1424b527 --- /dev/null +++ b/mixs6/room_connected.md @@ -0,0 +1,48 @@ + +# Slot: room_connected + + +List of rooms connected to the sampling room by a doorway + +URI: [mixs.vocab:room_connected](https://w3id.org/mixs/vocab/room_connected) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms connected by a doorway | +| **Mappings:** | | MIXS:0000826 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 116 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='office', description=None) | + diff --git a/mixs6/room_count.md b/mixs6/room_count.md new file mode 100644 index 00000000..1de37476 --- /dev/null +++ b/mixs6/room_count.md @@ -0,0 +1,48 @@ + +# Slot: room_count + + +The total count of rooms in the built structure including all room types + +URI: [mixs.vocab:room_count](https://w3id.org/mixs/vocab/room_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room count | +| **Mappings:** | | MIXS:0000234 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 105 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_dim.md b/mixs6/room_dim.md new file mode 100644 index 00000000..7ced664d --- /dev/null +++ b/mixs6/room_dim.md @@ -0,0 +1,48 @@ + +# Slot: room_dim + + +The length, width and height of sampling room + +URI: [mixs.vocab:room_dim](https://w3id.org/mixs/vocab/room_dim) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room dimensions | +| **Mappings:** | | MIXS:0000192 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 106 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_door_dist.md b/mixs6/room_door_dist.md new file mode 100644 index 00000000..8d4f36fa --- /dev/null +++ b/mixs6/room_door_dist.md @@ -0,0 +1,48 @@ + +# Slot: room_door_dist + + +Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + +URI: [mixs.vocab:room_door_dist](https://w3id.org/mixs/vocab/room_door_dist) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room door distance | +| **Mappings:** | | MIXS:0000193 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 107 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_door_share.md b/mixs6/room_door_share.md new file mode 100644 index 00000000..4bc1e713 --- /dev/null +++ b/mixs6/room_door_share.md @@ -0,0 +1,48 @@ + +# Slot: room_door_share + + +List of room(s) (room number, room name) sharing a door with the sampling room + +URI: [mixs.vocab:room_door_share](https://w3id.org/mixs/vocab/room_door_share) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that share a door with sampling room | +| **Mappings:** | | MIXS:0000242 | +| **Comments:** | | Expected value: room name;room number | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 118 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_hallway.md b/mixs6/room_hallway.md new file mode 100644 index 00000000..f2a23571 --- /dev/null +++ b/mixs6/room_hallway.md @@ -0,0 +1,48 @@ + +# Slot: room_hallway + + +List of room(s) (room number, room name) located in the same hallway as sampling room + +URI: [mixs.vocab:room_hallway](https://w3id.org/mixs/vocab/room_hallway) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that are on the same hallway | +| **Mappings:** | | MIXS:0000238 | +| **Comments:** | | Expected value: room name;room number | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 117 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_loc.md b/mixs6/room_loc.md new file mode 100644 index 00000000..2b3784a1 --- /dev/null +++ b/mixs6/room_loc.md @@ -0,0 +1,48 @@ + +# Slot: room_loc + + +The position of the room within the building + +URI: [mixs.vocab:room_loc](https://w3id.org/mixs/vocab/room_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room location in building | +| **Mappings:** | | MIXS:0000823 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 108 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='interior room', description=None) | + diff --git a/mixs6/room_moist_damage_hist.md b/mixs6/room_moist_damage_hist.md new file mode 100644 index 00000000..c5a5953f --- /dev/null +++ b/mixs6/room_moist_damage_hist.md @@ -0,0 +1,48 @@ + +# Slot: room_moist_damage_hist + + +The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + +URI: [mixs.vocab:room_moist_damage_hist](https://w3id.org/mixs/vocab/room_moist_damage_hist) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room moisture damage or mold history | +| **Mappings:** | | MIXS:0000235 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 109 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_net_area.md b/mixs6/room_net_area.md new file mode 100644 index 00000000..dbaa11b4 --- /dev/null +++ b/mixs6/room_net_area.md @@ -0,0 +1,48 @@ + +# Slot: room_net_area + + +The net floor area of sampling room. Net area excludes wall thicknesses + +URI: [mixs.vocab:room_net_area](https://w3id.org/mixs/vocab/room_net_area) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room net area | +| **Mappings:** | | MIXS:0000194 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square feet, square meter | +| | | Occurrence: 1 | +| | | Position: 110 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_occup.md b/mixs6/room_occup.md new file mode 100644 index 00000000..16a26a99 --- /dev/null +++ b/mixs6/room_occup.md @@ -0,0 +1,48 @@ + +# Slot: room_occup + + +Count of room occupancy at time of sampling + +URI: [mixs.vocab:room_occup](https://w3id.org/mixs/vocab/room_occup) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room occupancy | +| **Mappings:** | | MIXS:0000236 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 111 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_samp_pos.md b/mixs6/room_samp_pos.md new file mode 100644 index 00000000..f2f2039c --- /dev/null +++ b/mixs6/room_samp_pos.md @@ -0,0 +1,48 @@ + +# Slot: room_samp_pos + + +The horizontal sampling position in the room relative to architectural elements + +URI: [mixs.vocab:room_samp_pos](https://w3id.org/mixs/vocab/room_samp_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room sampling position | +| **Mappings:** | | MIXS:0000824 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 112 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='south corner', description=None) | + diff --git a/mixs6/room_type.md b/mixs6/room_type.md new file mode 100644 index 00000000..31daca4d --- /dev/null +++ b/mixs6/room_type.md @@ -0,0 +1,48 @@ + +# Slot: room_type + + +The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + +URI: [mixs.vocab:room_type](https://w3id.org/mixs/vocab/room_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room type | +| **Mappings:** | | MIXS:0000825 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 113 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='bathroom', description=None) | + diff --git a/mixs6/room_vol.md b/mixs6/room_vol.md new file mode 100644 index 00000000..4663e653 --- /dev/null +++ b/mixs6/room_vol.md @@ -0,0 +1,48 @@ + +# Slot: room_vol + + +Volume of sampling room + +URI: [mixs.vocab:room_vol](https://w3id.org/mixs/vocab/room_vol) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room volume | +| **Mappings:** | | MIXS:0000195 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic feet, cubic meter | +| | | Occurrence: 1 | +| | | Position: 114 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_wall_share.md b/mixs6/room_wall_share.md new file mode 100644 index 00000000..6a251043 --- /dev/null +++ b/mixs6/room_wall_share.md @@ -0,0 +1,48 @@ + +# Slot: room_wall_share + + +List of room(s) (room number, room name) sharing a wall with the sampling room + +URI: [mixs.vocab:room_wall_share](https://w3id.org/mixs/vocab/room_wall_share) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooms that share a wall with sampling room | +| **Mappings:** | | MIXS:0000243 | +| **Comments:** | | Expected value: room name;room number | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 119 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/room_window_count.md b/mixs6/room_window_count.md new file mode 100644 index 00000000..111ac2db --- /dev/null +++ b/mixs6/room_window_count.md @@ -0,0 +1,48 @@ + +# Slot: room_window_count + + +Number of windows in the room + +URI: [mixs.vocab:room_window_count](https://w3id.org/mixs/vocab/room_window_count) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | room window count | +| **Mappings:** | | MIXS:0000237 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 115 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/root_cond.md b/mixs6/root_cond.md new file mode 100644 index 00000000..ce56ec62 --- /dev/null +++ b/mixs6/root_cond.md @@ -0,0 +1,48 @@ + +# Slot: root_cond + + +Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + +URI: [mixs.vocab:root_cond](https://w3id.org/mixs/vocab/root_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting conditions | +| **Mappings:** | | MIXS:0001061 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | + diff --git a/mixs6/root_med_carbon.md b/mixs6/root_med_carbon.md new file mode 100644 index 00000000..35d0c799 --- /dev/null +++ b/mixs6/root_med_carbon.md @@ -0,0 +1,48 @@ + +# Slot: root_med_carbon + + +Source of organic carbon in the culture rooting medium; e.g. sucrose. + +URI: [mixs.vocab:root_med_carbon](https://w3id.org/mixs/vocab/root_med_carbon) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium carbon | +| **Mappings:** | | MIXS:0000577 | +| **Comments:** | | Expected value: carbon source name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='sucrose', description=None) | + diff --git a/mixs6/root_med_macronutr.md b/mixs6/root_med_macronutr.md new file mode 100644 index 00000000..957c9d89 --- /dev/null +++ b/mixs6/root_med_macronutr.md @@ -0,0 +1,48 @@ + +# Slot: root_med_macronutr + + +Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + +URI: [mixs.vocab:root_med_macronutr](https://w3id.org/mixs/vocab/root_med_macronutr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium macronutrients | +| **Mappings:** | | MIXS:0000578 | +| **Comments:** | | Expected value: macronutrient name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='KH2PO4;170¬†milligram per liter', description=None) | + diff --git a/mixs6/root_med_micronutr.md b/mixs6/root_med_micronutr.md new file mode 100644 index 00000000..3a2aca8c --- /dev/null +++ b/mixs6/root_med_micronutr.md @@ -0,0 +1,48 @@ + +# Slot: root_med_micronutr + + +Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + +URI: [mixs.vocab:root_med_micronutr](https://w3id.org/mixs/vocab/root_med_micronutr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium micronutrients | +| **Mappings:** | | MIXS:0000579 | +| **Comments:** | | Expected value: micronutrient name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='H3BO3;6.2¬†milligram per liter', description=None) | + diff --git a/mixs6/root_med_ph.md b/mixs6/root_med_ph.md new file mode 100644 index 00000000..ba42760a --- /dev/null +++ b/mixs6/root_med_ph.md @@ -0,0 +1,48 @@ + +# Slot: root_med_ph + + +pH measurement of the culture rooting medium; e.g. 5.5. + +URI: [mixs.vocab:root_med_ph](https://w3id.org/mixs/vocab/root_med_ph) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium pH | +| **Mappings:** | | MIXS:0001062 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='7.5', description=None) | + diff --git a/mixs6/root_med_regl.md b/mixs6/root_med_regl.md new file mode 100644 index 00000000..2d927495 --- /dev/null +++ b/mixs6/root_med_regl.md @@ -0,0 +1,48 @@ + +# Slot: root_med_regl + + +Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + +URI: [mixs.vocab:root_med_regl](https://w3id.org/mixs/vocab/root_med_regl) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium regulators | +| **Mappings:** | | MIXS:0000581 | +| **Comments:** | | Expected value: regulator name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='abscisic acid;0.75 milligram per liter', description=None) | + diff --git a/mixs6/root_med_solid.md b/mixs6/root_med_solid.md new file mode 100644 index 00000000..67ce74d3 --- /dev/null +++ b/mixs6/root_med_solid.md @@ -0,0 +1,48 @@ + +# Slot: root_med_solid + + +Specification of the solidifying agent in the culture rooting medium; e.g. agar. + +URI: [mixs.vocab:root_med_solid](https://w3id.org/mixs/vocab/root_med_solid) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium solidifier | +| **Mappings:** | | MIXS:0001063 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='agar', description=None) | + diff --git a/mixs6/root_med_suppl.md b/mixs6/root_med_suppl.md new file mode 100644 index 00000000..6c57ad83 --- /dev/null +++ b/mixs6/root_med_suppl.md @@ -0,0 +1,48 @@ + +# Slot: root_med_suppl + + +Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + +URI: [mixs.vocab:root_med_suppl](https://w3id.org/mixs/vocab/root_med_suppl) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | rooting medium organic supplements | +| **Mappings:** | | MIXS:0000580 | +| **Comments:** | | Expected value: supplement name;measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='nicotinic acid;0.5 milligram per liter', description=None) | + diff --git a/mixs6/salinity.md b/mixs6/salinity.md new file mode 100644 index 00000000..e45db0af --- /dev/null +++ b/mixs6/salinity.md @@ -0,0 +1,84 @@ + +# Slot: salinity + + +Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + +URI: [mixs.vocab:salinity](https://w3id.org/mixs/vocab/salinity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | salinity | +| **Mappings:** | | MIXS:0000183 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: practical salinity unit, percentage | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='25 practical salinity unit', description=None) | + diff --git a/mixs6/salinity_meth.md b/mixs6/salinity_meth.md new file mode 100644 index 00000000..0176960e --- /dev/null +++ b/mixs6/salinity_meth.md @@ -0,0 +1,48 @@ + +# Slot: salinity_meth + + +Reference or method used in determining salinity + +URI: [mixs.vocab:salinity_meth](https://w3id.org/mixs/vocab/salinity_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | extreme_unusual_properties/salinity method | +| **Mappings:** | | MIXS:0000341 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 47 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/salt_regm.md b/mixs6/salt_regm.md new file mode 100644 index 00000000..e0f9c9f1 --- /dev/null +++ b/mixs6/salt_regm.md @@ -0,0 +1,48 @@ + +# Slot: salt_regm + + +Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + +URI: [mixs.vocab:salt_regm](https://w3id.org/mixs/vocab/salt_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | salt regimen | +| **Mappings:** | | MIXS:0000582 | +| **Comments:** | | Expected value: salt name;salt amount;treatment interval and duration | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/samp_capt_status.md b/mixs6/samp_capt_status.md new file mode 100644 index 00000000..881385b1 --- /dev/null +++ b/mixs6/samp_capt_status.md @@ -0,0 +1,60 @@ + +# Slot: samp_capt_status + + +Reason for the sample + +URI: [mixs.vocab:samp_capt_status](https://w3id.org/mixs/vocab/samp_capt_status) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample capture status | +| **Mappings:** | | MIXS:0000860 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 5 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='farm sample', description=None) | + diff --git a/mixs6/samp_collect_device.md b/mixs6/samp_collect_device.md new file mode 100644 index 00000000..c00d5059 --- /dev/null +++ b/mixs6/samp_collect_device.md @@ -0,0 +1,56 @@ + +# Slot: samp_collect_device + + +The method or device employed for collecting the sample + +URI: [mixs.vocab:samp_collect_device](https://w3id.org/mixs/vocab/samp_collect_device) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection device or method | +| **Comments:** | | Expected value: type name | +| | | Preferred unit: | +| | | Position: 31.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: X | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='environmental swab sampling, biopsy, niskin bottle, push core', description=None) | + diff --git a/mixs6/samp_collection_point.md b/mixs6/samp_collection_point.md new file mode 100644 index 00000000..8eb85a36 --- /dev/null +++ b/mixs6/samp_collection_point.md @@ -0,0 +1,48 @@ + +# Slot: samp_collection_point + + +Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_collection_point](https://w3id.org/mixs/vocab/samp_collection_point) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection point | +| **Mappings:** | | MIXS:0001015 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 39 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='well', description=None) | + diff --git a/mixs6/samp_dis_stage.md b/mixs6/samp_dis_stage.md new file mode 100644 index 00000000..c86d8255 --- /dev/null +++ b/mixs6/samp_dis_stage.md @@ -0,0 +1,60 @@ + +# Slot: samp_dis_stage + + +Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + +URI: [mixs.vocab:samp_dis_stage](https://w3id.org/mixs/vocab/samp_dis_stage) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample disease stage | +| **Mappings:** | | MIXS:0000249 | +| **Comments:** | | Expected value: free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 6 | +| | | This field is used in: 2 packages: host-associated, plant-associated | +| **Examples:** | | Example(value='infection', description=None) | + diff --git a/mixs6/samp_floor.md b/mixs6/samp_floor.md new file mode 100644 index 00000000..46cf32c1 --- /dev/null +++ b/mixs6/samp_floor.md @@ -0,0 +1,48 @@ + +# Slot: samp_floor + + +The floor of the building, where the sampling room is located + +URI: [mixs.vocab:samp_floor](https://w3id.org/mixs/vocab/samp_floor) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling floor | +| **Mappings:** | | MIXS:0000828 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 121 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='4th floor', description=None) | + diff --git a/mixs6/samp_loc_corr_rate.md b/mixs6/samp_loc_corr_rate.md new file mode 100644 index 00000000..3e1ce93f --- /dev/null +++ b/mixs6/samp_loc_corr_rate.md @@ -0,0 +1,48 @@ + +# Slot: samp_loc_corr_rate + + +Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + +URI: [mixs.vocab:samp_loc_corr_rate](https://w3id.org/mixs/vocab/samp_loc_corr_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | corrosion rate at sample location | +| **Mappings:** | | MIXS:0000136 | +| **Comments:** | | Expected value: measurement value range | +| | | Preferred unit: millimeter per year | +| | | Occurrence: 1 | +| | | Position: 34 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_mat_process.md b/mixs6/samp_mat_process.md new file mode 100644 index 00000000..96a3bae2 --- /dev/null +++ b/mixs6/samp_mat_process.md @@ -0,0 +1,56 @@ + +# Slot: samp_mat_process + + +Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + +URI: [mixs.vocab:samp_mat_process](https://w3id.org/mixs/vocab/samp_mat_process) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample material processing | +| **Comments:** | | Expected value: text or OBI | +| | | Preferred unit: | +| | | Position: 32.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='filtering of seawater, storing samples in ethanol', description=None) | + diff --git a/mixs6/samp_md.md b/mixs6/samp_md.md new file mode 100644 index 00000000..206adb58 --- /dev/null +++ b/mixs6/samp_md.md @@ -0,0 +1,48 @@ + +# Slot: samp_md + + +In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_md](https://w3id.org/mixs/vocab/samp_md) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample measured depth | +| **Mappings:** | | MIXS:0000413 | +| **Comments:** | | Expected value: measurement value;enumeration | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 43 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='1534 meter;MSL', description=None) | + diff --git a/mixs6/samp_preserv.md b/mixs6/samp_preserv.md new file mode 100644 index 00000000..4af0496f --- /dev/null +++ b/mixs6/samp_preserv.md @@ -0,0 +1,48 @@ + +# Slot: samp_preserv + + +Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + +URI: [mixs.vocab:samp_preserv](https://w3id.org/mixs/vocab/samp_preserv) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | preservative added to sample | +| **Mappings:** | | MIXS:0000463 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: milliliter | +| | | Occurrence: 1 | +| | | Position: 46 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_room_id.md b/mixs6/samp_room_id.md new file mode 100644 index 00000000..8a47e40f --- /dev/null +++ b/mixs6/samp_room_id.md @@ -0,0 +1,48 @@ + +# Slot: samp_room_id + + +Sampling room number. This ID should be consistent with the designations on the building floor plans + +URI: [mixs.vocab:samp_room_id](https://w3id.org/mixs/vocab/samp_room_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling room ID or name | +| **Mappings:** | | MIXS:0000244 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 122 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_salinity.md b/mixs6/samp_salinity.md new file mode 100644 index 00000000..297340dc --- /dev/null +++ b/mixs6/samp_salinity.md @@ -0,0 +1,168 @@ + +# Slot: samp_salinity + + +Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + +URI: [mixs.vocab:samp_salinity](https://w3id.org/mixs/vocab/samp_salinity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample salinity | +| **Mappings:** | | MIXS:0000109 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, practical salinity unit, percentage | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 11 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, plant-associated, wastewater_sludge | +| **Examples:** | | Example(value='1 milligram per liter', description=None) | + diff --git a/mixs6/samp_size.md b/mixs6/samp_size.md new file mode 100644 index 00000000..95a1ffa6 --- /dev/null +++ b/mixs6/samp_size.md @@ -0,0 +1,56 @@ + +# Slot: samp_size + + +Amount or size of sample (volume, mass or area) that was collected + +URI: [mixs.vocab:samp_size](https://w3id.org/mixs/vocab/samp_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | amount or size of sample collected | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millliter, gram, milligram, liter | +| | | Position: 34.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: X | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='5 liter', description=None) | + diff --git a/mixs6/samp_sort_meth.md b/mixs6/samp_sort_meth.md new file mode 100644 index 00000000..004d852a --- /dev/null +++ b/mixs6/samp_sort_meth.md @@ -0,0 +1,48 @@ + +# Slot: samp_sort_meth + + +Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + +URI: [mixs.vocab:samp_sort_meth](https://w3id.org/mixs/vocab/samp_sort_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample size sorting method | +| **Mappings:** | | MIXS:0000216 | +| **Comments:** | | Expected value: description of method | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 22 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_store_dur.md b/mixs6/samp_store_dur.md new file mode 100644 index 00000000..7535d16d --- /dev/null +++ b/mixs6/samp_store_dur.md @@ -0,0 +1,216 @@ + +# Slot: samp_store_dur + + +Duration for which the sample was stored + +URI: [mixs.vocab:samp_store_dur](https://w3id.org/mixs/vocab/samp_store_dur) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage duration | +| **Mappings:** | | MIXS:0000116 | +| **Comments:** | | Expected value: duration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='P1Y6M', description=None) | + diff --git a/mixs6/samp_store_loc.md b/mixs6/samp_store_loc.md new file mode 100644 index 00000000..2ba8cda8 --- /dev/null +++ b/mixs6/samp_store_loc.md @@ -0,0 +1,216 @@ + +# Slot: samp_store_loc + + +Location at which sample was stored, usually name of a specific freezer/room + +URI: [mixs.vocab:samp_store_loc](https://w3id.org/mixs/vocab/samp_store_loc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage location | +| **Mappings:** | | MIXS:0000755 | +| **Comments:** | | Expected value: location name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='Freezer no:5', description=None) | + diff --git a/mixs6/samp_store_temp.md b/mixs6/samp_store_temp.md new file mode 100644 index 00000000..1066a15e --- /dev/null +++ b/mixs6/samp_store_temp.md @@ -0,0 +1,216 @@ + +# Slot: samp_store_temp + + +Temperature at which sample was stored, e.g. -80 degree Celsius + +URI: [mixs.vocab:samp_store_temp](https://w3id.org/mixs/vocab/samp_store_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample storage temperature | +| **Mappings:** | | MIXS:0000110 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='-80 degree Celsius', description=None) | + diff --git a/mixs6/samp_subtype.md b/mixs6/samp_subtype.md new file mode 100644 index 00000000..9c8baebf --- /dev/null +++ b/mixs6/samp_subtype.md @@ -0,0 +1,60 @@ + +# Slot: samp_subtype + + +Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_subtype](https://w3id.org/mixs/vocab/samp_subtype) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample subtype | +| **Mappings:** | | MIXS:0000999 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 38 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='biofilm', description=None) | + diff --git a/mixs6/samp_time_out.md b/mixs6/samp_time_out.md new file mode 100644 index 00000000..4262dc73 --- /dev/null +++ b/mixs6/samp_time_out.md @@ -0,0 +1,48 @@ + +# Slot: samp_time_out + + +The recent and long term history of outside sampling + +URI: [mixs.vocab:samp_time_out](https://w3id.org/mixs/vocab/samp_time_out) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling time outside | +| **Mappings:** | | MIXS:0000196 | +| **Comments:** | | Expected value: time | +| | | Preferred unit: hour | +| | | Occurrence: 1 | +| | | Position: 123 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_transport_cond.md b/mixs6/samp_transport_cond.md new file mode 100644 index 00000000..fc356d57 --- /dev/null +++ b/mixs6/samp_transport_cond.md @@ -0,0 +1,60 @@ + +# Slot: samp_transport_cond + + +Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + +URI: [mixs.vocab:samp_transport_cond](https://w3id.org/mixs/vocab/samp_transport_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample transport conditions | +| **Mappings:** | | MIXS:0000410 | +| **Comments:** | | Expected value: measurement value;measurement value | +| | | Preferred unit: days;degree Celsius | +| | | Occurrence: 1 | +| | | Position: 47 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='5 days;-20 degree Celsius', description=None) | + diff --git a/mixs6/samp_tvdss.md b/mixs6/samp_tvdss.md new file mode 100644 index 00000000..b5796c80 --- /dev/null +++ b/mixs6/samp_tvdss.md @@ -0,0 +1,48 @@ + +# Slot: samp_tvdss + + +Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + +URI: [mixs.vocab:samp_tvdss](https://w3id.org/mixs/vocab/samp_tvdss) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample true vertical depth subsea | +| **Mappings:** | | MIXS:0000409 | +| **Comments:** | | Expected value: measurement value or measurement value range | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 42 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/samp_type.md b/mixs6/samp_type.md new file mode 100644 index 00000000..8a4f67da --- /dev/null +++ b/mixs6/samp_type.md @@ -0,0 +1,60 @@ + +# Slot: samp_type + + +Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:samp_type](https://w3id.org/mixs/vocab/samp_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample type | +| **Mappings:** | | MIXS:0000998 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 37 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='solid deposit', description=None) | + diff --git a/mixs6/samp_vol_we_dna_ext.md b/mixs6/samp_vol_we_dna_ext.md new file mode 100644 index 00000000..d2e98a32 --- /dev/null +++ b/mixs6/samp_vol_we_dna_ext.md @@ -0,0 +1,228 @@ + +# Slot: samp_vol_we_dna_ext + + +Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + +URI: [mixs.vocab:samp_vol_we_dna_ext](https://w3id.org/mixs/vocab/samp_vol_we_dna_ext) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample volume or weight for DNA extraction | +| **Mappings:** | | MIXS:0000111 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millliter, gram, milligram, square centimeter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | +| **Examples:** | | Example(value='1500 milliliter', description=None) | + diff --git a/mixs6/samp_weather.md b/mixs6/samp_weather.md new file mode 100644 index 00000000..159a6454 --- /dev/null +++ b/mixs6/samp_weather.md @@ -0,0 +1,48 @@ + +# Slot: samp_weather + + +The weather on the sampling day + +URI: [mixs.vocab:samp_weather](https://w3id.org/mixs/vocab/samp_weather) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sampling day weather | +| **Mappings:** | | MIXS:0000827 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 120 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='foggy', description=None) | + diff --git a/mixs6/samp_well_name.md b/mixs6/samp_well_name.md new file mode 100644 index 00000000..d9d76e6f --- /dev/null +++ b/mixs6/samp_well_name.md @@ -0,0 +1,60 @@ + +# Slot: samp_well_name + + +Name of the well (e.g. BXA1123) where sample was taken + +URI: [mixs.vocab:samp_well_name](https://w3id.org/mixs/vocab/samp_well_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample well name | +| **Mappings:** | | MIXS:0000296 | +| **Comments:** | | Expected value: name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 35 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sample_name.md b/mixs6/sample_name.md new file mode 100644 index 00000000..30a30ebe --- /dev/null +++ b/mixs6/sample_name.md @@ -0,0 +1,56 @@ + +# Slot: sample_name + + +Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + +URI: [mixs.vocab:sample_name](https://w3id.org/mixs/vocab/sample_name) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [core field](core_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample name | +| **Comments:** | | Expected value: | +| | | Preferred unit: | +| | | Position: | +| | | CHECKLIST migs_eu: | +| | | CHECKLIST migs_ba: | +| | | CHECKLIST migs_pl: | +| | | CHECKLIST migs_vi: | +| | | CHECKLIST migs_org: | +| | | CHECKLIST me: | +| | | CHECKLIST mimarks_s: | +| | | CHECKLIST mimarks_c: | +| | | CHECKLIST misag: | +| | | CHECKLIST mimag: | +| | | CHECKLIST miuvig: | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/saturates_pc.md b/mixs6/saturates_pc.md new file mode 100644 index 00000000..4694e2ab --- /dev/null +++ b/mixs6/saturates_pc.md @@ -0,0 +1,60 @@ + +# Slot: saturates_pc + + +Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + +URI: [mixs.vocab:saturates_pc](https://w3id.org/mixs/vocab/saturates_pc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | saturates wt% | +| **Mappings:** | | MIXS:0000131 | +| **Comments:** | | Expected value: name;measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 89 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/season.md b/mixs6/season.md new file mode 100644 index 00000000..6d1ddbef --- /dev/null +++ b/mixs6/season.md @@ -0,0 +1,48 @@ + +# Slot: season + + +The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + +URI: [mixs.vocab:season](https://w3id.org/mixs/vocab/season) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | season | +| **Mappings:** | | MIXS:0000829 | +| **Comments:** | | Expected value: NCIT:C94729 | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 124 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='autumn [NCIT:C94733]', description=None) | + diff --git a/mixs6/season_environment.md b/mixs6/season_environment.md new file mode 100644 index 00000000..012d4f20 --- /dev/null +++ b/mixs6/season_environment.md @@ -0,0 +1,48 @@ + +# Slot: season_environment + + +Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + +URI: [mixs.vocab:season_environment](https://w3id.org/mixs/vocab/season_environment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | seasonal environment | +| **Mappings:** | | MIXS:0001068 | +| **Comments:** | | Expected value: seasonal environment name;treatment interval and duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/season_precpt.md b/mixs6/season_precpt.md new file mode 100644 index 00000000..345b211e --- /dev/null +++ b/mixs6/season_precpt.md @@ -0,0 +1,48 @@ + +# Slot: season_precpt + + +The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + +URI: [mixs.vocab:season_precpt](https://w3id.org/mixs/vocab/season_precpt) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean seasonal precipitation | +| **Mappings:** | | MIXS:0000645 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: millimeter | +| | | Occurrence: 1 | +| | | Position: 24 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/season_temp.md b/mixs6/season_temp.md new file mode 100644 index 00000000..1195a4b3 --- /dev/null +++ b/mixs6/season_temp.md @@ -0,0 +1,48 @@ + +# Slot: season_temp + + +Mean seasonal temperature + +URI: [mixs.vocab:season_temp](https://w3id.org/mixs/vocab/season_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | mean seasonal temperature | +| **Mappings:** | | MIXS:0000643 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 22 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='18 degree Celsius', description=None) | + diff --git a/mixs6/season_use.md b/mixs6/season_use.md new file mode 100644 index 00000000..a29f954b --- /dev/null +++ b/mixs6/season_use.md @@ -0,0 +1,48 @@ + +# Slot: season_use + + +The seasons the space is occupied + +URI: [mixs.vocab:season_use](https://w3id.org/mixs/vocab/season_use) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | seasonal use | +| **Mappings:** | | MIXS:0000830 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 125 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='Winter', description=None) | + diff --git a/mixs6/secondary_treatment.md b/mixs6/secondary_treatment.md new file mode 100644 index 00000000..e1ea5fc4 --- /dev/null +++ b/mixs6/secondary_treatment.md @@ -0,0 +1,48 @@ + +# Slot: secondary_treatment + + +The process for substantially degrading the biological content of the sewage + +URI: [mixs.vocab:secondary_treatment](https://w3id.org/mixs/vocab/secondary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | secondary treatment | +| **Mappings:** | | MIXS:0000351 | +| **Comments:** | | Expected value: secondary treatment type | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sediment_type.md b/mixs6/sediment_type.md new file mode 100644 index 00000000..57eba3fe --- /dev/null +++ b/mixs6/sediment_type.md @@ -0,0 +1,48 @@ + +# Slot: sediment_type + + +Information about the sediment type based on major constituents + +URI: [mixs.vocab:sediment_type](https://w3id.org/mixs/vocab/sediment_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sediment type | +| **Mappings:** | | MIXS:0001078 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: sediment | +| **Examples:** | | Example(value='biogenous', description=None) | + diff --git a/mixs6/seq_meth.md b/mixs6/seq_meth.md new file mode 100644 index 00000000..aa474909 --- /dev/null +++ b/mixs6/seq_meth.md @@ -0,0 +1,56 @@ + +# Slot: seq_meth + + +Sequencing method used; e.g. Sanger, ABI-solid + +URI: [mixs.vocab:seq_meth](https://w3id.org/mixs/vocab/seq_meth) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sequencing method | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 50.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='Illumina HiSeq 1500', description=None) | + diff --git a/mixs6/seq_quality_check.md b/mixs6/seq_quality_check.md new file mode 100644 index 00000000..77e5500f --- /dev/null +++ b/mixs6/seq_quality_check.md @@ -0,0 +1,56 @@ + +# Slot: seq_quality_check + + +Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + +URI: [mixs.vocab:seq_quality_check](https://w3id.org/mixs/vocab/seq_quality_check) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sequence quality check | +| **Comments:** | | Expected value: none or manually edited | +| | | Preferred unit: | +| | | Position: 51.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='none', description=None) | + diff --git a/mixs6/sequencing_field.md b/mixs6/sequencing_field.md new file mode 100644 index 00000000..a85367e3 --- /dev/null +++ b/mixs6/sequencing_field.md @@ -0,0 +1,78 @@ + +# Slot: sequencing_field + + + + +URI: [mixs.vocab:sequencing_field](https://w3id.org/mixs/vocab/sequencing_field) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + * [adapters](adapters.md) + * [annot](annot.md) + * [assembly_name](assembly_name.md) + * [assembly_qual](assembly_qual.md) + * [assembly_software](assembly_software.md) + * [bin_param](bin_param.md) + * [bin_software](bin_software.md) + * [chimera_check](chimera_check.md) + * [compl_appr](compl_appr.md) + * [compl_score](compl_score.md) + * [compl_software](compl_software.md) + * [contam_score](contam_score.md) + * [contam_screen_input](contam_screen_input.md) + * [contam_screen_param](contam_screen_param.md) + * [decontam_software](decontam_software.md) + * [detec_type](detec_type.md) + * [feat_pred](feat_pred.md) + * [host_pred_appr](host_pred_appr.md) + * [host_pred_est_acc](host_pred_est_acc.md) + * [lib_layout](lib_layout.md) + * [lib_reads_seqd](lib_reads_seqd.md) + * [lib_screen](lib_screen.md) + * [lib_size](lib_size.md) + * [lib_vector](lib_vector.md) + * [mag_cov_software](mag_cov_software.md) + * [mid](mid.md) + * [nucl_acid_amp](nucl_acid_amp.md) + * [nucl_acid_ext](nucl_acid_ext.md) + * [number_contig](number_contig.md) + * [pcr_cond](pcr_cond.md) + * [pcr_primers](pcr_primers.md) + * [pred_genome_struc](pred_genome_struc.md) + * [pred_genome_type](pred_genome_type.md) + * [reassembly_bin](reassembly_bin.md) + * [ref_db](ref_db.md) + * [seq_meth](seq_meth.md) + * [seq_quality_check](seq_quality_check.md) + * [sim_search_meth](sim_search_meth.md) + * [single_cell_lysis_appr](single_cell_lysis_appr.md) + * [single_cell_lysis_prot](single_cell_lysis_prot.md) + * [sop](sop.md) + * [sort_tech](sort_tech.md) + * [target_gene](target_gene.md) + * [target_subfragment](target_subfragment.md) + * [tax_class](tax_class.md) + * [tax_ident](tax_ident.md) + * [trna_ext_software](trna_ext_software.md) + * [trnas](trnas.md) + * [url](url.md) + * [vir_ident_software](vir_ident_software.md) + * [votu_class_appr](votu_class_appr.md) + * [votu_db](votu_db.md) + * [votu_seq_comp_appr](votu_seq_comp_appr.md) + * [wga_amp_appr](wga_amp_appr.md) + * [wga_amp_kit](wga_amp_kit.md) + * [x_16s_recover](x_16s_recover.md) + * [x_16s_recover_software](x_16s_recover_software.md) + +## Used by + diff --git a/mixs6/sewage_type.md b/mixs6/sewage_type.md new file mode 100644 index 00000000..899b2ea2 --- /dev/null +++ b/mixs6/sewage_type.md @@ -0,0 +1,48 @@ + +# Slot: sewage_type + + +Type of wastewater treatment plant as municipial or industrial + +URI: [mixs.vocab:sewage_type](https://w3id.org/mixs/vocab/sewage_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sewage type | +| **Mappings:** | | MIXS:0000215 | +| **Comments:** | | Expected value: sewage type name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sexual_act.md b/mixs6/sexual_act.md new file mode 100644 index 00000000..c2db90cf --- /dev/null +++ b/mixs6/sexual_act.md @@ -0,0 +1,48 @@ + +# Slot: sexual_act + + +Current sexual partner and frequency of sex + +URI: [mixs.vocab:sexual_act](https://w3id.org/mixs/vocab/sexual_act) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sexual activity | +| **Mappings:** | | MIXS:0000285 | +| **Comments:** | | Expected value: partner sex;frequency | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/shading_device_cond.md b/mixs6/shading_device_cond.md new file mode 100644 index 00000000..1f9431d0 --- /dev/null +++ b/mixs6/shading_device_cond.md @@ -0,0 +1,48 @@ + +# Slot: shading_device_cond + + +The physical condition of the shading device at the time of sampling + +URI: [mixs.vocab:shading_device_cond](https://w3id.org/mixs/vocab/shading_device_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device condition | +| **Mappings:** | | MIXS:0000831 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 126 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='new', description=None) | + diff --git a/mixs6/shading_device_loc.md b/mixs6/shading_device_loc.md new file mode 100644 index 00000000..684cb04f --- /dev/null +++ b/mixs6/shading_device_loc.md @@ -0,0 +1,48 @@ + +# Slot: shading_device_loc + + +The location of the shading device in relation to the built structure + +URI: [mixs.vocab:shading_device_loc](https://w3id.org/mixs/vocab/shading_device_loc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device location | +| **Mappings:** | | MIXS:0000832 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 127 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='exterior', description=None) | + diff --git a/mixs6/shading_device_mat.md b/mixs6/shading_device_mat.md new file mode 100644 index 00000000..a523c6a7 --- /dev/null +++ b/mixs6/shading_device_mat.md @@ -0,0 +1,48 @@ + +# Slot: shading_device_mat + + +The material the shading device is composed of + +URI: [mixs.vocab:shading_device_mat](https://w3id.org/mixs/vocab/shading_device_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device material | +| **Mappings:** | | MIXS:0000245 | +| **Comments:** | | Expected value: material name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 128 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/shading_device_type.md b/mixs6/shading_device_type.md new file mode 100644 index 00000000..65f64e8d --- /dev/null +++ b/mixs6/shading_device_type.md @@ -0,0 +1,48 @@ + +# Slot: shading_device_type + + +The type of shading device + +URI: [mixs.vocab:shading_device_type](https://w3id.org/mixs/vocab/shading_device_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device type | +| **Mappings:** | | MIXS:0000835 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 130 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='slatted aluminum awning', description=None) | + diff --git a/mixs6/shading_device_water_mold.md b/mixs6/shading_device_water_mold.md new file mode 100644 index 00000000..b70560d5 --- /dev/null +++ b/mixs6/shading_device_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: shading_device_water_mold + + +Signs of the presence of mold or mildew on the shading device + +URI: [mixs.vocab:shading_device_water_mold](https://w3id.org/mixs/vocab/shading_device_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | shading device signs of water/mold | +| **Mappings:** | | MIXS:0000834 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 129 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/sieving.md b/mixs6/sieving.md new file mode 100644 index 00000000..dae90345 --- /dev/null +++ b/mixs6/sieving.md @@ -0,0 +1,48 @@ + +# Slot: sieving + + +Collection design of pooled samples and/or sieve size and amount of sample sieved + +URI: [mixs.vocab:sieving](https://w3id.org/mixs/vocab/sieving) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | composite design/sieving (if any) | +| **Mappings:** | | MIXS:0000322 | +| **Comments:** | | Expected value: design name and/or size;amount | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 14 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/silicate.md b/mixs6/silicate.md new file mode 100644 index 00000000..dff17edc --- /dev/null +++ b/mixs6/silicate.md @@ -0,0 +1,84 @@ + +# Slot: silicate + + +Concentration of silicate + +URI: [mixs.vocab:silicate](https://w3id.org/mixs/vocab/silicate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | silicate | +| **Mappings:** | | MIXS:0000184 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='0.05 micromole per liter', description=None) | + diff --git a/mixs6/sim_search_meth.md b/mixs6/sim_search_meth.md new file mode 100644 index 00000000..36457ce7 --- /dev/null +++ b/mixs6/sim_search_meth.md @@ -0,0 +1,56 @@ + +# Slot: sim_search_meth + + +Tool used to compare ORFs with database, along with version and cutoffs used + +URI: [mixs.vocab:sim_search_meth](https://w3id.org/mixs/vocab/sim_search_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | similarity search method | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Preferred unit: | +| | | Position: 61.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='HMMER3;3.1b2;hmmsearch, cutoff of 50 on score', description=None) | + diff --git a/mixs6/single_cell_lysis_appr.md b/mixs6/single_cell_lysis_appr.md new file mode 100644 index 00000000..626203c3 --- /dev/null +++ b/mixs6/single_cell_lysis_appr.md @@ -0,0 +1,56 @@ + +# Slot: single_cell_lysis_appr + + +Method used to free DNA from interior of the cell(s) or particle(s) + +URI: [mixs.vocab:single_cell_lysis_appr](https://w3id.org/mixs/vocab/single_cell_lysis_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | single cell or viral particle lysis approach | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 75.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='enzymatic', description=None) | + diff --git a/mixs6/single_cell_lysis_prot.md b/mixs6/single_cell_lysis_prot.md new file mode 100644 index 00000000..e1abf739 --- /dev/null +++ b/mixs6/single_cell_lysis_prot.md @@ -0,0 +1,56 @@ + +# Slot: single_cell_lysis_prot + + +Name of the kit or standard protocol used for cell(s) or particle(s) lysis + +URI: [mixs.vocab:single_cell_lysis_prot](https://w3id.org/mixs/vocab/single_cell_lysis_prot) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | single cell or viral particle lysis kit protocol | +| **Comments:** | | Expected value: kit, protocol name | +| | | Preferred unit: | +| | | Position: 76.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='ambion single cell lysis kit', description=None) | + diff --git a/mixs6/size_frac.md b/mixs6/size_frac.md new file mode 100644 index 00000000..f2604800 --- /dev/null +++ b/mixs6/size_frac.md @@ -0,0 +1,56 @@ + +# Slot: size_frac + + +Filtering pore size used in sample preparation + +URI: [mixs.vocab:size_frac](https://w3id.org/mixs/vocab/size_frac) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size fraction selected | +| **Comments:** | | Expected value: filter size value range | +| | | Preferred unit: | +| | | Position: 33.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: X | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='0-0.22 micrometer', description=None) | + diff --git a/mixs6/size_frac_low.md b/mixs6/size_frac_low.md new file mode 100644 index 00000000..ea597466 --- /dev/null +++ b/mixs6/size_frac_low.md @@ -0,0 +1,48 @@ + +# Slot: size_frac_low + + +Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + +URI: [mixs.vocab:size_frac_low](https://w3id.org/mixs/vocab/size_frac_low) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size-fraction lower threshold | +| **Mappings:** | | MIXS:0000735 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: micrometer | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.2 micrometer', description=None) | + diff --git a/mixs6/size_frac_up.md b/mixs6/size_frac_up.md new file mode 100644 index 00000000..18765b27 --- /dev/null +++ b/mixs6/size_frac_up.md @@ -0,0 +1,48 @@ + +# Slot: size_frac_up + + +Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + +URI: [mixs.vocab:size_frac_up](https://w3id.org/mixs/vocab/size_frac_up) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | size-fraction upper threshold | +| **Mappings:** | | MIXS:0000736 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: micrometer | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='20 micrometer', description=None) | + diff --git a/mixs6/slope_aspect.md b/mixs6/slope_aspect.md new file mode 100644 index 00000000..6f664fe0 --- /dev/null +++ b/mixs6/slope_aspect.md @@ -0,0 +1,48 @@ + +# Slot: slope_aspect + + +The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + +URI: [mixs.vocab:slope_aspect](https://w3id.org/mixs/vocab/slope_aspect) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | slope aspect | +| **Mappings:** | | MIXS:0000647 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree | +| | | Occurrence: 1 | +| | | Position: 32 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/slope_gradient.md b/mixs6/slope_gradient.md new file mode 100644 index 00000000..69cd1df9 --- /dev/null +++ b/mixs6/slope_gradient.md @@ -0,0 +1,48 @@ + +# Slot: slope_gradient + + +Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + +URI: [mixs.vocab:slope_gradient](https://w3id.org/mixs/vocab/slope_gradient) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | slope gradient | +| **Mappings:** | | MIXS:0000646 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 31 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sludge_retent_time.md b/mixs6/sludge_retent_time.md new file mode 100644 index 00000000..57a9189c --- /dev/null +++ b/mixs6/sludge_retent_time.md @@ -0,0 +1,48 @@ + +# Slot: sludge_retent_time + + +The time activated sludge remains in reactor + +URI: [mixs.vocab:sludge_retent_time](https://w3id.org/mixs/vocab/sludge_retent_time) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sludge retention time | +| **Mappings:** | | MIXS:0000669 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: hours | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/smoker.md b/mixs6/smoker.md new file mode 100644 index 00000000..a7732ae2 --- /dev/null +++ b/mixs6/smoker.md @@ -0,0 +1,48 @@ + +# Slot: smoker + + +Specification of smoking status + +URI: [mixs.vocab:smoker](https://w3id.org/mixs/vocab/smoker) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | smoker | +| **Mappings:** | | MIXS:0000262 | +| **Comments:** | | Expected value: smoking status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 17 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/sodium.md b/mixs6/sodium.md new file mode 100644 index 00000000..5f2a2f9c --- /dev/null +++ b/mixs6/sodium.md @@ -0,0 +1,120 @@ + +# Slot: sodium + + +Sodium concentration in the sample + +URI: [mixs.vocab:sodium](https://w3id.org/mixs/vocab/sodium) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sodium | +| **Mappings:** | | MIXS:0000428 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 66 | +| | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='10.5 milligram per liter', description=None) | + diff --git a/mixs6/soil_type.md b/mixs6/soil_type.md new file mode 100644 index 00000000..672119ae --- /dev/null +++ b/mixs6/soil_type.md @@ -0,0 +1,48 @@ + +# Slot: soil_type + + +Soil series name or other lower-level classification + +URI: [mixs.vocab:soil_type](https://w3id.org/mixs/vocab/soil_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil type | +| **Mappings:** | | MIXS:0000332 | +| **Comments:** | | Expected value: soil type name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 29 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soil_type_meth.md b/mixs6/soil_type_meth.md new file mode 100644 index 00000000..c7c6f633 --- /dev/null +++ b/mixs6/soil_type_meth.md @@ -0,0 +1,48 @@ + +# Slot: soil_type_meth + + +Reference or method used in determining soil series name or other lower-level classification + +URI: [mixs.vocab:soil_type_meth](https://w3id.org/mixs/vocab/soil_type_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soil type method | +| **Mappings:** | | MIXS:0000334 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 30 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/solar_irradiance.md b/mixs6/solar_irradiance.md new file mode 100644 index 00000000..9630b3d0 --- /dev/null +++ b/mixs6/solar_irradiance.md @@ -0,0 +1,48 @@ + +# Slot: solar_irradiance + + +The amount of solar energy that arrives at a specific area of a surface during a specific time interval + +URI: [mixs.vocab:solar_irradiance](https://w3id.org/mixs/vocab/solar_irradiance) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | solar irradiance | +| **Mappings:** | | MIXS:0000112 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: kilowatts per square meter per day, ergs per square centimeter per second | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='1.36 kilowatts per square meter per day', description=None) | + diff --git a/mixs6/soluble_inorg_mat.md b/mixs6/soluble_inorg_mat.md new file mode 100644 index 00000000..8499cd26 --- /dev/null +++ b/mixs6/soluble_inorg_mat.md @@ -0,0 +1,48 @@ + +# Slot: soluble_inorg_mat + + +Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + +URI: [mixs.vocab:soluble_inorg_mat](https://w3id.org/mixs/vocab/soluble_inorg_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble inorganic material | +| **Mappings:** | | MIXS:0000672 | +| **Comments:** | | Expected value: soluble inorganic material name;measurement value | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soluble_org_mat.md b/mixs6/soluble_org_mat.md new file mode 100644 index 00000000..6d80cc6e --- /dev/null +++ b/mixs6/soluble_org_mat.md @@ -0,0 +1,48 @@ + +# Slot: soluble_org_mat + + +Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + +URI: [mixs.vocab:soluble_org_mat](https://w3id.org/mixs/vocab/soluble_org_mat) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble organic material | +| **Mappings:** | | MIXS:0000673 | +| **Comments:** | | Expected value: soluble organic material name;measurement value | +| | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/soluble_react_phosp.md b/mixs6/soluble_react_phosp.md new file mode 100644 index 00000000..5bba34f5 --- /dev/null +++ b/mixs6/soluble_react_phosp.md @@ -0,0 +1,48 @@ + +# Slot: soluble_react_phosp + + +Concentration of soluble reactive phosphorus + +URI: [mixs.vocab:soluble_react_phosp](https://w3id.org/mixs/vocab/soluble_react_phosp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | soluble reactive phosphorus | +| **Mappings:** | | MIXS:0000738 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.1 milligram per liter', description=None) | + diff --git a/mixs6/sop.md b/mixs6/sop.md new file mode 100644 index 00000000..9df0caa5 --- /dev/null +++ b/mixs6/sop.md @@ -0,0 +1,56 @@ + +# Slot: sop + + +Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + +URI: [mixs.vocab:sop](https://w3id.org/mixs/vocab/sop) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relevant standard operating procedures | +| **Comments:** | | Expected value: reference to SOP | +| | | Preferred unit: | +| | | Position: 93.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/', description=None) | + diff --git a/mixs6/sort_tech.md b/mixs6/sort_tech.md new file mode 100644 index 00000000..f7bf8c35 --- /dev/null +++ b/mixs6/sort_tech.md @@ -0,0 +1,56 @@ + +# Slot: sort_tech + + +Method used to sort/isolate cells or particles of interest + +URI: [mixs.vocab:sort_tech](https://w3id.org/mixs/vocab/sort_tech) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sorting technology | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 74.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='optical manipulation', description=None) | + diff --git a/mixs6/source_mat_id.md b/mixs6/source_mat_id.md new file mode 100644 index 00000000..54519094 --- /dev/null +++ b/mixs6/source_mat_id.md @@ -0,0 +1,56 @@ + +# Slot: source_mat_id + + +A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + +URI: [mixs.vocab:source_mat_id](https://w3id.org/mixs/vocab/source_mat_id) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source material identifiers | +| **Comments:** | | Expected value: for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer | +| | | Preferred unit: | +| | | Position: 20.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='MPI012345', description=None) | + diff --git a/mixs6/source_uvig.md b/mixs6/source_uvig.md new file mode 100644 index 00000000..a545013c --- /dev/null +++ b/mixs6/source_uvig.md @@ -0,0 +1,56 @@ + +# Slot: source_uvig + + +Type of dataset from which the UViG was obtained + +URI: [mixs.vocab:source_uvig](https://w3id.org/mixs/vocab/source_uvig) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source of UViGs | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 35.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='viral fraction metagenome (virome)', description=None) | + diff --git a/mixs6/space_typ_state.md b/mixs6/space_typ_state.md new file mode 100644 index 00000000..88faee27 --- /dev/null +++ b/mixs6/space_typ_state.md @@ -0,0 +1,48 @@ + +# Slot: space_typ_state + + +Customary or normal state of the space + +URI: [mixs.vocab:space_typ_state](https://w3id.org/mixs/vocab/space_typ_state) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | space typical state | +| **Mappings:** | | MIXS:0000770 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 23 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='typically occupied', description=None) | + diff --git a/mixs6/special_diet.md b/mixs6/special_diet.md new file mode 100644 index 00000000..89bef30a --- /dev/null +++ b/mixs6/special_diet.md @@ -0,0 +1,48 @@ + +# Slot: special_diet + + +Specification of special diet; can include multiple special diets + +URI: [mixs.vocab:special_diet](https://w3id.org/mixs/vocab/special_diet) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | special diet | +| **Mappings:** | | MIXS:0000905 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 3 | +| | | This field is used uniquely in: human-gut | +| **Examples:** | | Example(value='other:vegan', description=None) | + diff --git a/mixs6/specific.md b/mixs6/specific.md new file mode 100644 index 00000000..2d860090 --- /dev/null +++ b/mixs6/specific.md @@ -0,0 +1,48 @@ + +# Slot: specific + + +The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + +URI: [mixs.vocab:specific](https://w3id.org/mixs/vocab/specific) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specifications | +| **Mappings:** | | MIXS:0000836 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 132 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='construction', description=None) | + diff --git a/mixs6/specific_host.md b/mixs6/specific_host.md new file mode 100644 index 00000000..73ee2288 --- /dev/null +++ b/mixs6/specific_host.md @@ -0,0 +1,56 @@ + +# Slot: specific_host + + +If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + +URI: [mixs.vocab:specific_host](https://w3id.org/mixs/vocab/specific_host) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specific host | +| **Comments:** | | Expected value: host taxid, unknown, environmental | +| | | Preferred unit: | +| | | Position: 23.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='9606', description=None) | + diff --git a/mixs6/specific_humidity.md b/mixs6/specific_humidity.md new file mode 100644 index 00000000..ebc14a64 --- /dev/null +++ b/mixs6/specific_humidity.md @@ -0,0 +1,48 @@ + +# Slot: specific_humidity + + +The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + +URI: [mixs.vocab:specific_humidity](https://w3id.org/mixs/vocab/specific_humidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | specific humidity | +| **Mappings:** | | MIXS:0000214 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram of air, kilogram of air | +| | | Occurrence: 1 | +| | | Position: 131 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15 per kilogram of air', description=None) | + diff --git a/mixs6/sr_dep_env.md b/mixs6/sr_dep_env.md new file mode 100644 index 00000000..e07282fd --- /dev/null +++ b/mixs6/sr_dep_env.md @@ -0,0 +1,48 @@ + +# Slot: sr_dep_env + + +Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_dep_env](https://w3id.org/mixs/vocab/sr_dep_env) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock depositional environment | +| **Mappings:** | | MIXS:0000996 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 21 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Marine', description=None) | + diff --git a/mixs6/sr_geol_age.md b/mixs6/sr_geol_age.md new file mode 100644 index 00000000..aff7e4fa --- /dev/null +++ b/mixs6/sr_geol_age.md @@ -0,0 +1,48 @@ + +# Slot: sr_geol_age + + +Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_geol_age](https://w3id.org/mixs/vocab/sr_geol_age) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock geological age | +| **Mappings:** | | MIXS:0000997 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 22 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Silurian', description=None) | + diff --git a/mixs6/sr_kerog_type.md b/mixs6/sr_kerog_type.md new file mode 100644 index 00000000..b1ab2783 --- /dev/null +++ b/mixs6/sr_kerog_type.md @@ -0,0 +1,48 @@ + +# Slot: sr_kerog_type + + +Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_kerog_type](https://w3id.org/mixs/vocab/sr_kerog_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock kerogen type | +| **Mappings:** | | MIXS:0000994 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 19 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Type IV', description=None) | + diff --git a/mixs6/sr_lithology.md b/mixs6/sr_lithology.md new file mode 100644 index 00000000..e21f1d23 --- /dev/null +++ b/mixs6/sr_lithology.md @@ -0,0 +1,48 @@ + +# Slot: sr_lithology + + +Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + +URI: [mixs.vocab:sr_lithology](https://w3id.org/mixs/vocab/sr_lithology) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | source rock lithology | +| **Mappings:** | | MIXS:0000995 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 20 | +| | | This field is used uniquely in: hydrocarbon resources-cores | +| **Examples:** | | Example(value='Coal', description=None) | + diff --git a/mixs6/standing_water_regm.md b/mixs6/standing_water_regm.md new file mode 100644 index 00000000..43ebb4c8 --- /dev/null +++ b/mixs6/standing_water_regm.md @@ -0,0 +1,48 @@ + +# Slot: standing_water_regm + + +Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:standing_water_regm](https://w3id.org/mixs/vocab/standing_water_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | standing water regimen | +| **Mappings:** | | MIXS:0001069 | +| **Comments:** | | Expected value: standing water type;treatment interval and duration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/store_cond.md b/mixs6/store_cond.md new file mode 100644 index 00000000..a2440559 --- /dev/null +++ b/mixs6/store_cond.md @@ -0,0 +1,48 @@ + +# Slot: store_cond + + +Explain how and for how long the soil sample was stored before DNA extraction + +URI: [mixs.vocab:store_cond](https://w3id.org/mixs/vocab/store_cond) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | storage conditions (fresh/frozen/other) | +| **Mappings:** | | MIXS:0000327 | +| **Comments:** | | Expected value: storage condition type;duration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 19 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='-20 degree Celsius freezer;P2Y10D', description=None) | + diff --git a/mixs6/study_complt_stat.md b/mixs6/study_complt_stat.md new file mode 100644 index 00000000..ee18ece4 --- /dev/null +++ b/mixs6/study_complt_stat.md @@ -0,0 +1,48 @@ + +# Slot: study_complt_stat + + +Specification of study completion status, if no the reason should be specified + +URI: [mixs.vocab:study_complt_stat](https://w3id.org/mixs/vocab/study_complt_stat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | study completion status | +| **Mappings:** | | MIXS:0000898 | +| **Comments:** | | Expected value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow up (4)other-specify | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 29 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='no;non-compliance', description=None) | + diff --git a/mixs6/submitted_to_insdc.md b/mixs6/submitted_to_insdc.md new file mode 100644 index 00000000..cff6d74e --- /dev/null +++ b/mixs6/submitted_to_insdc.md @@ -0,0 +1,56 @@ + +# Slot: submitted_to_insdc + + +Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + +URI: [mixs.vocab:submitted_to_insdc](https://w3id.org/mixs/vocab/submitted_to_insdc) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [investigation field](investigation_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | submitted to insdc | +| **Comments:** | | Expected value: boolean | +| | | Preferred unit: | +| | | Position: 1.0 | +| | | CHECKLIST migs_eu: M | +| | | CHECKLIST migs_ba: M | +| | | CHECKLIST migs_pl: M | +| | | CHECKLIST migs_vi: M | +| | | CHECKLIST migs_org: M | +| | | CHECKLIST me: M | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/subspecf_gen_lin.md b/mixs6/subspecf_gen_lin.md new file mode 100644 index 00000000..e86bf8b4 --- /dev/null +++ b/mixs6/subspecf_gen_lin.md @@ -0,0 +1,56 @@ + +# Slot: subspecf_gen_lin + + +This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + +URI: [mixs.vocab:subspecf_gen_lin](https://w3id.org/mixs/vocab/subspecf_gen_lin) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | subspecific genetic lineage | +| **Comments:** | | Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype | +| | | Preferred unit: | +| | | Position: 14.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='serovar:Newport', description=None) | + diff --git a/mixs6/substructure_type.md b/mixs6/substructure_type.md new file mode 100644 index 00000000..21139c53 --- /dev/null +++ b/mixs6/substructure_type.md @@ -0,0 +1,48 @@ + +# Slot: substructure_type + + +The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + +URI: [mixs.vocab:substructure_type](https://w3id.org/mixs/vocab/substructure_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | substructure type | +| **Mappings:** | | MIXS:0000767 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 19 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='basement', description=None) | + diff --git a/mixs6/sulfate.md b/mixs6/sulfate.md new file mode 100644 index 00000000..6443288f --- /dev/null +++ b/mixs6/sulfate.md @@ -0,0 +1,108 @@ + +# Slot: sulfate + + +Concentration of sulfate in the sample + +URI: [mixs.vocab:sulfate](https://w3id.org/mixs/vocab/sulfate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfate | +| **Mappings:** | | MIXS:0000423 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 58 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='5 micromole per liter', description=None) | + diff --git a/mixs6/sulfate_fw.md b/mixs6/sulfate_fw.md new file mode 100644 index 00000000..4e776bf4 --- /dev/null +++ b/mixs6/sulfate_fw.md @@ -0,0 +1,60 @@ + +# Slot: sulfate_fw + + +Original sulfate concentration in the hydrocarbon resource + +URI: [mixs.vocab:sulfate_fw](https://w3id.org/mixs/vocab/sulfate_fw) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfate in formation water | +| **Mappings:** | | MIXS:0000407 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 17 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/sulfide.md b/mixs6/sulfide.md new file mode 100644 index 00000000..03d3e550 --- /dev/null +++ b/mixs6/sulfide.md @@ -0,0 +1,108 @@ + +# Slot: sulfide + + +Concentration of sulfide in the sample + +URI: [mixs.vocab:sulfide](https://w3id.org/mixs/vocab/sulfide) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sulfide | +| **Mappings:** | | MIXS:0000424 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 59 | +| | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | +| **Examples:** | | Example(value='2 micromole per liter', description=None) | + diff --git a/mixs6/surf_air_cont.md b/mixs6/surf_air_cont.md new file mode 100644 index 00000000..77192770 --- /dev/null +++ b/mixs6/surf_air_cont.md @@ -0,0 +1,48 @@ + +# Slot: surf_air_cont + + +Contaminant identified on surface + +URI: [mixs.vocab:surf_air_cont](https://w3id.org/mixs/vocab/surf_air_cont) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface-air contaminant | +| **Mappings:** | | MIXS:0000759 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 2 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='radon', description=None) | + diff --git a/mixs6/surf_humidity.md b/mixs6/surf_humidity.md new file mode 100644 index 00000000..85ef1c33 --- /dev/null +++ b/mixs6/surf_humidity.md @@ -0,0 +1,48 @@ + +# Slot: surf_humidity + + +Surfaces: water activity as a function of air and material moisture + +URI: [mixs.vocab:surf_humidity](https://w3id.org/mixs/vocab/surf_humidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface humidity | +| **Mappings:** | | MIXS:0000123 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percentage | +| | | Occurrence: 1 | +| | | Position: 5 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='10%', description=None) | + diff --git a/mixs6/surf_material.md b/mixs6/surf_material.md new file mode 100644 index 00000000..ed72044b --- /dev/null +++ b/mixs6/surf_material.md @@ -0,0 +1,48 @@ + +# Slot: surf_material + + +Surface materials at the point of sampling + +URI: [mixs.vocab:surf_material](https://w3id.org/mixs/vocab/surf_material) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface material | +| **Mappings:** | | MIXS:0000758 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/surf_moisture.md b/mixs6/surf_moisture.md new file mode 100644 index 00000000..ac51ab2d --- /dev/null +++ b/mixs6/surf_moisture.md @@ -0,0 +1,48 @@ + +# Slot: surf_moisture + + +Water held on a surface + +URI: [mixs.vocab:surf_moisture](https://w3id.org/mixs/vocab/surf_moisture) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface moisture | +| **Mappings:** | | MIXS:0000128 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: parts per million, gram per cubic meter, gram per square meter | +| | | Occurrence: 1 | +| | | Position: 10 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='0.01 gram per square meter', description=None) | + diff --git a/mixs6/surf_moisture_ph.md b/mixs6/surf_moisture_ph.md new file mode 100644 index 00000000..801a5714 --- /dev/null +++ b/mixs6/surf_moisture_ph.md @@ -0,0 +1,48 @@ + +# Slot: surf_moisture_ph + + +ph measurement of surface + +URI: [mixs.vocab:surf_moisture_ph](https://w3id.org/mixs/vocab/surf_moisture_ph) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface moisture pH | +| **Mappings:** | | MIXS:0000760 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 8 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='7', description=None) | + diff --git a/mixs6/surf_temp.md b/mixs6/surf_temp.md new file mode 100644 index 00000000..1b9dc1c6 --- /dev/null +++ b/mixs6/surf_temp.md @@ -0,0 +1,48 @@ + +# Slot: surf_temp + + +Temperature of the surface at the time of sampling + +URI: [mixs.vocab:surf_temp](https://w3id.org/mixs/vocab/surf_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | surface temperature | +| **Mappings:** | | MIXS:0000125 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 7 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='15 degree Celsius', description=None) | + diff --git a/mixs6/suspend_part_matter.md b/mixs6/suspend_part_matter.md new file mode 100644 index 00000000..e3dc4793 --- /dev/null +++ b/mixs6/suspend_part_matter.md @@ -0,0 +1,48 @@ + +# Slot: suspend_part_matter + + +Concentration of suspended particulate matter + +URI: [mixs.vocab:suspend_part_matter](https://w3id.org/mixs/vocab/suspend_part_matter) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | suspended particulate matter | +| **Mappings:** | | MIXS:0000741 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='0.5 milligram per liter', description=None) | + diff --git a/mixs6/suspend_solids.md b/mixs6/suspend_solids.md new file mode 100644 index 00000000..1b3206b3 --- /dev/null +++ b/mixs6/suspend_solids.md @@ -0,0 +1,72 @@ + +# Slot: suspend_solids + + +Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + +URI: [mixs.vocab:suspend_solids](https://w3id.org/mixs/vocab/suspend_solids) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | suspended solids | +| **Mappings:** | | MIXS:0000150 | +| **Comments:** | | Expected value: suspended solid name;measurement value | +| | | Preferred unit: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million | +| | | Occurrence: m | +| | | Position: 76 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tan.md b/mixs6/tan.md new file mode 100644 index 00000000..c28cc21b --- /dev/null +++ b/mixs6/tan.md @@ -0,0 +1,60 @@ + +# Slot: tan + + +Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + +URI: [mixs.vocab:tan](https://w3id.org/mixs/vocab/tan) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total acid number | +| **Mappings:** | | MIXS:0000120 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 86 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/target_gene.md b/mixs6/target_gene.md new file mode 100644 index 00000000..864490b9 --- /dev/null +++ b/mixs6/target_gene.md @@ -0,0 +1,56 @@ + +# Slot: target_gene + + +Targeted gene or locus name for marker gene studies + +URI: [mixs.vocab:target_gene](https://w3id.org/mixs/vocab/target_gene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | target gene | +| **Comments:** | | Expected value: gene name | +| | | Preferred unit: | +| | | Position: 44.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: M | +| | | CHECKLIST mimarks_c: M | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='16S rRNA, 18S rRNA, nif, amoA, rpo', description=None) | + diff --git a/mixs6/target_subfragment.md b/mixs6/target_subfragment.md new file mode 100644 index 00000000..02cc401c --- /dev/null +++ b/mixs6/target_subfragment.md @@ -0,0 +1,56 @@ + +# Slot: target_subfragment + + +Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + +URI: [mixs.vocab:target_subfragment](https://w3id.org/mixs/vocab/target_subfragment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | target subfragment | +| **Comments:** | | Expected value: gene fragment name | +| | | Preferred unit: | +| | | Position: 45.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='V6, V9, ITS', description=None) | + diff --git a/mixs6/tax_class.md b/mixs6/tax_class.md new file mode 100644 index 00000000..48a9c22d --- /dev/null +++ b/mixs6/tax_class.md @@ -0,0 +1,56 @@ + +# Slot: tax_class + + +Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + +URI: [mixs.vocab:tax_class](https://w3id.org/mixs/vocab/tax_class) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | taxonomic classification | +| **Comments:** | | Expected value: classification method, database name, and other parameters | +| | | Preferred unit: | +| | | Position: 62.0 | +| | | CHECKLIST migs_eu: X | +| | | CHECKLIST migs_ba: X | +| | | CHECKLIST migs_pl: X | +| | | CHECKLIST migs_vi: X | +| | | CHECKLIST migs_org: X | +| | | CHECKLIST me: X | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)', description=None) | + diff --git a/mixs6/tax_ident.md b/mixs6/tax_ident.md new file mode 100644 index 00000000..21c7a4d0 --- /dev/null +++ b/mixs6/tax_ident.md @@ -0,0 +1,56 @@ + +# Slot: tax_ident + + +The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + +URI: [mixs.vocab:tax_ident](https://w3id.org/mixs/vocab/tax_ident) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | taxonomic identity marker | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 53.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: M | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='other: rpoB gene', description=None) | + diff --git a/mixs6/temp.md b/mixs6/temp.md new file mode 100644 index 00000000..80501f4b --- /dev/null +++ b/mixs6/temp.md @@ -0,0 +1,216 @@ + +# Slot: temp + + +Temperature of the sample at the time of sampling + +URI: [mixs.vocab:temp](https://w3id.org/mixs/vocab/temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | temperature | +| **Mappings:** | | MIXS:0000113 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | +| **Examples:** | | Example(value='25 degree Celsius', description=None) | + diff --git a/mixs6/temp_out.md b/mixs6/temp_out.md new file mode 100644 index 00000000..7d2cf27a --- /dev/null +++ b/mixs6/temp_out.md @@ -0,0 +1,48 @@ + +# Slot: temp_out + + +The recorded temperature value at sampling time outside + +URI: [mixs.vocab:temp_out](https://w3id.org/mixs/vocab/temp_out) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | temperature outside house | +| **Mappings:** | | MIXS:0000197 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: degree Celsius | +| | | Occurrence: 1 | +| | | Position: 133 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='5 degree Celsius', description=None) | + diff --git a/mixs6/tertiary_treatment.md b/mixs6/tertiary_treatment.md new file mode 100644 index 00000000..d17d162d --- /dev/null +++ b/mixs6/tertiary_treatment.md @@ -0,0 +1,48 @@ + +# Slot: tertiary_treatment + + +The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + +URI: [mixs.vocab:tertiary_treatment](https://w3id.org/mixs/vocab/tertiary_treatment) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tertiary treatment | +| **Mappings:** | | MIXS:0000352 | +| **Comments:** | | Expected value: tertiary treatment type | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/texture.md b/mixs6/texture.md new file mode 100644 index 00000000..ea9f7a8e --- /dev/null +++ b/mixs6/texture.md @@ -0,0 +1,48 @@ + +# Slot: texture + + +The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + +URI: [mixs.vocab:texture](https://w3id.org/mixs/vocab/texture) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | texture | +| **Mappings:** | | MIXS:0000335 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 35 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/texture_meth.md b/mixs6/texture_meth.md new file mode 100644 index 00000000..9903f4f8 --- /dev/null +++ b/mixs6/texture_meth.md @@ -0,0 +1,48 @@ + +# Slot: texture_meth + + +Reference or method used in determining soil texture + +URI: [mixs.vocab:texture_meth](https://w3id.org/mixs/vocab/texture_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | texture method | +| **Mappings:** | | MIXS:0000336 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 36 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tidal_stage.md b/mixs6/tidal_stage.md new file mode 100644 index 00000000..1c0e07dc --- /dev/null +++ b/mixs6/tidal_stage.md @@ -0,0 +1,60 @@ + +# Slot: tidal_stage + + +Stage of tide + +URI: [mixs.vocab:tidal_stage](https://w3id.org/mixs/vocab/tidal_stage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tidal stage | +| **Mappings:** | | MIXS:0000750 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: sediment, water | +| **Examples:** | | Example(value='high tide', description=None) | + diff --git a/mixs6/tillage.md b/mixs6/tillage.md new file mode 100644 index 00000000..45daa747 --- /dev/null +++ b/mixs6/tillage.md @@ -0,0 +1,48 @@ + +# Slot: tillage + + +Note method(s) used for tilling + +URI: [mixs.vocab:tillage](https://w3id.org/mixs/vocab/tillage) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | history/tillage | +| **Mappings:** | | MIXS:0001081 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 8 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='chisel', description=None) | + diff --git a/mixs6/time_last_toothbrush.md b/mixs6/time_last_toothbrush.md new file mode 100644 index 00000000..89db40f0 --- /dev/null +++ b/mixs6/time_last_toothbrush.md @@ -0,0 +1,48 @@ + +# Slot: time_last_toothbrush + + +Specification of the time since last toothbrushing + +URI: [mixs.vocab:time_last_toothbrush](https://w3id.org/mixs/vocab/time_last_toothbrush) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | time since last toothbrushing | +| **Mappings:** | | MIXS:0000924 | +| **Comments:** | | Expected value: duration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used uniquely in: human-oral | +| **Examples:** | | Example(value='P2H45M', description=None) | + diff --git a/mixs6/time_since_last_wash.md b/mixs6/time_since_last_wash.md new file mode 100644 index 00000000..d0634785 --- /dev/null +++ b/mixs6/time_since_last_wash.md @@ -0,0 +1,48 @@ + +# Slot: time_since_last_wash + + +Specification of the time since last wash + +URI: [mixs.vocab:time_since_last_wash](https://w3id.org/mixs/vocab/time_since_last_wash) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | time since last wash | +| **Mappings:** | | MIXS:0000943 | +| **Comments:** | | Expected value: duration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 2 | +| | | This field is used uniquely in: human-skin | +| **Examples:** | | Example(value='P1D', description=None) | + diff --git a/mixs6/tiss_cult_growth_med.md b/mixs6/tiss_cult_growth_med.md new file mode 100644 index 00000000..857a908e --- /dev/null +++ b/mixs6/tiss_cult_growth_med.md @@ -0,0 +1,48 @@ + +# Slot: tiss_cult_growth_med + + +Description of plant tissue culture growth media used + +URI: [mixs.vocab:tiss_cult_growth_med](https://w3id.org/mixs/vocab/tiss_cult_growth_med) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tissue culture growth media | +| **Mappings:** | | MIXS:0001070 | +| **Comments:** | | Expected value: PMID,DOI,url or free text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='https://link.springer.com/content/pdf/10.1007/BF02796489.pdf', description=None) | + diff --git a/mixs6/toluene.md b/mixs6/toluene.md new file mode 100644 index 00000000..2243078c --- /dev/null +++ b/mixs6/toluene.md @@ -0,0 +1,60 @@ + +# Slot: toluene + + +Concentration of toluene in the sample + +URI: [mixs.vocab:toluene](https://w3id.org/mixs/vocab/toluene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | toluene | +| **Mappings:** | | MIXS:0000154 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 82 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_carb.md b/mixs6/tot_carb.md new file mode 100644 index 00000000..7ba6f8e3 --- /dev/null +++ b/mixs6/tot_carb.md @@ -0,0 +1,60 @@ + +# Slot: tot_carb + + +Total carbon content + +URI: [mixs.vocab:tot_carb](https://w3id.org/mixs/vocab/tot_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total carbon | +| **Mappings:** | | MIXS:0000525 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: microbial mat_biofilm, sediment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_depth_water_col.md b/mixs6/tot_depth_water_col.md new file mode 100644 index 00000000..8de8c90d --- /dev/null +++ b/mixs6/tot_depth_water_col.md @@ -0,0 +1,60 @@ + +# Slot: tot_depth_water_col + + +Measurement of total depth of water column + +URI: [mixs.vocab:tot_depth_water_col](https://w3id.org/mixs/vocab/tot_depth_water_col) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total depth of water column | +| **Mappings:** | | MIXS:0000634 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: sediment, water | +| **Examples:** | | Example(value='500 meter', description=None) | + diff --git a/mixs6/tot_diss_nitro.md b/mixs6/tot_diss_nitro.md new file mode 100644 index 00000000..37c49b31 --- /dev/null +++ b/mixs6/tot_diss_nitro.md @@ -0,0 +1,48 @@ + +# Slot: tot_diss_nitro + + +Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + +URI: [mixs.vocab:tot_diss_nitro](https://w3id.org/mixs/vocab/tot_diss_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total dissolved nitrogen | +| **Mappings:** | | MIXS:0000744 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='40 microgram per liter', description=None) | + diff --git a/mixs6/tot_inorg_nitro.md b/mixs6/tot_inorg_nitro.md new file mode 100644 index 00000000..976d47a7 --- /dev/null +++ b/mixs6/tot_inorg_nitro.md @@ -0,0 +1,48 @@ + +# Slot: tot_inorg_nitro + + +Total inorganic nitrogen content + +URI: [mixs.vocab:tot_inorg_nitro](https://w3id.org/mixs/vocab/tot_inorg_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total inorganic nitrogen | +| **Mappings:** | | MIXS:0000745 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='40 microgram per liter', description=None) | + diff --git a/mixs6/tot_iron.md b/mixs6/tot_iron.md new file mode 100644 index 00000000..08386946 --- /dev/null +++ b/mixs6/tot_iron.md @@ -0,0 +1,60 @@ + +# Slot: tot_iron + + +Concentration of total iron in the sample + +URI: [mixs.vocab:tot_iron](https://w3id.org/mixs/vocab/tot_iron) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total iron | +| **Mappings:** | | MIXS:0000105 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, milligram per kilogram | +| | | Occurrence: 1 | +| | | Position: 71 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_nitro.md b/mixs6/tot_nitro.md new file mode 100644 index 00000000..565e282e --- /dev/null +++ b/mixs6/tot_nitro.md @@ -0,0 +1,84 @@ + +# Slot: tot_nitro + + +Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + +URI: [mixs.vocab:tot_nitro](https://w3id.org/mixs/vocab/tot_nitro) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen concentration | +| **Mappings:** | | MIXS:0000102 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 64 | +| | | This field is used in: 4 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge, water | +| **Examples:** | | Example(value='50 micromole per liter', description=None) | + diff --git a/mixs6/tot_nitro_content.md b/mixs6/tot_nitro_content.md new file mode 100644 index 00000000..3e287979 --- /dev/null +++ b/mixs6/tot_nitro_content.md @@ -0,0 +1,72 @@ + +# Slot: tot_nitro_content + + +Total nitrogen content of the sample + +URI: [mixs.vocab:tot_nitro_content](https://w3id.org/mixs/vocab/tot_nitro_content) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen content | +| **Mappings:** | | MIXS:0000530 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_nitro_content_meth.md b/mixs6/tot_nitro_content_meth.md new file mode 100644 index 00000000..c6b97597 --- /dev/null +++ b/mixs6/tot_nitro_content_meth.md @@ -0,0 +1,48 @@ + +# Slot: tot_nitro_content_meth + + +Reference or method used in determining the total nitrogen + +URI: [mixs.vocab:tot_nitro_content_meth](https://w3id.org/mixs/vocab/tot_nitro_content_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total nitrogen content method | +| **Mappings:** | | MIXS:0000338 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 42 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_org_c_meth.md b/mixs6/tot_org_c_meth.md new file mode 100644 index 00000000..a16da9d8 --- /dev/null +++ b/mixs6/tot_org_c_meth.md @@ -0,0 +1,48 @@ + +# Slot: tot_org_c_meth + + +Reference or method used in determining total organic carbon + +URI: [mixs.vocab:tot_org_c_meth](https://w3id.org/mixs/vocab/tot_org_c_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total organic carbon method | +| **Mappings:** | | MIXS:0000337 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 40 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_org_carb.md b/mixs6/tot_org_carb.md new file mode 100644 index 00000000..18a46583 --- /dev/null +++ b/mixs6/tot_org_carb.md @@ -0,0 +1,72 @@ + +# Slot: tot_org_carb + + +Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + +URI: [mixs.vocab:tot_org_carb](https://w3id.org/mixs/vocab/tot_org_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total organic carbon | +| **Mappings:** | | MIXS:0000533 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram Carbon per kilogram sample material | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_part_carb.md b/mixs6/tot_part_carb.md new file mode 100644 index 00000000..0c92d522 --- /dev/null +++ b/mixs6/tot_part_carb.md @@ -0,0 +1,48 @@ + +# Slot: tot_part_carb + + +Total particulate carbon content + +URI: [mixs.vocab:tot_part_carb](https://w3id.org/mixs/vocab/tot_part_carb) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total particulate carbon | +| **Mappings:** | | MIXS:0000747 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: water | +| **Examples:** | | Example(value='35 micromole per liter', description=None) | + diff --git a/mixs6/tot_phosp.md b/mixs6/tot_phosp.md new file mode 100644 index 00000000..97314e15 --- /dev/null +++ b/mixs6/tot_phosp.md @@ -0,0 +1,72 @@ + +# Slot: tot_phosp + + +Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + +URI: [mixs.vocab:tot_phosp](https://w3id.org/mixs/vocab/tot_phosp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total phosphorus | +| **Mappings:** | | MIXS:0000117 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: micromole per liter, milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 75 | +| | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | +| **Examples:** | | Example(value='0.03 milligram per liter', description=None) | + diff --git a/mixs6/tot_phosphate.md b/mixs6/tot_phosphate.md new file mode 100644 index 00000000..48546f13 --- /dev/null +++ b/mixs6/tot_phosphate.md @@ -0,0 +1,48 @@ + +# Slot: tot_phosphate + + +Total amount or concentration of phosphate + +URI: [mixs.vocab:tot_phosphate](https://w3id.org/mixs/vocab/tot_phosphate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total phosphate | +| **Mappings:** | | MIXS:0000689 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: microgram per liter, micromole per liter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tot_sulfur.md b/mixs6/tot_sulfur.md new file mode 100644 index 00000000..335f5de9 --- /dev/null +++ b/mixs6/tot_sulfur.md @@ -0,0 +1,60 @@ + +# Slot: tot_sulfur + + +Concentration of total sulfur in the sample + +URI: [mixs.vocab:tot_sulfur](https://w3id.org/mixs/vocab/tot_sulfur) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | total sulfur | +| **Mappings:** | | MIXS:0000419 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 60 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/train_line.md b/mixs6/train_line.md new file mode 100644 index 00000000..1774bab1 --- /dev/null +++ b/mixs6/train_line.md @@ -0,0 +1,48 @@ + +# Slot: train_line + + +The subway line name + +URI: [mixs.vocab:train_line](https://w3id.org/mixs/vocab/train_line) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train line | +| **Mappings:** | | MIXS:0000837 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 134 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='red', description=None) | + diff --git a/mixs6/train_stat_loc.md b/mixs6/train_stat_loc.md new file mode 100644 index 00000000..939233ac --- /dev/null +++ b/mixs6/train_stat_loc.md @@ -0,0 +1,48 @@ + +# Slot: train_stat_loc + + +The train station collection location + +URI: [mixs.vocab:train_stat_loc](https://w3id.org/mixs/vocab/train_stat_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train station collection location | +| **Mappings:** | | MIXS:0000838 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 135 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='forest hills', description=None) | + diff --git a/mixs6/train_stop_loc.md b/mixs6/train_stop_loc.md new file mode 100644 index 00000000..a4cff1b8 --- /dev/null +++ b/mixs6/train_stop_loc.md @@ -0,0 +1,48 @@ + +# Slot: train_stop_loc + + +The train stop collection location + +URI: [mixs.vocab:train_stop_loc](https://w3id.org/mixs/vocab/train_stop_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | train stop collection location | +| **Mappings:** | | MIXS:0000839 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 136 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='end', description=None) | + diff --git a/mixs6/travel_out_six_month.md b/mixs6/travel_out_six_month.md new file mode 100644 index 00000000..aa1d0be1 --- /dev/null +++ b/mixs6/travel_out_six_month.md @@ -0,0 +1,48 @@ + +# Slot: travel_out_six_month + + +Specification of the countries travelled in the last six months; can include multiple travels + +URI: [mixs.vocab:travel_out_six_month](https://w3id.org/mixs/vocab/travel_out_six_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | travel outside the country in last six months | +| **Mappings:** | | MIXS:0000268 | +| **Comments:** | | Expected value: country name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 26 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/trna_ext_software.md b/mixs6/trna_ext_software.md new file mode 100644 index 00000000..49683728 --- /dev/null +++ b/mixs6/trna_ext_software.md @@ -0,0 +1,56 @@ + +# Slot: trna_ext_software + + +Tools used for tRNA identification + +URI: [mixs.vocab:trna_ext_software](https://w3id.org/mixs/vocab/trna_ext_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | tRNA extraction software | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Preferred unit: | +| | | Position: 66.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='infernal;v2;default parameters', description=None) | + diff --git a/mixs6/trnas.md b/mixs6/trnas.md new file mode 100644 index 00000000..398bb910 --- /dev/null +++ b/mixs6/trnas.md @@ -0,0 +1,56 @@ + +# Slot: trnas + + +The total number of tRNAs identified from the SAG or MAG + +URI: [mixs.vocab:trnas](https://w3id.org/mixs/vocab/trnas) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | number of standard tRNAs extracted | +| **Comments:** | | Expected value: value from 0-21 | +| | | Preferred unit: | +| | | Position: 65.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: X | +| **Examples:** | | Example(value='18', description=None) | + diff --git a/mixs6/trophic_level.md b/mixs6/trophic_level.md new file mode 100644 index 00000000..bf95829b --- /dev/null +++ b/mixs6/trophic_level.md @@ -0,0 +1,56 @@ + +# Slot: trophic_level + + +Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + +URI: [mixs.vocab:trophic_level](https://w3id.org/mixs/vocab/trophic_level) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | trophic level | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 26.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='heterotroph', description=None) | + diff --git a/mixs6/turbidity.md b/mixs6/turbidity.md new file mode 100644 index 00000000..1c1de5b3 --- /dev/null +++ b/mixs6/turbidity.md @@ -0,0 +1,72 @@ + +# Slot: turbidity + + +Measure of the amount of cloudiness or haziness in water caused by individual particles + +URI: [mixs.vocab:turbidity](https://w3id.org/mixs/vocab/turbidity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | turbidity | +| **Mappings:** | | MIXS:0000191 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: formazin turbidity unit, formazin nephelometric units | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | +| **Examples:** | | Example(value='0.3 nephelometric turbidity units', description=None) | + diff --git a/mixs6/tvdss_of_hcr_pressure.md b/mixs6/tvdss_of_hcr_pressure.md new file mode 100644 index 00000000..f146c44a --- /dev/null +++ b/mixs6/tvdss_of_hcr_pressure.md @@ -0,0 +1,60 @@ + +# Slot: tvdss_of_hcr_pressure + + +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + +URI: [mixs.vocab:tvdss_of_hcr_pressure](https://w3id.org/mixs/vocab/tvdss_of_hcr_pressure) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depth (TVDSS) of hydrocarbon resource pressure | +| **Mappings:** | | MIXS:0000397 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 9 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/tvdss_of_hcr_temp.md b/mixs6/tvdss_of_hcr_temp.md new file mode 100644 index 00000000..682fac52 --- /dev/null +++ b/mixs6/tvdss_of_hcr_temp.md @@ -0,0 +1,60 @@ + +# Slot: tvdss_of_hcr_temp + + +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + +URI: [mixs.vocab:tvdss_of_hcr_temp](https://w3id.org/mixs/vocab/tvdss_of_hcr_temp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | depth (TVDSS) of hydrocarbon resource temperature | +| **Mappings:** | | MIXS:0000394 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter | +| | | Occurrence: 1 | +| | | Position: 7 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/twin_sibling.md b/mixs6/twin_sibling.md new file mode 100644 index 00000000..9d7e99d2 --- /dev/null +++ b/mixs6/twin_sibling.md @@ -0,0 +1,48 @@ + +# Slot: twin_sibling + + +Specification of twin sibling presence + +URI: [mixs.vocab:twin_sibling](https://w3id.org/mixs/vocab/twin_sibling) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | twin sibling presence | +| **Mappings:** | | MIXS:0000326 | +| **Comments:** | | Expected value: presence status | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 27 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/typ_occup_density.md b/mixs6/typ_occup_density.md new file mode 100644 index 00000000..35be40c3 --- /dev/null +++ b/mixs6/typ_occup_density.md @@ -0,0 +1,48 @@ + +# Slot: typ_occup_density + + +Customary or normal density of occupants + +URI: [mixs.vocab:typ_occup_density](https://w3id.org/mixs/vocab/typ_occup_density) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | typical occupant density | +| **Mappings:** | | MIXS:0000771 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 24 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='25', description=None) | + diff --git a/mixs6/urine_collect_meth.md b/mixs6/urine_collect_meth.md new file mode 100644 index 00000000..9983fbcb --- /dev/null +++ b/mixs6/urine_collect_meth.md @@ -0,0 +1,48 @@ + +# Slot: urine_collect_meth + + +Specification of urine collection method + +URI: [mixs.vocab:urine_collect_meth](https://w3id.org/mixs/vocab/urine_collect_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/collection method | +| **Mappings:** | | MIXS:0000899 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 43 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='catheter', description=None) | + diff --git a/mixs6/url.md b/mixs6/url.md new file mode 100644 index 00000000..0dfa22e0 --- /dev/null +++ b/mixs6/url.md @@ -0,0 +1,56 @@ + +# Slot: url + + + + +URI: [mixs.vocab:url](https://w3id.org/mixs/vocab/url) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | relevant electronic resources | +| **Comments:** | | Expected value: URL | +| | | Preferred unit: | +| | | Position: 92.0 | +| | | CHECKLIST migs_eu: C | +| | | CHECKLIST migs_ba: C | +| | | CHECKLIST migs_pl: C | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: C | +| | | CHECKLIST me: C | +| | | CHECKLIST mimarks_s: C | +| | | CHECKLIST mimarks_c: C | +| | | CHECKLIST misag: C | +| | | CHECKLIST mimag: C | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='http://www.earthmicrobiome.org/', description=None) | + diff --git a/mixs6/urogenit_disord.md b/mixs6/urogenit_disord.md new file mode 100644 index 00000000..f970859c --- /dev/null +++ b/mixs6/urogenit_disord.md @@ -0,0 +1,48 @@ + +# Slot: urogenit_disord + + +History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + +URI: [mixs.vocab:urogenit_disord](https://w3id.org/mixs/vocab/urogenit_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urogenital disorder | +| **Mappings:** | | MIXS:0000289 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 10 | +| | | This field is used uniquely in: human-vaginal | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/urogenit_tract_disor.md b/mixs6/urogenit_tract_disor.md new file mode 100644 index 00000000..4e8637ef --- /dev/null +++ b/mixs6/urogenit_tract_disor.md @@ -0,0 +1,48 @@ + +# Slot: urogenit_tract_disor + + +History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + +URI: [mixs.vocab:urogenit_tract_disor](https://w3id.org/mixs/vocab/urogenit_tract_disor) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/urogenital tract disorder | +| **Mappings:** | | MIXS:0000278 | +| **Comments:** | | Expected value: disorder name | +| | | Preferred unit: | +| | | Occurrence: m | +| | | Position: 41 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/ventilation_rate.md b/mixs6/ventilation_rate.md new file mode 100644 index 00000000..4bdecf2b --- /dev/null +++ b/mixs6/ventilation_rate.md @@ -0,0 +1,48 @@ + +# Slot: ventilation_rate + + +Ventilation rate of the system in the sampled premises + +URI: [mixs.vocab:ventilation_rate](https://w3id.org/mixs/vocab/ventilation_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ventilation rate | +| **Mappings:** | | MIXS:0000114 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per minute, liters per second | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='750 cubic meter per minute', description=None) | + diff --git a/mixs6/ventilation_type.md b/mixs6/ventilation_type.md new file mode 100644 index 00000000..45386e92 --- /dev/null +++ b/mixs6/ventilation_type.md @@ -0,0 +1,60 @@ + +# Slot: ventilation_type + + +Ventilation system used in the sampled premises + +URI: [mixs.vocab:ventilation_type](https://w3id.org/mixs/vocab/ventilation_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ventilation type | +| **Mappings:** | | MIXS:0000756 | +| **Comments:** | | Expected value: ventilation type name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: air, built environment | +| **Examples:** | | Example(value='Operable windows', description=None) | + diff --git a/mixs6/vfa.md b/mixs6/vfa.md new file mode 100644 index 00000000..4914d32d --- /dev/null +++ b/mixs6/vfa.md @@ -0,0 +1,60 @@ + +# Slot: vfa + + +Concentration of Volatile Fatty Acids in the sample + +URI: [mixs.vocab:vfa](https://w3id.org/mixs/vocab/vfa) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | volatile fatty acids | +| **Mappings:** | | MIXS:0000152 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 80 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/vfa_fw.md b/mixs6/vfa_fw.md new file mode 100644 index 00000000..9194aa70 --- /dev/null +++ b/mixs6/vfa_fw.md @@ -0,0 +1,60 @@ + +# Slot: vfa_fw + + +Original volatile fatty acid concentration in the hydrocarbon resource + +URI: [mixs.vocab:vfa_fw](https://w3id.org/mixs/vocab/vfa_fw) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vfa in formation water | +| **Mappings:** | | MIXS:0000408 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter | +| | | Occurrence: 1 | +| | | Position: 18 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/vir_ident_software.md b/mixs6/vir_ident_software.md new file mode 100644 index 00000000..47cb8637 --- /dev/null +++ b/mixs6/vir_ident_software.md @@ -0,0 +1,56 @@ + +# Slot: vir_ident_software + + +Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + +URI: [mixs.vocab:vir_ident_software](https://w3id.org/mixs/vocab/vir_ident_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | viral identification software | +| **Comments:** | | Expected value: software name, version and relevant parameters | +| | | Preferred unit: | +| | | Position: 83.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='VirSorter; 1.0.4; Virome database, category 2', description=None) | + diff --git a/mixs6/virus_enrich_appr.md b/mixs6/virus_enrich_appr.md new file mode 100644 index 00000000..a021c28c --- /dev/null +++ b/mixs6/virus_enrich_appr.md @@ -0,0 +1,56 @@ + +# Slot: virus_enrich_appr + + +List of approaches used to enrich the sample for viruses, if any + +URI: [mixs.vocab:virus_enrich_appr](https://w3id.org/mixs/vocab/virus_enrich_appr) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | virus enrichment approach | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 36.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: C | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: M | +| **Examples:** | | Example(value='filtration + FeCl Precipitation + ultracentrifugation + DNAse', description=None) | + diff --git a/mixs6/vis_media.md b/mixs6/vis_media.md new file mode 100644 index 00000000..c17a1e9f --- /dev/null +++ b/mixs6/vis_media.md @@ -0,0 +1,48 @@ + +# Slot: vis_media + + +The building visual media + +URI: [mixs.vocab:vis_media](https://w3id.org/mixs/vocab/vis_media) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | visual media | +| **Mappings:** | | MIXS:0000840 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 137 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='3D scans', description=None) | + diff --git a/mixs6/viscosity.md b/mixs6/viscosity.md new file mode 100644 index 00000000..853feb60 --- /dev/null +++ b/mixs6/viscosity.md @@ -0,0 +1,60 @@ + +# Slot: viscosity + + +A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + +URI: [mixs.vocab:viscosity](https://w3id.org/mixs/vocab/viscosity) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | viscosity | +| **Mappings:** | | MIXS:0000126 | +| **Comments:** | | Expected value: measurement value;measurement value | +| | | Preferred unit: cP at degree Celsius | +| | | Occurrence: 1 | +| | | Position: 87 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/volatile_org_comp.md b/mixs6/volatile_org_comp.md new file mode 100644 index 00000000..f0273bfd --- /dev/null +++ b/mixs6/volatile_org_comp.md @@ -0,0 +1,48 @@ + +# Slot: volatile_org_comp + + +Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + +URI: [mixs.vocab:volatile_org_comp](https://w3id.org/mixs/vocab/volatile_org_comp) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | volatile organic compounds | +| **Mappings:** | | MIXS:0000115 | +| **Comments:** | | Expected value: volatile organic compound name;measurement value | +| | | Preferred unit: microgram per cubic meter, parts per million, nanogram per liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='formaldehyde;500 nanogram per liter', description=None) | + diff --git a/mixs6/votu_class_appr.md b/mixs6/votu_class_appr.md new file mode 100644 index 00000000..0240f9fd --- /dev/null +++ b/mixs6/votu_class_appr.md @@ -0,0 +1,56 @@ + +# Slot: votu_class_appr + + +Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + +URI: [mixs.vocab:votu_class_appr](https://w3id.org/mixs/vocab/votu_class_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU classification approach | +| **Comments:** | | Expected value: cutoffs and method used | +| | | Preferred unit: | +| | | Position: 87.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='95% ANI;85% AF; greedy incremental clustering', description=None) | + diff --git a/mixs6/votu_db.md b/mixs6/votu_db.md new file mode 100644 index 00000000..0bf67ee2 --- /dev/null +++ b/mixs6/votu_db.md @@ -0,0 +1,56 @@ + +# Slot: votu_db + + +Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + +URI: [mixs.vocab:votu_db](https://w3id.org/mixs/vocab/votu_db) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU database | +| **Comments:** | | Expected value: database and version | +| | | Preferred unit: | +| | | Position: 89.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='NCBI Viral RefSeq;83', description=None) | + diff --git a/mixs6/votu_seq_comp_appr.md b/mixs6/votu_seq_comp_appr.md new file mode 100644 index 00000000..4719341b --- /dev/null +++ b/mixs6/votu_seq_comp_appr.md @@ -0,0 +1,56 @@ + +# Slot: votu_seq_comp_appr + + +Tool and thresholds used to compare sequences when computing "species-level" vOTUs + +URI: [mixs.vocab:votu_seq_comp_appr](https://w3id.org/mixs/vocab/votu_seq_comp_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | vOTU sequence comparison approach | +| **Comments:** | | Expected value: software name, version and relevant parameters | +| | | Preferred unit: | +| | | Position: 88.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: - | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='blastn;2.6.0+;e-value cutoff: 0.001', description=None) | + diff --git a/mixs6/wall_area.md b/mixs6/wall_area.md new file mode 100644 index 00000000..7e5a2395 --- /dev/null +++ b/mixs6/wall_area.md @@ -0,0 +1,48 @@ + +# Slot: wall_area + + +The total area of the sampled room's walls + +URI: [mixs.vocab:wall_area](https://w3id.org/mixs/vocab/wall_area) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall area | +| **Mappings:** | | MIXS:0000198 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 138 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_const_type.md b/mixs6/wall_const_type.md new file mode 100644 index 00000000..ff7f2f8d --- /dev/null +++ b/mixs6/wall_const_type.md @@ -0,0 +1,48 @@ + +# Slot: wall_const_type + + +The building class of the wall defined by the composition of the building elements and fire-resistance rating. + +URI: [mixs.vocab:wall_const_type](https://w3id.org/mixs/vocab/wall_const_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall construction type | +| **Mappings:** | | MIXS:0000841 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 139 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='fire resistive', description=None) | + diff --git a/mixs6/wall_finish_mat.md b/mixs6/wall_finish_mat.md new file mode 100644 index 00000000..1d795065 --- /dev/null +++ b/mixs6/wall_finish_mat.md @@ -0,0 +1,48 @@ + +# Slot: wall_finish_mat + + +The material utilized to finish the outer most layer of the wall + +URI: [mixs.vocab:wall_finish_mat](https://w3id.org/mixs/vocab/wall_finish_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall finish material | +| **Mappings:** | | MIXS:0000842 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 140 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/wall_height.md b/mixs6/wall_height.md new file mode 100644 index 00000000..79e4a6cd --- /dev/null +++ b/mixs6/wall_height.md @@ -0,0 +1,48 @@ + +# Slot: wall_height + + +The average height of the walls in the sampled room + +URI: [mixs.vocab:wall_height](https://w3id.org/mixs/vocab/wall_height) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall height | +| **Mappings:** | | MIXS:0000221 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: centimeter | +| | | Occurrence: 1 | +| | | Position: 141 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_loc.md b/mixs6/wall_loc.md new file mode 100644 index 00000000..f4e384cb --- /dev/null +++ b/mixs6/wall_loc.md @@ -0,0 +1,48 @@ + +# Slot: wall_loc + + +The relative location of the wall within the room + +URI: [mixs.vocab:wall_loc](https://w3id.org/mixs/vocab/wall_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall location | +| **Mappings:** | | MIXS:0000843 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 142 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='north', description=None) | + diff --git a/mixs6/wall_surf_treatment.md b/mixs6/wall_surf_treatment.md new file mode 100644 index 00000000..29854833 --- /dev/null +++ b/mixs6/wall_surf_treatment.md @@ -0,0 +1,48 @@ + +# Slot: wall_surf_treatment + + +The surface treatment of interior wall + +URI: [mixs.vocab:wall_surf_treatment](https://w3id.org/mixs/vocab/wall_surf_treatment) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall surface treatment | +| **Mappings:** | | MIXS:0000845 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 144 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='paneling', description=None) | + diff --git a/mixs6/wall_texture.md b/mixs6/wall_texture.md new file mode 100644 index 00000000..87c9d56b --- /dev/null +++ b/mixs6/wall_texture.md @@ -0,0 +1,48 @@ + +# Slot: wall_texture + + +The feel, appearance, or consistency of a wall surface + +URI: [mixs.vocab:wall_texture](https://w3id.org/mixs/vocab/wall_texture) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall texture | +| **Mappings:** | | MIXS:0000846 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 145 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='popcorn', description=None) | + diff --git a/mixs6/wall_thermal_mass.md b/mixs6/wall_thermal_mass.md new file mode 100644 index 00000000..fdcfcd6a --- /dev/null +++ b/mixs6/wall_thermal_mass.md @@ -0,0 +1,48 @@ + +# Slot: wall_thermal_mass + + +The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + +URI: [mixs.vocab:wall_thermal_mass](https://w3id.org/mixs/vocab/wall_thermal_mass) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall thermal mass | +| **Mappings:** | | MIXS:0000222 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: joule per degree Celsius | +| | | Occurrence: 1 | +| | | Position: 146 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wall_water_mold.md b/mixs6/wall_water_mold.md new file mode 100644 index 00000000..a54cda50 --- /dev/null +++ b/mixs6/wall_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: wall_water_mold + + +Signs of the presence of mold or mildew on a wall + +URI: [mixs.vocab:wall_water_mold](https://w3id.org/mixs/vocab/wall_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wall signs of water/mold | +| **Mappings:** | | MIXS:0000844 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 143 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/wastewater_type.md b/mixs6/wastewater_type.md new file mode 100644 index 00000000..cf4c7f2c --- /dev/null +++ b/mixs6/wastewater_type.md @@ -0,0 +1,48 @@ + +# Slot: wastewater_type + + +The origin of wastewater such as human waste, rainfall, storm drains, etc. + +URI: [mixs.vocab:wastewater_type](https://w3id.org/mixs/vocab/wastewater_type) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wastewater type | +| **Mappings:** | | MIXS:0000353 | +| **Comments:** | | Expected value: wastewater type name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: wastewater_sludge | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_content.md b/mixs6/water_content.md new file mode 100644 index 00000000..5f93f11e --- /dev/null +++ b/mixs6/water_content.md @@ -0,0 +1,72 @@ + +# Slot: water_content + + +Water content measurement + +URI: [mixs.vocab:water_content](https://w3id.org/mixs/vocab/water_content) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water content | +| **Mappings:** | | MIXS:0000185 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: gram per gram or cubic centimeter per cubic centimeter | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_content_soil_meth.md b/mixs6/water_content_soil_meth.md new file mode 100644 index 00000000..19052919 --- /dev/null +++ b/mixs6/water_content_soil_meth.md @@ -0,0 +1,48 @@ + +# Slot: water_content_soil_meth + + +Reference or method used in determining the water content of soil + +URI: [mixs.vocab:water_content_soil_meth](https://w3id.org/mixs/vocab/water_content_soil_meth) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water content method | +| **Mappings:** | | MIXS:0000323 | +| **Comments:** | | Expected value: PMID,DOI or url | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 16 | +| | | This field is used uniquely in: soil | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_current.md b/mixs6/water_current.md new file mode 100644 index 00000000..fdffd7f1 --- /dev/null +++ b/mixs6/water_current.md @@ -0,0 +1,60 @@ + +# Slot: water_current + + +Measurement of magnitude and direction of flow within a fluid + +URI: [mixs.vocab:water_current](https://w3id.org/mixs/vocab/water_current) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water current | +| **Mappings:** | | MIXS:0000203 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per second, knots | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used in: 2 packages: miscellaneous natural or artificial environment, water | +| **Examples:** | | Example(value='10 cubic meter per second', description=None) | + diff --git a/mixs6/water_cut.md b/mixs6/water_cut.md new file mode 100644 index 00000000..d6e1b7f4 --- /dev/null +++ b/mixs6/water_cut.md @@ -0,0 +1,48 @@ + +# Slot: water_cut + + +Current amount of water (%) in a produced fluid stream; or the average of the combined streams + +URI: [mixs.vocab:water_cut](https://w3id.org/mixs/vocab/water_cut) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water cut | +| **Mappings:** | | MIXS:0000454 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: percent | +| | | Occurrence: 1 | +| | | Position: 26 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_feat_size.md b/mixs6/water_feat_size.md new file mode 100644 index 00000000..79f91383 --- /dev/null +++ b/mixs6/water_feat_size.md @@ -0,0 +1,48 @@ + +# Slot: water_feat_size + + +The size of the water feature + +URI: [mixs.vocab:water_feat_size](https://w3id.org/mixs/vocab/water_feat_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water feature size | +| **Mappings:** | | MIXS:0000223 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: square meter | +| | | Occurrence: 1 | +| | | Position: 147 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_feat_type.md b/mixs6/water_feat_type.md new file mode 100644 index 00000000..2dd2a699 --- /dev/null +++ b/mixs6/water_feat_type.md @@ -0,0 +1,48 @@ + +# Slot: water_feat_type + + +The type of water feature present within the building being sampled + +URI: [mixs.vocab:water_feat_type](https://w3id.org/mixs/vocab/water_feat_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water feature type | +| **Mappings:** | | MIXS:0000847 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 148 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='stream', description=None) | + diff --git a/mixs6/water_production_rate.md b/mixs6/water_production_rate.md new file mode 100644 index 00000000..02b022a0 --- /dev/null +++ b/mixs6/water_production_rate.md @@ -0,0 +1,48 @@ + +# Slot: water_production_rate + + +Water production rates per well (e.g. 987 m3 / day) + +URI: [mixs.vocab:water_production_rate](https://w3id.org/mixs/vocab/water_production_rate) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water production rate | +| **Mappings:** | | MIXS:0000453 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: cubic meter per day | +| | | Occurrence: 1 | +| | | Position: 25 | +| | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/water_temp_regm.md b/mixs6/water_temp_regm.md new file mode 100644 index 00000000..0cc55c5a --- /dev/null +++ b/mixs6/water_temp_regm.md @@ -0,0 +1,48 @@ + +# Slot: water_temp_regm + + +Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:water_temp_regm](https://w3id.org/mixs/vocab/water_temp_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | water temperature regimen | +| **Mappings:** | | MIXS:0000590 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: degree Celsius | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/watering_regm.md b/mixs6/watering_regm.md new file mode 100644 index 00000000..c9db20cf --- /dev/null +++ b/mixs6/watering_regm.md @@ -0,0 +1,48 @@ + +# Slot: watering_regm + + +Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + +URI: [mixs.vocab:watering_regm](https://w3id.org/mixs/vocab/watering_regm) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | watering regimen | +| **Mappings:** | | MIXS:0000591 | +| **Comments:** | | Expected value: measurement value;treatment interval and duration | +| | | Preferred unit: milliliter, liter | +| | | Occurrence: m | +| | | Position: 1 | +| | | This field is used uniquely in: plant-associated | +| **Examples:** | | Example(value='1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | + diff --git a/mixs6/weekday.md b/mixs6/weekday.md new file mode 100644 index 00000000..c60c7720 --- /dev/null +++ b/mixs6/weekday.md @@ -0,0 +1,48 @@ + +# Slot: weekday + + +The day of the week when sampling occurred + +URI: [mixs.vocab:weekday](https://w3id.org/mixs/vocab/weekday) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | weekday | +| **Mappings:** | | MIXS:0000848 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 149 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='Sunday', description=None) | + diff --git a/mixs6/weight_loss_3_month.md b/mixs6/weight_loss_3_month.md new file mode 100644 index 00000000..51d4263c --- /dev/null +++ b/mixs6/weight_loss_3_month.md @@ -0,0 +1,48 @@ + +# Slot: weight_loss_3_month + + +Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + +URI: [mixs.vocab:weight_loss_3_month](https://w3id.org/mixs/vocab/weight_loss_3_month) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | weight loss in last three months | +| **Mappings:** | | MIXS:0000295 | +| **Comments:** | | Expected value: weight loss specification;measurement value | +| | | Preferred unit: kilogram, gram | +| | | Occurrence: 1 | +| | | Position: 22 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='yes;5 kilogram', description=None) | + diff --git a/mixs6/wga_amp_appr.md b/mixs6/wga_amp_appr.md new file mode 100644 index 00000000..90170ae6 --- /dev/null +++ b/mixs6/wga_amp_appr.md @@ -0,0 +1,56 @@ + +# Slot: wga_amp_appr + + +Method used to amplify genomic DNA in preparation for sequencing + +URI: [mixs.vocab:wga_amp_appr](https://w3id.org/mixs/vocab/wga_amp_appr) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | WGA amplification approach | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Position: 77.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: M | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='mda based', description=None) | + diff --git a/mixs6/wga_amp_kit.md b/mixs6/wga_amp_kit.md new file mode 100644 index 00000000..b2990e73 --- /dev/null +++ b/mixs6/wga_amp_kit.md @@ -0,0 +1,56 @@ + +# Slot: wga_amp_kit + + +Kit used to amplify genomic DNA in preparation for sequencing + +URI: [mixs.vocab:wga_amp_kit](https://w3id.org/mixs/vocab/wga_amp_kit) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | WGA amplification kit | +| **Comments:** | | Expected value: kit name | +| | | Preferred unit: | +| | | Position: 78.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: - | +| | | CHECKLIST miuvig: C | +| **Examples:** | | Example(value='qiagen repli-g', description=None) | + diff --git a/mixs6/win.md b/mixs6/win.md new file mode 100644 index 00000000..797260ea --- /dev/null +++ b/mixs6/win.md @@ -0,0 +1,60 @@ + +# Slot: win + + +A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + +URI: [mixs.vocab:win](https://w3id.org/mixs/vocab/win) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | well identification number | +| **Mappings:** | | MIXS:0000297 | +| **Comments:** | | Expected value: text | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 36 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/wind_direction.md b/mixs6/wind_direction.md new file mode 100644 index 00000000..b9e9ddac --- /dev/null +++ b/mixs6/wind_direction.md @@ -0,0 +1,48 @@ + +# Slot: wind_direction + + +Wind direction is the direction from which a wind originates + +URI: [mixs.vocab:wind_direction](https://w3id.org/mixs/vocab/wind_direction) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wind direction | +| **Mappings:** | | MIXS:0000757 | +| **Comments:** | | Expected value: wind direction name | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='Northwest', description=None) | + diff --git a/mixs6/wind_speed.md b/mixs6/wind_speed.md new file mode 100644 index 00000000..1afeea98 --- /dev/null +++ b/mixs6/wind_speed.md @@ -0,0 +1,48 @@ + +# Slot: wind_speed + + +Speed of wind measured at the time of sampling + +URI: [mixs.vocab:wind_speed](https://w3id.org/mixs/vocab/wind_speed) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | wind speed | +| **Mappings:** | | MIXS:0000118 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: meter per second, kilometer per hour | +| | | Occurrence: 1 | +| | | Position: 1 | +| | | This field is used uniquely in: air | +| **Examples:** | | Example(value='21 kilometer per hour', description=None) | + diff --git a/mixs6/window_cond.md b/mixs6/window_cond.md new file mode 100644 index 00000000..6d12942a --- /dev/null +++ b/mixs6/window_cond.md @@ -0,0 +1,48 @@ + +# Slot: window_cond + + +The physical condition of the window at the time of sampling + +URI: [mixs.vocab:window_cond](https://w3id.org/mixs/vocab/window_cond) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window condition | +| **Mappings:** | | MIXS:0000849 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 151 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='rupture', description=None) | + diff --git a/mixs6/window_cover.md b/mixs6/window_cover.md new file mode 100644 index 00000000..ecc8031a --- /dev/null +++ b/mixs6/window_cover.md @@ -0,0 +1,48 @@ + +# Slot: window_cover + + +The type of window covering + +URI: [mixs.vocab:window_cover](https://w3id.org/mixs/vocab/window_cover) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window covering | +| **Mappings:** | | MIXS:0000850 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 152 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='curtains', description=None) | + diff --git a/mixs6/window_horiz_pos.md b/mixs6/window_horiz_pos.md new file mode 100644 index 00000000..67651ac1 --- /dev/null +++ b/mixs6/window_horiz_pos.md @@ -0,0 +1,48 @@ + +# Slot: window_horiz_pos + + +The horizontal position of the window on the wall + +URI: [mixs.vocab:window_horiz_pos](https://w3id.org/mixs/vocab/window_horiz_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window horizontal position | +| **Mappings:** | | MIXS:0000851 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 153 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='middle', description=None) | + diff --git a/mixs6/window_loc.md b/mixs6/window_loc.md new file mode 100644 index 00000000..1136f85a --- /dev/null +++ b/mixs6/window_loc.md @@ -0,0 +1,48 @@ + +# Slot: window_loc + + +The relative location of the window within the room + +URI: [mixs.vocab:window_loc](https://w3id.org/mixs/vocab/window_loc) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window location | +| **Mappings:** | | MIXS:0000852 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 154 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='west', description=None) | + diff --git a/mixs6/window_mat.md b/mixs6/window_mat.md new file mode 100644 index 00000000..4fb2fe65 --- /dev/null +++ b/mixs6/window_mat.md @@ -0,0 +1,48 @@ + +# Slot: window_mat + + +The type of material used to finish a window + +URI: [mixs.vocab:window_mat](https://w3id.org/mixs/vocab/window_mat) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window material | +| **Mappings:** | | MIXS:0000853 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 155 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='wood', description=None) | + diff --git a/mixs6/window_open_freq.md b/mixs6/window_open_freq.md new file mode 100644 index 00000000..37a6b932 --- /dev/null +++ b/mixs6/window_open_freq.md @@ -0,0 +1,48 @@ + +# Slot: window_open_freq + + +The number of times windows are opened per week + +URI: [mixs.vocab:window_open_freq](https://w3id.org/mixs/vocab/window_open_freq) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window open frequency | +| **Mappings:** | | MIXS:0000246 | +| **Comments:** | | Expected value: value | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 156 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/window_size.md b/mixs6/window_size.md new file mode 100644 index 00000000..62f82b71 --- /dev/null +++ b/mixs6/window_size.md @@ -0,0 +1,48 @@ + +# Slot: window_size + + +The window's length and width + +URI: [mixs.vocab:window_size](https://w3id.org/mixs/vocab/window_size) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window area/size | +| **Mappings:** | | MIXS:0000224 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: inch, meter | +| | | Occurrence: 1 | +| | | Position: 150 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/window_status.md b/mixs6/window_status.md new file mode 100644 index 00000000..e6d835d5 --- /dev/null +++ b/mixs6/window_status.md @@ -0,0 +1,48 @@ + +# Slot: window_status + + +Defines whether the windows were open or closed during environmental testing + +URI: [mixs.vocab:window_status](https://w3id.org/mixs/vocab/window_status) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window status | +| **Mappings:** | | MIXS:0000855 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 158 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='open', description=None) | + diff --git a/mixs6/window_type.md b/mixs6/window_type.md new file mode 100644 index 00000000..97b4928b --- /dev/null +++ b/mixs6/window_type.md @@ -0,0 +1,48 @@ + +# Slot: window_type + + +The type of windows + +URI: [mixs.vocab:window_type](https://w3id.org/mixs/vocab/window_type) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window type | +| **Mappings:** | | MIXS:0000856 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 159 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='fixed window', description=None) | + diff --git a/mixs6/window_vert_pos.md b/mixs6/window_vert_pos.md new file mode 100644 index 00000000..b6b3a807 --- /dev/null +++ b/mixs6/window_vert_pos.md @@ -0,0 +1,48 @@ + +# Slot: window_vert_pos + + +The vertical position of the window on the wall + +URI: [mixs.vocab:window_vert_pos](https://w3id.org/mixs/vocab/window_vert_pos) + + +## Domain and Range + +None -> OPT + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window vertical position | +| **Mappings:** | | MIXS:0000857 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 160 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='middle', description=None) | + diff --git a/mixs6/window_water_mold.md b/mixs6/window_water_mold.md new file mode 100644 index 00000000..0a137088 --- /dev/null +++ b/mixs6/window_water_mold.md @@ -0,0 +1,48 @@ + +# Slot: window_water_mold + + +Signs of the presence of mold or mildew on the window. + +URI: [mixs.vocab:window_water_mold](https://w3id.org/mixs/vocab/window_water_mold) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | window signs of water/mold | +| **Mappings:** | | MIXS:0000854 | +| **Comments:** | | Expected value: enumeration | +| | | Preferred unit: | +| | | Occurrence: 1 | +| | | Position: 157 | +| | | This field is used uniquely in: built environment | +| **Examples:** | | Example(value='no presence of mold visible', description=None) | + diff --git a/mixs6/x_16s_recover.md b/mixs6/x_16s_recover.md new file mode 100644 index 00000000..509515be --- /dev/null +++ b/mixs6/x_16s_recover.md @@ -0,0 +1,56 @@ + +# Slot: x_16s_recover + + +Can a 16S gene be recovered from the submitted SAG or MAG? + +URI: [mixs.vocab:x_16s_recover](https://w3id.org/mixs/vocab/x_16s_recover) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | 16S recovered | +| **Comments:** | | Expected value: boolean | +| | | Preferred unit: | +| | | Position: 63.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='yes', description=None) | + diff --git a/mixs6/x_16s_recover_software.md b/mixs6/x_16s_recover_software.md new file mode 100644 index 00000000..34c2a9fa --- /dev/null +++ b/mixs6/x_16s_recover_software.md @@ -0,0 +1,56 @@ + +# Slot: x_16s_recover_software + + +Tools used for 16S rRNA gene extraction + +URI: [mixs.vocab:x_16s_recover_software](https://w3id.org/mixs/vocab/x_16s_recover_software) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [sequencing field](sequencing_field.md) + +## Children + + +## Used by + + * [Core](Core.md) + * [CoreMe](CoreMe.md) + * [CoreMigsBa](CoreMigsBa.md) + * [CoreMigsEu](CoreMigsEu.md) + * [CoreMigsOrg](CoreMigsOrg.md) + * [CoreMigsPl](CoreMigsPl.md) + * [CoreMigsVi](CoreMigsVi.md) + * [CoreMimag](CoreMimag.md) + * [CoreMimarksC](CoreMimarksC.md) + * [CoreMimarksS](CoreMimarksS.md) + * [CoreMisag](CoreMisag.md) + * [CoreMiuvig](CoreMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | 16S recovery software | +| **Comments:** | | Expected value: names and versions of software(s), parameters used | +| | | Preferred unit: | +| | | Position: 64.0 | +| | | CHECKLIST migs_eu: - | +| | | CHECKLIST migs_ba: - | +| | | CHECKLIST migs_pl: - | +| | | CHECKLIST migs_vi: - | +| | | CHECKLIST migs_org: - | +| | | CHECKLIST me: - | +| | | CHECKLIST mimarks_s: - | +| | | CHECKLIST mimarks_c: - | +| | | CHECKLIST misag: X | +| | | CHECKLIST mimag: X | +| | | CHECKLIST miuvig: - | +| **Examples:** | | Example(value='rambl;v2;default parameters', description=None) | + diff --git a/mixs6/xylene.md b/mixs6/xylene.md new file mode 100644 index 00000000..97ee680d --- /dev/null +++ b/mixs6/xylene.md @@ -0,0 +1,60 @@ + +# Slot: xylene + + +Concentration of xylene in the sample + +URI: [mixs.vocab:xylene](https://w3id.org/mixs/vocab/xylene) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | xylene | +| **Mappings:** | | MIXS:0000156 | +| **Comments:** | | Expected value: measurement value | +| | | Preferred unit: milligram per liter, parts per million | +| | | Occurrence: 1 | +| | | Position: 84 | +| | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | +| **Examples:** | | Example(value='', description=None) | + From 4d9d4837b18bda124026dfa64abfdb326a04d21d Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 12:39:32 -0700 Subject: [PATCH 2/7] docs --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index bbfc7f3e..66136973 100644 --- a/index.md +++ b/index.md @@ -1,7 +1,7 @@ {% include header.html %}
-

THIS IS A DEVELOPMENT VERSION OF THE GSC Website

+

THIS IS A DEVELOPMENT VERSION OF THE GSC Website (cjm version)

For the live website, please visit https://gensc.org/.


From 0f0d6ebe2064c637e6f1e65cdcbefde7bedaf773 Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 12:47:41 -0700 Subject: [PATCH 3/7] test --- Makefile | 107 + requirements.txt | 2 + src/schema/mixs.yaml | 14263 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 14372 insertions(+) create mode 100644 Makefile create mode 100644 requirements.txt create mode 100644 src/schema/mixs.yaml diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..21e90294 --- /dev/null +++ b/Makefile @@ -0,0 +1,107 @@ +SRC_DIR = src +SCHEMA_DIR = $(SRC_DIR)/schema +SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml') +SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES)) + +SCHEMA_NAME = mixs +SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml +TGTS = graphql jsonschema docs shex owl csv graphql python + +#GEN_OPTS = --no-mergeimports +GEN_OPTS = + +all: stage-docs +gen: $(patsubst %,gen-%,$(TGTS)) +clean: + rm -rf target/ + rm -rf docs/ + +t: + echo $(SCHEMA_NAMES) + +echo: + echo $(patsubst %,gen-%,$(TGTS)) + +test: all + +install: + . environment.sh + pip install -r requirements.txt + +tdir-%: + mkdir -p target/$* +docs: + mkdir $@ + +stage: $(patsubst %,stage-%,$(TGTS)) +stage-%: gen-% + cp -pr target/$* . + + +### -- MARKDOWN DOCS -- +# Generate documentation ready for mkdocs +# TODO: modularize imports +gen-docs: target/docs/index.md +.PHONY: gen-docs +#copy-src-docs: +# cp $(SRC_DIR)/docs/*md target/docs/ +target/docs/%.md: $(SCHEMA_SRC) tdir-docs + gen-markdown $(GEN_OPTS) --dir target/docs $< +stage-docs: gen-docs + cp -pr target/docs mixs6 + +### -- MARKDOWN DOCS -- +# TODO: modularize imports +gen-python: $(patsubst %, target/python/%.py, $(SCHEMA_NAMES)) +.PHONY: gen-python +target/python/%.py: $(SCHEMA_DIR)/%.yaml tdir-python + gen-py-classes --no-mergeimports $(GEN_OPTS) $< > $@ + +### -- MARKDOWN DOCS -- +# TODO: modularize imports. For now imports are merged. +gen-graphql:target/graphql/$(SCHEMA_NAME).graphql +target/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql + gen-graphql $(GEN_OPTS) $< > $@ + +### -- JSON schema -- +# TODO: modularize imports. For now imports are merged. +gen-jsonschema: target/jsonschema/$(SCHEMA_NAME).schema.json +target/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema + gen-json-schema $(GEN_OPTS) -t transaction $< > $@ + +### -- Shex -- +# one file per module +gen-shex: $(patsubst %, target/shex/%.shex, $(SCHEMA_NAMES)) +target/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex + gen-shex --no-mergeimports $(GEN_OPTS) $< > $@ + +### -- CSV -- +# one file per module +gen-csv: $(patsubst %, target/csv/%.csv, $(SCHEMA_NAMES)) +target/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv + gen-csv $(GEN_OPTS) $< > $@ + +### -- OWL -- +# TODO: modularize imports. For now imports are merged. +gen-owl: target/owl/$(SCHEMA_NAME).owl.ttl +.PHONY: gen-owl +target/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl + gen-owl $(GEN_OPTS) $< > $@ + +### -- RDF (direct mapping) -- +# TODO: modularize imports. For now imports are merged. +gen-rdf: target/rdf/$(SCHEMA_NAME).ttl +target/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf + gen-rdf $(GEN_OPTS) $< > $@ + +### -- LinkML -- +# linkml (copy) +# one file per module +gen-linkml: target/linkml/$(SCHEMA_NAME).yaml +target/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml + cp $< > $@ + +# test docs locally. +docserve: + mkdocs serve + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..1a3a849f --- /dev/null +++ b/requirements.txt @@ -0,0 +1,2 @@ +linkml + diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml new file mode 100644 index 00000000..5c5bb293 --- /dev/null +++ b/src/schema/mixs.yaml @@ -0,0 +1,14263 @@ +id: http://w3id.org/mixs6 +description: MIxS 6 linkml rendering (experimental) +imports: +- biolinkml:types +prefixes: + biolinkml: https://w3id.org/biolink/biolinkml/ + mixs.vocab: https://w3id.org/mixs/vocab/ + MIXS: https://w3id.org/mixs/terms/ +default_prefix: mixs.vocab +slots: + core field: + description: basic fields + investigation field: + description: field describing aspect of the investigation/study to which the sample + belongs + nucleic acid sequence source field: {} + sequencing field: {} + mixs extension field: {} + environment field: + description: field describing environmental aspect of a sample + submitted_to_insdc: + is_a: investigation field + aliases: + - submitted to insdc + description: Depending on the study (large-scale e.g. done with next generation + sequencing technology, or small-scale) sequences have to be submitted to SRA + (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin + systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant + as a self-test field, therefore it is not necessary to include this field in + contextual data submitted to databases + pattern: '{boolean}' + examples: + - value: 'yes' + comments: + - 'Expected value: boolean' + - 'Preferred unit: ' + - 'Position: 1.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + investigation_type: + is_a: investigation field + aliases: + - investigation type + description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS + compliant reports as standardized by Genomic Standards Consortium. This field + is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, + mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled + genome, or uncultivated viral genome + pattern: '[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig]' + examples: + - value: metagenome + comments: + - 'Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, + mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled + genome, or uncultivated viral genomes' + - 'Preferred unit: ' + - 'Position: 2.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + range: investigation_type_enum + sample_name: + is_a: core field + aliases: + - 'sample name ' + description: 'Sample Name is a name that you choose for the sample. It can have + any format, but we suggest that you make it concise, unique and consistent within + your lab, and as informative as possible. Every Sample Name from a single Submitter + must be unique. ' + pattern: '' + examples: + - value: '' + comments: + - 'Expected value: ' + - 'Preferred unit: ' + - 'Position: ' + - 'CHECKLIST migs_eu: ' + - 'CHECKLIST migs_ba: ' + - 'CHECKLIST migs_pl: ' + - 'CHECKLIST migs_vi: ' + - 'CHECKLIST migs_org: ' + - 'CHECKLIST me: ' + - 'CHECKLIST mimarks_s: ' + - 'CHECKLIST mimarks_c: ' + - 'CHECKLIST misag: ' + - 'CHECKLIST mimag: ' + - 'CHECKLIST miuvig: ' + project_name: + is_a: investigation field + aliases: + - project name + description: Name of the project within which the sequencing was organized + pattern: '{text}' + examples: + - value: Forest soil metagenome + comments: + - 'Expected value: ' + - 'Preferred unit: ' + - 'Position: 3.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + experimental_factor: + is_a: investigation field + aliases: + - experimental factor + description: Experimental factors are essentially the variable aspects of an experiment + design which can be used to describe an experiment, or set of experiments, in + an increasingly detailed manner. This field accepts ontology terms from Experimental + Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For + a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; + for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + pattern: '{termLabel} {[termID]}|{text}' + examples: + - value: time series design [EFO:EFO_0001779] + comments: + - 'Expected value: text or EFO and/or OBI' + - 'Preferred unit: ' + - 'Position: 4.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: X' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + lat_lon: + is_a: environment field + aliases: + - geographic location (latitude and longitude) + description: The geographical origin of the sample as defined by latitude and + longitude. The values should be reported in decimal degrees and in WGS84 system + pattern: '{float} {float}' + examples: + - value: 50.586825 6.408977 + comments: + - 'Expected value: decimal degrees' + - 'Preferred unit: ' + - 'Position: 5.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + depth: + is_a: environment field + aliases: + - geographic location (depth) + description: Please refer to the definitions of depth in the environmental packages + pattern: '-' + examples: + - value: '' + comments: + - 'Expected value: -' + - 'Preferred unit: ' + - 'Position: 6.0' + - 'CHECKLIST migs_eu: E' + - 'CHECKLIST migs_ba: E' + - 'CHECKLIST migs_pl: E' + - 'CHECKLIST migs_vi: E' + - 'CHECKLIST migs_org: E' + - 'CHECKLIST me: E' + - 'CHECKLIST mimarks_s: E' + - 'CHECKLIST mimarks_c: E' + - 'CHECKLIST misag: E' + - 'CHECKLIST mimag: E' + - 'CHECKLIST miuvig: E' + - 'This field is used in: 8 packages: host-associated, microbial mat_biofilm, + miscellaneous natural or artificial environment, plant-associated, sediment, + soil, wastewater_sludge, water' + alt: + is_a: environment field + aliases: + - altitude + description: "Altitude is a term used to identify heights of objects such as airplanes,\ + \ space shuttles, rockets, atmospheric balloons and heights of places such as\ + \ atmospheric layers and clouds. It is used to measure the height of an object\ + \ which is above the earth\u201A\xC4\xF4s surface. In this context, the altitude\ + \ measurement is the vertical distance between the earth's surface above sea\ + \ level and the sampled position in the air" + pattern: '{float} {unit}' + examples: + - value: 100 meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Position: ' + - 'CHECKLIST migs_eu: E' + - 'CHECKLIST migs_ba: E' + - 'CHECKLIST migs_pl: E' + - 'CHECKLIST migs_vi: E' + - 'CHECKLIST migs_org: E' + - 'CHECKLIST me: E' + - 'CHECKLIST mimarks_s: E' + - 'CHECKLIST mimarks_c: E' + - 'CHECKLIST misag: E' + - 'CHECKLIST mimag: E' + - 'CHECKLIST miuvig: E' + - 'This field is used in: 3 packages: air, host-associated, miscellaneous natural + or artificial environment' + elev: + is_a: environment field + aliases: + - elevation + description: Elevation of the sampling site is its height above a fixed reference + point, most commonly the mean sea level. Elevation is mainly used when referring + to points on the earth's surface, while altitude is used for points above the + surface, such as an aircraft in flight or a spacecraft in orbit + pattern: '{float} {unit}' + examples: + - value: 100 meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Position: 7.0' + - 'CHECKLIST migs_eu: E' + - 'CHECKLIST migs_ba: E' + - 'CHECKLIST migs_pl: E' + - 'CHECKLIST migs_vi: E' + - 'CHECKLIST migs_org: E' + - 'CHECKLIST me: E' + - 'CHECKLIST mimarks_s: E' + - 'CHECKLIST mimarks_c: E' + - 'CHECKLIST misag: E' + - 'CHECKLIST mimag: E' + - 'CHECKLIST miuvig: E' + - 'This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, + microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, + sediment, soil, water' + geo_loc_name: + is_a: environment field + aliases: + - geographic location (country and/or sea,region) + description: The geographical origin of the sample as defined by the country or + sea name followed by specific region name. Country or sea names should be chosen + from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology + (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + pattern: '{term};{term};{text}' + examples: + - value: Germany;North Rhine-Westphalia;Eifel National Park + comments: + - 'Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location + name' + - 'Preferred unit: ' + - 'Position: 8.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + collection_date: + is_a: environment field + aliases: + - collection date + description: 'The time of sampling, either as an instance (single point in time) + or interval. In case no exact time is available, the date/time can be right + truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; + 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' + pattern: '{timestamp}' + examples: + - value: '2018-05-11T10:00:00+01:00' + comments: + - 'Expected value: date and time' + - 'Preferred unit: ' + - 'Position: 9.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + env_broad_scale: + is_a: environment field + aliases: + - broad-scale environmental context + description: "In this field, report which major environmental system your sample\ + \ or specimen came from. The systems identified should have a coarse spatial\ + \ grain, to provide the general environmental context of where the sampling\ + \ was done (e.g. were you in the desert or a rainforest?). We recommend using\ + \ subclasses of ENVO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\ + \ Format (one term): termLabel [termID], Format (multiple terms): termLabel\ + \ [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water\ + \ sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic\ + \ epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the\ + \ Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228].\ + \ If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" + pattern: '{termLabel} {[termID]}' + examples: + - value: forest biome [ENVO:01000174] + comments: + - 'Expected value: Add terms that identify the major environment type(s) where + your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple + terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine + biome [ENVO:01000020]' + - 'Preferred unit: ' + - 'Position: 10.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + env_local_scale: + is_a: environment field + aliases: + - local environmental context + description: "In this field, report the entity or entities which are in your sample\ + \ or specimen\u2019s local vicinity and which you believe have significant causal\ + \ influences on your sample or specimen. Please use terms that are present in\ + \ ENVO and which are of smaller spatial grain than your entry for env_broad_scale.\ + \ Format (one term): termLabel [termID]; Format (multiple terms): termLabel\ + \ [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled\ + \ sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb\ + \ and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub\ + \ layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified\ + \ here: http://www.obofoundry.org/ontology/envo.html" + pattern: '{termLabel} {[termID]}' + examples: + - value: litter layer [ENVO:01000338] + comments: + - 'Expected value: Add terms that identify environmental entities having causal + influences upon the entity at time of sampling, multiple terms can be separated + by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]' + - 'Preferred unit: ' + - 'Position: 11.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + env_medium: + is_a: environment field + aliases: + - environmental medium + description: "In this field, report which environmental material or materials\ + \ (pipe separated) immediately surrounded your sample or specimen prior to sampling,\ + \ using one or more subclasses of ENVO\u2019s environmental material class:\ + \ http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel\ + \ [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel\ + \ [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic\ + \ Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on\ + \ a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed,\ + \ request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" + pattern: '{termLabel} {[termID]}' + examples: + - value: soil [ENVO:00001998] + comments: + - 'Expected value: Add terms that identify the material displaced by the entity + at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine + mud [ENVO:00002160]' + - 'Preferred unit: ' + - 'Position: 12.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + env_package: + is_a: mixs extension field + aliases: + - environmental package + description: MIxS extension for reporting of measurements and observations obtained + from one or more of the environments where the sample was obtained. All environmental + packages listed here are further defined in separate subtables. By giving the + name of the environmental package, a selection of fields can be made from the + subtables and can be reported + pattern: '[air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon + resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc + environment|plant-associated|sediment|soil|wastewater/sludge|water]' + examples: + - value: soil + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 13.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + range: env_package_enum + subspecf_gen_lin: + is_a: nucleic acid sequence source field + aliases: + - subspecific genetic lineage + description: This should provide further information about the genetic distinctness + of the sequenced organism by recording additional information e.g. serovar, + serotype, biotype, ecotype, or any relevant genetic typing schemes like Group + I plasmid. It can also contain alternative taxonomic information. It should + contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + pattern: '{rank name}:{text}' + examples: + - value: serovar:Newport + comments: + - 'Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is + subspecies, e.g. serovar, biotype, ecotype' + - 'Preferred unit: ' + - 'Position: 14.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + ploidy: + is_a: nucleic acid sequence source field + aliases: + - ploidy + description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, + triploid, tetraploid). It has implications for the downstream study of duplicated + gene and regions of the genomes (and perhaps for difficulties in assembly). + For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic + Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer + to http://purl.bioontology.org/ontology/PATO + pattern: '{termLabel} {[termID]}' + examples: + - value: allopolyploidy [PATO:0001379] + comments: + - 'Expected value: PATO' + - 'Preferred unit: ' + - 'Position: 15.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + num_replicons: + is_a: nucleic acid sequence source field + aliases: + - number of replicons + description: Reports the number of replicons in a nuclear genome of eukaryotes, + in the genome of a bacterium or archaea or the number of segments in a segmented + virus. Always applied to the haploid chromosome count of a eukaryote + pattern: '{integer}' + examples: + - value: '2' + comments: + - 'Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for + viruses: segments' + - 'Preferred unit: ' + - 'Position: 16.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + extrachrom_elements: + is_a: nucleic acid sequence source field + aliases: + - extrachromosomal elements + description: Do plasmids exist of significant phenotypic consequence (e.g. ones + that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids + (borrelia has 15+ plasmids) + pattern: '{integer}' + examples: + - value: '5' + comments: + - 'Expected value: number of extrachromosmal elements' + - 'Preferred unit: ' + - 'Position: 17.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: X' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + estimated_size: + is_a: nucleic acid sequence source field + aliases: + - estimated size + description: The estimated size of the genome prior to sequencing. Of particular + importance in the sequencing of (eukaryotic) genome which could remain in draft + form for a long or unspecified period. + pattern: '{integer} bp' + examples: + - value: 300000 bp + comments: + - 'Expected value: number of base pairs' + - 'Preferred unit: ' + - 'Position: 18.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: X' + ref_biomaterial: + is_a: nucleic acid sequence source field + aliases: + - reference for biomaterial + description: Primary publication if isolated before genome publication; otherwise, + primary genome report + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: doi:10.1016/j.syapm.2018.01.009 + comments: + - 'Expected value: PMID, DOI or URL' + - 'Preferred unit: ' + - 'Position: 19.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: X' + source_mat_id: + is_a: nucleic acid sequence source field + aliases: + - source material identifiers + description: A unique identifier assigned to a material sample (as defined by + http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular + digital record of a material sample) used for extracting nucleic acids, and + subsequent sequencing. The identifier can refer either to the original material + collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, + /bio_material, or /culture_collection may or may not share the same value as + the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id + may both contain 'UAM:Herps:14' , referring to both the specimen voucher and + sampled tissue with the same identifier. However, the /culture_collection qualifier + may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id + would refer to an identifier from some derived culture from which the nucleic + acids were extracted (e.g. xatc123 or ark:/2154/R2). + pattern: '{text}' + examples: + - value: MPI012345 + comments: + - 'Expected value: for cultures of microorganisms: identifiers for two culture + collections; for other material a unique arbitrary identifer' + - 'Preferred unit: ' + - 'Position: 20.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + pathogenicity: + is_a: nucleic acid sequence source field + aliases: + - known pathogenicity + description: To what is the entity pathogenic + pattern: '{text}' + examples: + - value: human, animal, plant, fungi, bacteria + comments: + - 'Expected value: names of organisms that the entity is pathogenic to' + - 'Preferred unit: ' + - 'Position: 21.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: X' + biotic_relationship: + is_a: nucleic acid sequence source field + aliases: + - observed biotic relationship + description: Description of relationship(s) between the subject organism and other + organism(s) it is associated with. E.g., parasite on species X; mutualist with + species Y. The target organism is the subject of the relationship, and the other + organism(s) is the object + pattern: '[free living|parasitism|commensalism|symbiotic|mutualism]' + examples: + - value: free living + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 22.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: X' + range: biotic_relationship_enum + specific_host: + is_a: nucleic acid sequence source field + aliases: + - specific host + description: If there is a host involved, please provide its taxid (or environmental + if not actually isolated from the dead or alive host - i.e. a pathogen could + be isolated from a swipe of a bench etc) and report whether it is a laboratory + or natural host) + pattern: '{NCBI taxid}|{text}' + examples: + - value: '9606' + comments: + - 'Expected value: host taxid, unknown, environmental' + - 'Preferred unit: ' + - 'Position: 23.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: X' + host_spec_range: + is_a: nucleic acid sequence source field + aliases: + - host specificity or range + description: The NCBI taxonomy identifier of the specific host if it is known + pattern: '{integer}' + examples: + - value: '9606' + comments: + - 'Expected value: NCBI taxid' + - 'Preferred unit: ' + - 'Position: 24.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: X' + health_disease_stat: + is_a: nucleic acid sequence source field + aliases: + - health or disease status of specific host at time of collection + description: Health or disease status of specific host at time of collection + pattern: '[healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing + condition|pathological|life threatening|congenital]' + examples: + - value: dead + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 25.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + range: health_disease_stat_enum + trophic_level: + is_a: nucleic acid sequence source field + aliases: + - trophic level + description: Trophic levels are the feeding position in a food chain. Microbes + can be a range of producers (e.g. chemolithotroph) + pattern: '[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]' + examples: + - value: heterotroph + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 26.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + range: trophic_level_enum + propagation: + is_a: nucleic acid sequence source field + aliases: + - propagation + description: 'This field is specific to different taxa. For phages: lytic/lysogenic, + for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there + is the strong opinion to name phage propagation obligately lytic or temperate, + therefore we also give this choice' + pattern: '{text}' + examples: + - value: lytic + comments: + - 'Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for + plasmid: incompatibility group; for eukaryote: asexual, sexual' + - 'Preferred unit: ' + - 'Position: 27.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + encoded_traits: + is_a: nucleic acid sequence source field + aliases: + - encoded traits + description: Should include key traits like antibiotic resistance or xenobiotic + degradation phenotypes for plasmids, converting genes for phage + pattern: '{text}' + examples: + - value: beta-lactamase class A + comments: + - 'Expected value: for plasmid: antibiotic resistance; for phage: converting genes' + - 'Preferred unit: ' + - 'Position: 28.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + rel_to_oxygen: + is_a: nucleic acid sequence source field + aliases: + - relationship to oxygen + description: Is this organism an aerobe, anaerobe? Please note that aerobic and + anaerobic are valid descriptors for microbial environments + pattern: '[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate + aerobe|obligate anaerobe]' + examples: + - value: aerobe + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 29.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: X' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + range: rel_to_oxygen_enum + isol_growth_condt: + is_a: nucleic acid sequence source field + aliases: + - isolation and growth condition + description: Publication reference in the form of pubmed ID (pmid), digital object + identifier (doi) or url for isolation and growth condition specifications of + the organism/material + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: 'doi: 10.1016/j.syapm.2018.01.009' + comments: + - 'Expected value: PMID,DOI or URL' + - 'Preferred unit: ' + - 'Position: 30.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + samp_collect_device: + is_a: nucleic acid sequence source field + aliases: + - sample collection device or method + description: The method or device employed for collecting the sample + pattern: '{text}' + examples: + - value: environmental swab sampling, biopsy, niskin bottle, push core + comments: + - 'Expected value: type name' + - 'Preferred unit: ' + - 'Position: 31.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: X' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + samp_mat_process: + is_a: nucleic acid sequence source field + aliases: + - sample material processing + description: Any processing applied to the sample during or after retrieving the + sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) + terms please see http://purl.bioontology.org/ontology/OBI + pattern: '{text}|{termLabel} {[termID]}' + examples: + - value: filtering of seawater, storing samples in ethanol + comments: + - 'Expected value: text or OBI' + - 'Preferred unit: ' + - 'Position: 32.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + size_frac: + is_a: nucleic acid sequence source field + aliases: + - size fraction selected + description: Filtering pore size used in sample preparation + pattern: '{float}-{float} {unit}' + examples: + - value: 0-0.22 micrometer + comments: + - 'Expected value: filter size value range' + - 'Preferred unit: ' + - 'Position: 33.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: X' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + samp_size: + is_a: nucleic acid sequence source field + aliases: + - amount or size of sample collected + description: Amount or size of sample (volume, mass or area) that was collected + pattern: '{float} {unit}' + examples: + - value: 5 liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millliter, gram, milligram, liter' + - 'Position: 34.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: X' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + source_uvig: + is_a: nucleic acid sequence source field + aliases: + - source of UViGs + description: Type of dataset from which the UViG was obtained + pattern: '[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted + metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome + (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome + (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]' + examples: + - value: viral fraction metagenome (virome) + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 35.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + range: source_uvig_enum + virus_enrich_appr: + is_a: nucleic acid sequence source field + aliases: + - virus enrichment approach + description: List of approaches used to enrich the sample for viruses, if any + pattern: '[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl + Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]' + examples: + - value: filtration + FeCl Precipitation + ultracentrifugation + DNAse + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 36.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + range: virus_enrich_appr_enum + nucl_acid_ext: + is_a: sequencing field + aliases: + - nucleic acid extraction + description: A link to a literature reference, electronic resource or a standard + operating procedure (SOP), that describes the material separation to recover + the nucleic acid fraction from a sample + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf + comments: + - 'Expected value: PMID, DOI or URL' + - 'Preferred unit: ' + - 'Position: 37.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + nucl_acid_amp: + is_a: sequencing field + aliases: + - nucleic acid amplification + description: A link to a literature reference, electronic resource or a standard + operating procedure (SOP), that describes the enzymatic amplification (PCR, + TMA, NASBA) of specific nucleic acids + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ + comments: + - 'Expected value: PMID, DOI or URL' + - 'Preferred unit: ' + - 'Position: 38.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + lib_size: + is_a: sequencing field + aliases: + - library size + description: Total number of clones in the library prepared for the project + pattern: '{integer}' + examples: + - value: '50' + comments: + - 'Expected value: number of clones' + - 'Preferred unit: ' + - 'Position: 39.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + lib_reads_seqd: + is_a: sequencing field + aliases: + - library reads sequenced + description: Total number of clones sequenced from the library + pattern: '{integer}' + examples: + - value: '20' + comments: + - 'Expected value: number of reads sequenced' + - 'Preferred unit: ' + - 'Position: 40.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + lib_layout: + is_a: sequencing field + aliases: + - library layout + description: Specify whether to expect single, paired, or other configuration + of reads + pattern: '[paired|single|vector|other]' + examples: + - value: paired + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 41.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + range: lib_layout_enum + lib_vector: + is_a: sequencing field + aliases: + - library vector + description: Cloning vector type(s) used in construction of libraries + pattern: '{text}' + examples: + - value: Bacteriophage P1 + comments: + - 'Expected value: vector' + - 'Preferred unit: ' + - 'Position: 42.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + lib_screen: + is_a: sequencing field + aliases: + - library screening strategy + description: Specific enrichment or screening methods applied before and/or after + creating libraries + pattern: '{text}' + examples: + - value: enriched, screened, normalized + comments: + - 'Expected value: screening strategy name' + - 'Preferred unit: ' + - 'Position: 43.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + target_gene: + is_a: sequencing field + aliases: + - target gene + description: Targeted gene or locus name for marker gene studies + pattern: '{text}' + examples: + - value: 16S rRNA, 18S rRNA, nif, amoA, rpo + comments: + - 'Expected value: gene name' + - 'Preferred unit: ' + - 'Position: 44.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + target_subfragment: + is_a: sequencing field + aliases: + - target subfragment + description: Name of subfragment of a gene or locus. Important to e.g. identify + special regions on marker genes like V6 on 16S rRNA + pattern: '{text}' + examples: + - value: V6, V9, ITS + comments: + - 'Expected value: gene fragment name' + - 'Preferred unit: ' + - 'Position: 45.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + pcr_primers: + is_a: sequencing field + aliases: + - pcr primers + description: PCR primers that were used to amplify the sequence of the targeted + gene, locus or subfragment. This field should contain all the primers used for + a single PCR reaction if multiple forward or reverse primers are present in + a single PCR reaction. The primer sequence should be reported in uppercase letters + pattern: FWD:{dna};REV:{dna} + examples: + - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT + comments: + - 'Expected value: FWD: forward primer sequence;REV:reverse primer sequence' + - 'Preferred unit: ' + - 'Position: 46.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + mid: + is_a: sequencing field + aliases: + - multiplex identifiers + description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are + used to specifically tag unique samples in a sequencing run. Sequence should + be reported in uppercase letters + pattern: '{dna}' + examples: + - value: GTGAATAT + comments: + - 'Expected value: multiplex identifier sequence' + - 'Preferred unit: ' + - 'Position: 47.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + adapters: + is_a: sequencing field + aliases: + - adapters + description: Adapters provide priming sequences for both amplification and sequencing + of the sample-library fragments. Both adapters should be reported; in uppercase + letters + pattern: '{dna};{dna}' + examples: + - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT + comments: + - 'Expected value: adapter A and B sequence' + - 'Preferred unit: ' + - 'Position: 48.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + pcr_cond: + is_a: sequencing field + aliases: + - pcr conditions + description: Description of reaction conditions and components of PCR in the form + of 'initial denaturation:94degC_1.5min; annealing=...' + pattern: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes;total cycles + examples: + - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 + comments: + - 'Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes;total cycles' + - 'Preferred unit: ' + - 'Position: 49.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + seq_meth: + is_a: sequencing field + aliases: + - sequencing method + description: Sequencing method used; e.g. Sanger, ABI-solid + pattern: '[454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS + Junior|AB 310 Genetic Analyzer|AB 3130 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB + 3500 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB + 3730xL Genetic Analyzer|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB + 5500xl-W Genetic Analysis System|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD + System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD + PI System|BGISEQ-500|GridION|Illumina Genome Analyzer|Illumina Genome Analyzer + II|Illumina Genome Analyzer IIx|Illumina HiSeq 1000|Illumina HiSeq 1500|Illumina + HiSeq 2000|Illumina HiSeq 2500|Illumina HiSeq 3000|Illumina HiSeq 4000|Illumina + HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina + NextSeq 500|Illumina NextSeq 550|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent + S5|Ion Torrent S5 XL|MinION|PacBio RS|PacBio RS II|PromethION|Sequel]' + examples: + - value: Illumina HiSeq 1500 + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 50.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: M' + - 'CHECKLIST mimarks_s: M' + - 'CHECKLIST mimarks_c: M' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + range: seq_meth_enum + seq_quality_check: + is_a: sequencing field + aliases: + - sequence quality check + description: Indicate if the sequence has been called by automatic systems (none) + or undergone a manual editing procedure (e.g. by inspecting the raw data or + chromatograms). Applied only for sequences that are not submitted to SRA,ENA + or DRA + pattern: '[none|manually edited]' + examples: + - value: none + comments: + - 'Expected value: none or manually edited' + - 'Preferred unit: ' + - 'Position: 51.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + chimera_check: + is_a: sequencing field + aliases: + - chimera check + description: A chimeric sequence, or chimera for short, is a sequence comprised + of two or more phylogenetically distinct parent sequences. Chimeras are usually + PCR artifacts thought to occur when a prematurely terminated amplicon reanneals + to a foreign DNA strand and is copied to completion in the following PCR cycles. + The point at which the chimeric sequence changes from one parent to the next + is called the breakpoint or conversion point + pattern: '{software};{version};{parameters}' + examples: + - value: uchime;v4.1;default parameters + comments: + - 'Expected value: name and version of software, parameters used' + - 'Preferred unit: ' + - 'Position: 52.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: -' + tax_ident: + is_a: sequencing field + aliases: + - taxonomic identity marker + description: The phylogenetic marker(s) used to assign an organism name to the + SAG or MAG + pattern: '[16S rRNA gene|multi-marker approach|other]' + examples: + - value: 'other: rpoB gene' + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 53.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: X' + range: tax_ident_enum + assembly_qual: + is_a: sequencing field + aliases: + - assembly quality + description: "The assembly quality category is based on sets of criteria outlined\ + \ for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,\ + \ contiguous sequence per replicon without gaps or ambiguities with a consensus\ + \ error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments\ + \ where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes\ + \ and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to\ + \ no review of assembly other than reporting of standard assembly statistics.\ + \ Low Quality Draft:Many fragments with little to no review of assembly other\ + \ than reporting of standard assembly statistics. Assembly statistics include,\ + \ but are not limited to total assembly size, number of contigs, contig N50/L50,\ + \ and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous\ + \ sequence per replicon without gaps or ambiguities, with extensive manual review\ + \ and editing to annotate putative gene functions and transcriptional units.\ + \ High-quality draft genome: One or multiple fragments, totaling \u2265 90%\ + \ of the expected genome or replicon sequence or predicted complete. Genome\ + \ fragment(s): One or multiple fragments, totalling < 90% of the expected genome\ + \ or replicon sequence, or for which no genome size could be estimated" + pattern: '[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality + draft genome|Genome fragment(s)]' + examples: + - value: High-quality draft genome + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 54.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + range: assembly_qual_enum + assembly_name: + is_a: sequencing field + aliases: + - assembly name + description: Name/version of the assembly provided by the submitter that is used + in the genome browsers and in the community + pattern: '{text} {text}' + examples: + - value: HuRef, JCVI_ISG_i3_1.0 + comments: + - 'Expected value: name and version of assembly' + - 'Preferred unit: ' + - 'Position: 55.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + assembly_software: + is_a: sequencing field + aliases: + - assembly software + description: Tool(s) used for assembly, including version number and parameters + pattern: '{software};{version};{parameters}' + examples: + - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise + comments: + - 'Expected value: name and version of software, parameters used' + - 'Preferred unit: ' + - 'Position: 56.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: M' + - 'CHECKLIST migs_vi: M' + - 'CHECKLIST migs_org: M' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: M' + annot: + is_a: sequencing field + aliases: + - annotation + description: Tool used for annotation, or for cases where annotation was provided + by a community jamboree or model organism database rather than by a specific + submitter + pattern: '{text}' + examples: + - value: prokka + comments: + - 'Expected value: name of tool or pipeline used, or annotation source description' + - 'Preferred unit: ' + - 'Position: 57.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: X' + number_contig: + is_a: sequencing field + aliases: + - number of contigs + description: Total number of contigs in the cleaned/submitted assembly that makes + up a given genome, SAG, MAG, or UViG + pattern: '{integer}' + examples: + - value: '40' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Position: 58.0' + - 'CHECKLIST migs_eu: M' + - 'CHECKLIST migs_ba: M' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: M' + feat_pred: + is_a: sequencing field + aliases: + - feature prediction + description: Method used to predict UViGs features such as ORFs, integration site, + etc. + pattern: '{software};{version};{parameters}' + examples: + - value: Prodigal;2.6.3;default parameters + comments: + - 'Expected value: names and versions of software(s), parameters used' + - 'Preferred unit: ' + - 'Position: 59.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + ref_db: + is_a: sequencing field + aliases: + - reference database(s) + description: List of database(s) used for ORF annotation, along with version number + and reference to website or publication + pattern: '{database};{version};{reference}' + examples: + - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 + doi:10.1093/nar/gkw975 + comments: + - 'Expected value: names, versions, and references of databases' + - 'Preferred unit: ' + - 'Position: 60.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + sim_search_meth: + is_a: sequencing field + aliases: + - similarity search method + description: Tool used to compare ORFs with database, along with version and cutoffs + used + pattern: '{software};{version};{parameters}' + examples: + - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score + comments: + - 'Expected value: names and versions of software(s), parameters used' + - 'Preferred unit: ' + - 'Position: 61.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + tax_class: + is_a: sequencing field + aliases: + - taxonomic classification + description: Method used for taxonomic classification, along with reference database + used, classification rank, and thresholds used to classify new genomes + pattern: '{text}' + examples: + - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, + default parameters) + comments: + - 'Expected value: classification method, database name, and other parameters' + - 'Preferred unit: ' + - 'Position: 62.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: X' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + x_16s_recover: + is_a: sequencing field + aliases: + - 16S recovered + description: Can a 16S gene be recovered from the submitted SAG or MAG? + pattern: '{boolean}' + examples: + - value: 'yes' + comments: + - 'Expected value: boolean' + - 'Preferred unit: ' + - 'Position: 63.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + x_16s_recover_software: + is_a: sequencing field + aliases: + - 16S recovery software + description: Tools used for 16S rRNA gene extraction + pattern: '{software};{version};{parameters}' + examples: + - value: rambl;v2;default parameters + comments: + - 'Expected value: names and versions of software(s), parameters used' + - 'Preferred unit: ' + - 'Position: 64.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + trnas: + is_a: sequencing field + aliases: + - number of standard tRNAs extracted + description: The total number of tRNAs identified from the SAG or MAG + pattern: '{integer}' + examples: + - value: '18' + comments: + - 'Expected value: value from 0-21' + - 'Preferred unit: ' + - 'Position: 65.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: X' + trna_ext_software: + is_a: sequencing field + aliases: + - tRNA extraction software + description: Tools used for tRNA identification + pattern: '{software};{version};{parameters}' + examples: + - value: infernal;v2;default parameters + comments: + - 'Expected value: names and versions of software(s), parameters used' + - 'Preferred unit: ' + - 'Position: 66.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: X' + compl_score: + is_a: sequencing field + aliases: + - completeness score + description: 'Completeness score is typically based on either the fraction of + markers found as compared to a database or the percent of a genome found as + compared to a closely related reference genome. High Quality Draft: >90%, Medium + Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated + completeness scores' + pattern: '[high|med|low];{percentage}' + examples: + - value: med;60% + comments: + - 'Expected value: quality;percent completeness' + - 'Preferred unit: ' + - 'Position: 67.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: C' + range: compl_score_enum + compl_software: + is_a: sequencing field + aliases: + - completeness software + description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + pattern: '{software};{version}' + examples: + - value: checkm + comments: + - 'Expected value: names and versions of software(s) used' + - 'Preferred unit: ' + - 'Position: 68.0' + - 'CHECKLIST migs_eu: X' + - 'CHECKLIST migs_ba: X' + - 'CHECKLIST migs_pl: X' + - 'CHECKLIST migs_vi: X' + - 'CHECKLIST migs_org: X' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: X' + compl_appr: + is_a: sequencing field + aliases: + - completeness approach + description: The approach used to determine the completeness of a given SAG or + MAG, which would typically make use of a set of conserved marker genes or a + closely related reference genome. For UViG completeness, include reference genome + or group used, and contig feature suggesting a complete genome + pattern: '[marker gene|reference based|other]' + examples: + - value: 'other: UViG length compared to the average length of reference genomes + from the P22virus genus (NCBI RefSeq v83)' + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 69.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + range: compl_appr_enum + contam_score: + is_a: sequencing field + aliases: + - contamination score + description: 'The contamination score is based on the fraction of single-copy + genes that are observed more than once in a query genome. The following scores + are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low + Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be + deposited into any of the public databases' + pattern: '{float} percentage' + examples: + - value: 1% + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Position: 70.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: -' + contam_screen_input: + is_a: sequencing field + aliases: + - contamination screening input + description: The type of sequence data used as input + pattern: '[reads| contigs]' + examples: + - value: contigs + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 71.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + contam_screen_param: + is_a: sequencing field + aliases: + - contamination screening parameters + description: Specific parameters used in the decontamination sofware, such as + reference database, coverage, and kmers. Combinations of these parameters may + also be used, i.e. kmer and coverage, or reference database and kmer + pattern: '[ref db|kmer|coverage|combination];{text|integer}' + examples: + - value: kmer + comments: + - 'Expected value: enumeration;value or name' + - 'Preferred unit: ' + - 'Position: 72.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + range: contam_screen_param_enum + decontam_software: + is_a: sequencing field + aliases: + - decontamination software + description: Tool(s) used in contamination screening + pattern: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' + examples: + - value: anvi'o + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 73.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: -' + range: decontam_software_enum + sort_tech: + is_a: sequencing field + aliases: + - sorting technology + description: Method used to sort/isolate cells or particles of interest + pattern: '[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]' + examples: + - value: optical manipulation + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 74.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + range: sort_tech_enum + single_cell_lysis_appr: + is_a: sequencing field + aliases: + - single cell or viral particle lysis approach + description: Method used to free DNA from interior of the cell(s) or particle(s) + pattern: '[chemical|enzymatic|physical|combination]' + examples: + - value: enzymatic + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 75.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + range: single_cell_lysis_appr_enum + single_cell_lysis_prot: + is_a: sequencing field + aliases: + - single cell or viral particle lysis kit protocol + description: Name of the kit or standard protocol used for cell(s) or particle(s) + lysis + pattern: '{text}' + examples: + - value: ambion single cell lysis kit + comments: + - 'Expected value: kit, protocol name' + - 'Preferred unit: ' + - 'Position: 76.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + wga_amp_appr: + is_a: sequencing field + aliases: + - WGA amplification approach + description: Method used to amplify genomic DNA in preparation for sequencing + pattern: '[pcr based|mda based]' + examples: + - value: mda based + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 77.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: M' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + wga_amp_kit: + is_a: sequencing field + aliases: + - WGA amplification kit + description: Kit used to amplify genomic DNA in preparation for sequencing + pattern: '{text}' + examples: + - value: qiagen repli-g + comments: + - 'Expected value: kit name' + - 'Preferred unit: ' + - 'Position: 78.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: X' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + bin_param: + is_a: sequencing field + aliases: + - binning parameters + description: The parameters that have been applied during the extraction of genomes + from metagenomic datasets + pattern: '[homology search|kmer|coverage|codon usage|combination]' + examples: + - value: coverage and kmer + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 79.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: C' + range: bin_param_enum + bin_software: + is_a: sequencing field + aliases: + - binning software + description: Tool(s) used for the extraction of genomes from metagenomic datasets + pattern: '[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]' + examples: + - value: concoct and maxbin + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 80.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: M' + - 'CHECKLIST miuvig: C' + range: bin_software_enum + reassembly_bin: + is_a: sequencing field + aliases: + - reassembly post binning + description: Has an assembly been performed on a genome bin extracted from a metagenomic + assembly? + pattern: '{boolean}' + examples: + - value: 'no' + comments: + - 'Expected value: boolean' + - 'Preferred unit: ' + - 'Position: 81.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: C' + mag_cov_software: + is_a: sequencing field + aliases: + - MAG coverage software + description: Tool(s) used to determine the genome coverage if coverage is used + as a binning parameter in the extraction of genomes from metagenomic datasets + pattern: '[bwa|bbmap|bowtie|other]' + examples: + - value: bbmap + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 82.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: X' + - 'CHECKLIST miuvig: X' + range: mag_cov_software_enum + vir_ident_software: + is_a: sequencing field + aliases: + - viral identification software + description: Tool(s) used for the identification of UViG as a viral genome, software + or protocol name including version number, parameters, and cutoffs used + pattern: '{software};{version};{parameters}' + examples: + - value: VirSorter; 1.0.4; Virome database, category 2 + comments: + - 'Expected value: software name, version and relevant parameters' + - 'Preferred unit: ' + - 'Position: 83.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + pred_genome_type: + is_a: sequencing field + aliases: + - predicted genome type + description: Type of genome predicted for the UViG + pattern: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' + examples: + - value: dsDNA + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 84.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + range: pred_genome_type_enum + pred_genome_struc: + is_a: sequencing field + aliases: + - predicted genome structure + description: Expected structure of the viral genome + pattern: '[segmented|non-segmented|undetermined]' + examples: + - value: non-segmented + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 85.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + range: pred_genome_struc_enum + detec_type: + is_a: sequencing field + aliases: + - detection type + description: Type of UViG detection + pattern: '[independent sequence (UViG)|provirus (UpViG)]' + examples: + - value: independent sequence (UViG) + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 86.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: M' + votu_class_appr: + is_a: sequencing field + aliases: + - vOTU classification approach + description: "Cutoffs and approach used when clustering new UViGs in \u201Cspecies-level\u201D\ + \ vOTUs. Note that results from standard 95% ANI / 85% AF clustering should\ + \ be provided alongside vOTUS defined from another set of thresholds, even if\ + \ the latter are the ones primarily used during the analysis" + pattern: '{ANI cutoff};{AF cutoff};{clustering method}' + examples: + - value: 95% ANI;85% AF; greedy incremental clustering + comments: + - 'Expected value: cutoffs and method used' + - 'Preferred unit: ' + - 'Position: 87.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + votu_seq_comp_appr: + is_a: sequencing field + aliases: + - vOTU sequence comparison approach + description: Tool and thresholds used to compare sequences when computing "species-level" + vOTUs + pattern: '{software};{version};{parameters}' + examples: + - value: 'blastn;2.6.0+;e-value cutoff: 0.001' + comments: + - 'Expected value: software name, version and relevant parameters' + - 'Preferred unit: ' + - 'Position: 88.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + votu_db: + is_a: sequencing field + aliases: + - vOTU database + description: Reference database (i.e. sequences not generated as part of the current + study) used to cluster new genomes in "species-level" vOTUs, if any + pattern: '{database};{version}' + examples: + - value: NCBI Viral RefSeq;83 + comments: + - 'Expected value: database and version' + - 'Preferred unit: ' + - 'Position: 89.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + host_pred_appr: + is_a: sequencing field + aliases: + - host prediction approach + description: Tool or approach used for host prediction + pattern: '[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co-occurrence|combination|other]' + examples: + - value: CRISPR spacer match + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 90.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + range: host_pred_appr_enum + host_pred_est_acc: + is_a: sequencing field + aliases: + - host prediction estimated accuracy + description: For each tool or approach used for host prediction, estimated false + discovery rates should be included, either computed de novo or from the literature + pattern: '{text}' + examples: + - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host + genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' + comments: + - 'Expected value: false discovery rate' + - 'Preferred unit: ' + - 'Position: 91.0' + - 'CHECKLIST migs_eu: -' + - 'CHECKLIST migs_ba: -' + - 'CHECKLIST migs_pl: -' + - 'CHECKLIST migs_vi: -' + - 'CHECKLIST migs_org: -' + - 'CHECKLIST me: -' + - 'CHECKLIST mimarks_s: -' + - 'CHECKLIST mimarks_c: -' + - 'CHECKLIST misag: -' + - 'CHECKLIST mimag: -' + - 'CHECKLIST miuvig: C' + url: + is_a: sequencing field + aliases: + - relevant electronic resources + description: '' + pattern: '{URL}' + examples: + - value: http://www.earthmicrobiome.org/ + comments: + - 'Expected value: URL' + - 'Preferred unit: ' + - 'Position: 92.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + sop: + is_a: sequencing field + aliases: + - relevant standard operating procedures + description: Standard operating procedures used in assembly and/or annotation + of genomes, metagenomes or environmental sequences + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ + comments: + - 'Expected value: reference to SOP' + - 'Preferred unit: ' + - 'Position: 93.0' + - 'CHECKLIST migs_eu: C' + - 'CHECKLIST migs_ba: C' + - 'CHECKLIST migs_pl: C' + - 'CHECKLIST migs_vi: C' + - 'CHECKLIST migs_org: C' + - 'CHECKLIST me: C' + - 'CHECKLIST mimarks_s: C' + - 'CHECKLIST mimarks_c: C' + - 'CHECKLIST misag: C' + - 'CHECKLIST mimag: C' + - 'CHECKLIST miuvig: C' + barometric_press: + is_a: environment field + aliases: + - barometric pressure + description: Force per unit area exerted against a surface by the weight of air + above that surface + pattern: '{float} {unit}' + examples: + - value: 5 millibar + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millibar' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000096 + carb_dioxide: + is_a: environment field + aliases: + - carbon dioxide + description: Carbon dioxide (gas) amount or concentration at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 410 parts per million + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: air, built environment' + slot_uri: MIXS:0000097 + carb_monoxide: + is_a: environment field + aliases: + - carbon monoxide + description: Carbon monoxide (gas) amount or concentration at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 0.1 parts per million + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000098 + chem_administration: + is_a: environment field + aliases: + - chemical administration + description: List of chemical compounds administered to the host or site where + sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can + include multiple compounds. For chemical entities of biological interest ontology + (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + pattern: '{termLabel} {[termID]};{timestamp}' + examples: + - value: agar [CHEBI:2509];2018-05-11T20:00Z + comments: + - 'Expected value: CHEBI;timestamp' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 13 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous + natural or artificial environment, plant-associated, sediment, wastewater_sludge, + water' + slot_uri: MIXS:0000751 + humidity: + is_a: environment field + aliases: + - humidity + description: Amount of water vapour in the air, at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 25 gram per cubic meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram per cubic meter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000100 + methane: + is_a: environment field + aliases: + - methane + description: Methane (gas) amount or concentration at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 1800 parts per billion + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, parts per billion, parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: air, microbial mat_biofilm, sediment' + slot_uri: MIXS:0000101 + misc_param: + is_a: environment field + aliases: + - miscellaneous parameter + description: Any other measurement performed or parameter collected, that is not + listed here + pattern: '{text};{float} {unit}' + examples: + - value: Bicarbonate ion concentration;2075 micromole per kilogram + comments: + - 'Expected value: parameter name;measurement value' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 16 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, soil, wastewater_sludge, + water' + slot_uri: MIXS:0000752 + organism_count: + is_a: environment field + aliases: + - organism count + description: 'Total cell count of any organism (or group of organisms) per gram, + volume or area of sample, should include name of organism followed by count. + The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should + also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' + pattern: '{text};{float} {unit};[qPCR|ATP|MPN|other]' + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + comments: + - 'Expected value: organism name;measurement value;enumeration' + - 'Preferred unit: number of cells per cubic meter, number of cells per milliliter, + number of cells per cubic centimeter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 16 packages: air, built environment, host-associated, + human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon + resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, + miscellaneous natural or artificial environment, plant-associated, sediment, + wastewater_sludge, water' + range: organism_count_enum + slot_uri: MIXS:0000103 + oxygen: + is_a: environment field + aliases: + - oxygen + description: Oxygen (gas) amount or concentration at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 600 parts per million + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000104 + oxy_stat_samp: + is_a: environment field + aliases: + - oxygenation status of sample + description: Oxygenation status of sample + pattern: '[aerobic|anaerobic|other]' + examples: + - value: aerobic + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 15 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, wastewater_sludge, water' + range: oxy_stat_samp_enum + slot_uri: MIXS:0000753 + perturbation: + is_a: environment field + aliases: + - perturbation + description: Type of perturbation, e.g. chemical administration, physical disturbance, + etc., coupled with perturbation regimen including how many times the perturbation + was repeated, how long each perturbation lasted, and the start and end time + of the entire perturbation period; can include multiple perturbation types + pattern: '{text};{Rn/start_time/end_time/duration}' + examples: + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + comments: + - 'Expected value: perturbation type name;perturbation interval and duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 13 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous + natural or artificial environment, plant-associated, sediment, wastewater_sludge, + water' + slot_uri: MIXS:0000754 + pollutants: + is_a: environment field + aliases: + - pollutants + description: Pollutant types and, amount or concentrations measured at the time + of sampling; can report multiple pollutants by entering numeric values preceded + by name of pollutant + pattern: '{text};{float} {unit}' + examples: + - value: lead;0.15 microgram per cubic meter + comments: + - 'Expected value: pollutant name;measurement value' + - 'Preferred unit: gram, mole per liter, milligram per liter, microgram per cubic + meter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000107 + resp_part_matter: + is_a: environment field + aliases: + - respirable particulate matter + description: Concentration of substances that remain suspended in the air, and + comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can + report multiple PM's by entering numeric values preceded by name of PM + pattern: '{text};{float} {unit}' + examples: + - value: PM2.5;10 microgram per cubic meter + comments: + - 'Expected value: particulate matter name;measurement value' + - 'Preferred unit: microgram per cubic meter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000108 + samp_salinity: + is_a: environment field + aliases: + - sample salinity + description: Salinity is the total concentration of all dissolved salts in a liquid + or solid (in the form of an extract obtained by centrifugation) sample. While + salinity can be measured by a complete chemical analysis, this method is difficult + and time consuming. More often, it is instead derived from the conductivity + measurement. This is known as practical salinity. These derivations compare + the specific conductance of the sample to a salinity standard such as seawater + pattern: '{float} {unit}' + examples: + - value: 1 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, practical salinity unit, percentage' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 11 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, plant-associated, wastewater_sludge' + slot_uri: MIXS:0000109 + samp_store_dur: + is_a: environment field + aliases: + - sample storage duration + description: Duration for which the sample was stored + pattern: '{duration}' + examples: + - value: P1Y6M + comments: + - 'Expected value: duration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 15 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000116 + samp_store_loc: + is_a: environment field + aliases: + - sample storage location + description: Location at which sample was stored, usually name of a specific freezer/room + pattern: '{text}' + examples: + - value: Freezer no:5 + comments: + - 'Expected value: location name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 15 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000755 + samp_store_temp: + is_a: environment field + aliases: + - sample storage temperature + description: Temperature at which sample was stored, e.g. -80 degree Celsius + pattern: '{float} {unit}' + examples: + - value: -80 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 15 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000110 + samp_vol_we_dna_ext: + is_a: environment field + aliases: + - sample volume or weight for DNA extraction + description: Volume (ml), weight (g) of processed sample, or surface area swabbed + from sample for DNA extraction + pattern: '{float} {unit}' + examples: + - value: 1500 milliliter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millliter, gram, milligram, square centimeter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 16 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, soil, wastewater_sludge, + water' + slot_uri: MIXS:0000111 + solar_irradiance: + is_a: environment field + aliases: + - solar irradiance + description: The amount of solar energy that arrives at a specific area of a surface + during a specific time interval + pattern: '{float} {unit}' + examples: + - value: 1.36 kilowatts per square meter per day + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilowatts per square meter per day, ergs per square centimeter + per second' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000112 + temp: + is_a: environment field + aliases: + - temperature + description: Temperature of the sample at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 25 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 15 packages: air, host-associated, human-associated, + human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, + hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural + or artificial environment, plant-associated, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000113 + ventilation_rate: + is_a: environment field + aliases: + - ventilation rate + description: Ventilation rate of the system in the sampled premises + pattern: '{float} {unit}' + examples: + - value: 750 cubic meter per minute + comments: + - 'Expected value: measurement value' + - 'Preferred unit: cubic meter per minute, liters per second' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000114 + ventilation_type: + is_a: environment field + aliases: + - ventilation type + description: Ventilation system used in the sampled premises + pattern: '{text}' + examples: + - value: Operable windows + comments: + - 'Expected value: ventilation type name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: air, built environment' + slot_uri: MIXS:0000756 + volatile_org_comp: + is_a: environment field + aliases: + - volatile organic compounds + description: Concentration of carbon-based chemicals that easily evaporate at + room temperature; can report multiple volatile organic compounds by entering + numeric values preceded by name of compound + pattern: '{text};{float} {unit}' + examples: + - value: formaldehyde;500 nanogram per liter + comments: + - 'Expected value: volatile organic compound name;measurement value' + - 'Preferred unit: microgram per cubic meter, parts per million, nanogram per + liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000115 + wind_direction: + is_a: environment field + aliases: + - wind direction + description: Wind direction is the direction from which a wind originates + pattern: '{text}' + examples: + - value: Northwest + comments: + - 'Expected value: wind direction name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000757 + wind_speed: + is_a: environment field + aliases: + - wind speed + description: Speed of wind measured at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 21 kilometer per hour + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter per second, kilometer per hour' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: air' + slot_uri: MIXS:0000118 + surf_material: + is_a: environment field + aliases: + - surface material + description: Surface materials at the point of sampling + pattern: '[adobe|carpet|cinder blocks|concrete|hay bales|glass|metal|paint|plastic|stainless + steel|stone|stucco|tile|vinyl|wood]' + examples: + - value: wood + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: built environment' + range: surf_material_enum + slot_uri: MIXS:0000758 + surf_air_cont: + is_a: environment field + aliases: + - surface-air contaminant + description: Contaminant identified on surface + pattern: '[dust|organic matter|particulate matter|volatile organic compounds|biological + contaminants|radon|nutrients|biocides]' + examples: + - value: radon + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 2' + - 'This field is used uniquely in: built environment' + range: surf_air_cont_enum + slot_uri: MIXS:0000759 + rel_air_humidity: + is_a: environment field + aliases: + - relative air humidity + description: Partial vapor and air pressure, density of the vapor and air, or + by the actual mass of the vapor and air + pattern: '{float} {unit}' + examples: + - value: 80% + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000121 + abs_air_humidity: + is_a: environment field + aliases: + - absolute air humidity + description: Actual mass of water vapor - mh20 - present in the air water vapor + mixture + pattern: '{float} {unit}' + examples: + - value: 9 gram per gram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram per gram, kilogram per kilogram, kilogram, pound' + - 'Occurrence: 1' + - 'Position: 4' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000122 + surf_humidity: + is_a: environment field + aliases: + - surface humidity + description: 'Surfaces: water activity as a function of air and material moisture' + pattern: '{float} {unit}' + examples: + - value: 10% + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 5' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000123 + air_temp: + is_a: environment field + aliases: + - air temperature + description: Temperature of the air at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 20 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 6' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000124 + surf_temp: + is_a: environment field + aliases: + - surface temperature + description: Temperature of the surface at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 15 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 7' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000125 + surf_moisture_ph: + is_a: environment field + aliases: + - surface moisture pH + description: ph measurement of surface + pattern: '{float}' + examples: + - value: '7' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 8' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000760 + build_occup_type: + is_a: environment field + aliases: + - building occupancy type + description: The primary function for which a building or discrete part of a building + is intended to be used + pattern: '[office|market|restaurant|residence|school|residential|commercial|low + rise|high rise|wood framed|office|health care|school|airport|sports complex]' + examples: + - value: market + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 9' + - 'This field is used uniquely in: built environment' + range: build_occup_type_enum + slot_uri: MIXS:0000761 + surf_moisture: + is_a: environment field + aliases: + - surface moisture + description: Water held on a surface + pattern: '{float} {unit}' + examples: + - value: 0.01 gram per square meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: parts per million, gram per cubic meter, gram per square meter' + - 'Occurrence: 1' + - 'Position: 10' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000128 + dew_point: + is_a: environment field + aliases: + - dew point + description: The temperature to which a given parcel of humid air must be cooled, + at constant barometric pressure, for water vapor to condense into water. + pattern: '{float} {unit}' + examples: + - value: 22 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 11' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000129 + indoor_space: + is_a: environment field + aliases: + - indoor space + description: A distinguishable space within a structure, the purpose for which + discrete areas of a building is used + pattern: '[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]' + examples: + - value: foyer + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 15' + - 'This field is used uniquely in: built environment' + range: indoor_space_enum + slot_uri: MIXS:0000763 + indoor_surf: + is_a: environment field + aliases: + - indoor surface + description: Type of indoor surface + pattern: '[cabinet|ceiling|counter top|door|shelving|vent cover|window|wall]' + examples: + - value: wall + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 16' + - 'This field is used uniquely in: built environment' + range: indoor_surf_enum + slot_uri: MIXS:0000764 + filter_type: + is_a: environment field + aliases: + - filter type + description: A device which removes solid particulates or airborne molecular contaminants + pattern: '[particulate air filter|chemical air filter|low-MERV pleated media|HEPA|electrostatic|gas-phase + or ultraviolet air treatments]' + examples: + - value: HEPA + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 17' + - 'This field is used uniquely in: built environment' + range: filter_type_enum + slot_uri: MIXS:0000765 + heat_cool_type: + is_a: environment field + aliases: + - heating and cooling system type + description: Methods of conditioning or heating a room or building + pattern: '[radiant system|heat pump|forced air system|steam forced heat|wood stove]' + examples: + - value: heat pump + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 18' + - 'This field is used uniquely in: built environment' + range: heat_cool_type_enum + slot_uri: MIXS:0000766 + substructure_type: + is_a: environment field + aliases: + - substructure type + description: The substructure or under building is that largely hidden section + of the building which is built off the foundations to the ground floor level + pattern: '[crawlspace|slab on grade|basement]' + examples: + - value: basement + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 19' + - 'This field is used uniquely in: built environment' + range: substructure_type_enum + slot_uri: MIXS:0000767 + building_setting: + is_a: environment field + aliases: + - building setting + description: A location (geography) where a building is set + pattern: '[urban|suburban|exurban|rural]' + examples: + - value: rural + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 20' + - 'This field is used uniquely in: built environment' + range: building_setting_enum + slot_uri: MIXS:0000768 + light_type: + is_a: environment field + aliases: + - light type + description: Application of light to achieve some practical or aesthetic effect. + Lighting includes the use of both artificial light sources such as lamps and + light fixtures, as well as natural illumination by capturing daylight. Can also + include absence of light + pattern: '[natural light|electric light|desk lamp|flourescent lights|natural light|none]' + examples: + - value: desk lamp + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 21' + - 'This field is used uniquely in: built environment' + range: light_type_enum + slot_uri: MIXS:0000769 + samp_sort_meth: + is_a: environment field + aliases: + - sample size sorting method + description: Method by which samples are sorted; open face filter collecting total + suspended particles, prefilter to remove particles larger than X micrometers + in diameter, where common values of X would be 10 and 2.5 full size sorting + in a cascade impactor. + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: description of method' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 22' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000216 + space_typ_state: + is_a: environment field + aliases: + - space typical state + description: Customary or normal state of the space + pattern: '[typically occupied|typically unoccupied]' + examples: + - value: typically occupied + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 23' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000770 + typ_occup_density: + is_a: environment field + aliases: + - typical occupant density + description: Customary or normal density of occupants + pattern: '{float}' + examples: + - value: '25' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 24' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000771 + occup_samp: + is_a: environment field + aliases: + - occupancy at sampling + description: Number of occupants present at time of sample within the given space + pattern: '{integer}' + examples: + - value: '10' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 25' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000772 + occup_density_samp: + is_a: environment field + aliases: + - occupant density at sampling + description: Average number of occupants at time of sampling per square footage + pattern: '{float}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 26' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000217 + address: + is_a: environment field + aliases: + - address + description: The street name and building number where the sampling occurred. + pattern: '{integer}{text}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 27' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000218 + adj_room: + is_a: environment field + aliases: + - adjacent rooms + description: List of rooms (room number, room name) immediately adjacent to the + sampling room + pattern: '{text};{integer}' + examples: + - value: '' + comments: + - 'Expected value: room name;room number' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 28' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000219 + aero_struc: + is_a: environment field + aliases: + - aerospace structure + description: Aerospace structures typically consist of thin plates with stiffeners + for the external surfaces, bulkheads and frames to support the shape and fasteners + such as welds, rivets, screws and bolts to hold the components together + pattern: '[plane|glider]' + examples: + - value: plane + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 29' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000773 + amount_light: + is_a: environment field + aliases: + - amount of light + description: The unit of illuminance and luminous emittance, measuring luminous + flux per unit area + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: lux, lumens per square meter' + - 'Occurrence: 1' + - 'Position: 30' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000140 + arch_struc: + is_a: environment field + aliases: + - architectural structure + description: An architectural structure is a human-made, free-standing, immobile + outdoor construction + pattern: '[building|shed|home]' + examples: + - value: shed + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 31' + - 'This field is used uniquely in: built environment' + range: arch_struc_enum + slot_uri: MIXS:0000774 + avg_occup: + is_a: environment field + aliases: + - average daily occupancy + description: Daily average occupancy of room + pattern: '{float}' + examples: + - value: '2' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 32' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000775 + avg_dew_point: + is_a: environment field + aliases: + - average dew point + description: The average of dew point measures taken at the beginning of every + hour over a 24 hour period on the sampling day + pattern: '{float} {unit}' + examples: + - value: 25.5 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 33' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000141 + avg_temp: + is_a: environment field + aliases: + - average temperature + description: The average of temperatures taken at the beginning of every hour + over a 24 hour period on the sampling day + pattern: '{float} {unit}' + examples: + - value: 12.5 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 34' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000142 + bathroom_count: + is_a: environment field + aliases: + - bathroom count + description: The number of bathrooms in the building + pattern: '{integer}' + examples: + - value: '1' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 35' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000776 + bedroom_count: + is_a: environment field + aliases: + - bedroom count + description: The number of bedrooms in the building + pattern: '{integer}' + examples: + - value: '2' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 36' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000777 + built_struc_age: + is_a: environment field + aliases: + - built structure age + description: The age of the built structure since construction + pattern: '{float} {unit}' + examples: + - value: '15' + comments: + - 'Expected value: value' + - 'Preferred unit: year' + - 'Occurrence: 1' + - 'Position: 37' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000145 + built_struc_set: + is_a: environment field + aliases: + - built structure setting + description: The characterization of the location of the built structure as high + or low human density + pattern: '[urban|rural]' + examples: + - value: rural + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 38' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000778 + built_struc_type: + is_a: environment field + aliases: + - built structure type + description: A physical structure that is a body or assemblage of bodies in space + to form a system capable of supporting loads + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 39' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000721 + ceil_area: + is_a: environment field + aliases: + - ceiling area + description: The area of the ceiling space within the room + pattern: '{float} {unit}' + examples: + - value: 25 square meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 40' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000148 + ceil_cond: + is_a: environment field + aliases: + - ceiling condition + description: The physical condition of the ceiling at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + pattern: '[new|visible wear|needs repair|damaged|rupture]' + examples: + - value: damaged + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 41' + - 'This field is used uniquely in: built environment' + range: ceil_cond_enum + slot_uri: MIXS:0000779 + ceil_finish_mat: + is_a: environment field + aliases: + - ceiling finish material + description: The type of material used to finish a ceiling + pattern: '[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral + wool/calcium silicate|wood]' + examples: + - value: stucco + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 42' + - 'This field is used uniquely in: built environment' + range: ceil_finish_mat_enum + slot_uri: MIXS:0000780 + ceil_water_mold: + is_a: environment field + aliases: + - ceiling signs of water/mold + description: Signs of the presence of mold or mildew on the ceiling + pattern: '[presence of mold visible|no presence of mold visible]' + examples: + - value: presence of mold visible + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 43' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000781 + ceil_struc: + is_a: environment field + aliases: + - ceiling structure + description: The construction format of the ceiling + pattern: '[wood frame|concrete]' + examples: + - value: concrete + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 44' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000782 + ceil_texture: + is_a: environment field + aliases: + - ceiling texture + description: The feel, appearance, or consistency of a ceiling surface + pattern: '[crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange + peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' + examples: + - value: popcorn + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 45' + - 'This field is used uniquely in: built environment' + range: ceil_texture_enum + slot_uri: MIXS:0000783 + ceil_thermal_mass: + is_a: environment field + aliases: + - ceiling thermal mass + description: The ability of the ceiling to provide inertia against temperature + fluctuations. Generally this means concrete that is exposed. A metal deck that + supports a concrete slab will act thermally as long as it is exposed to room + air flow + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: joule per degree Celsius' + - 'Occurrence: 1' + - 'Position: 46' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000143 + ceil_type: + is_a: environment field + aliases: + - ceiling type + description: The type of ceiling according to the ceiling's appearance or construction + pattern: '[cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched]' + examples: + - value: coffered + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 47' + - 'This field is used uniquely in: built environment' + range: ceil_type_enum + slot_uri: MIXS:0000784 + cool_syst_id: + is_a: environment field + aliases: + - cooling system identifier + description: The cooling system identifier + pattern: '{integer}' + examples: + - value: '12345' + comments: + - 'Expected value: unique identifier' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 48' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000785 + date_last_rain: + is_a: environment field + aliases: + - date last rain + description: The date of the last time it rained + pattern: '{timestamp}' + examples: + - value: 2018-05-11:T14:30Z + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 49' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000786 + build_docs: + is_a: environment field + aliases: + - design, construction, and operation documents + description: The building design, construction and operation documents + pattern: '[building information model|commissioning report|complaint logs|contract + administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop + drawings|submittals|ventilation system|windows]' + examples: + - value: maintenance plans + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 50' + - 'This field is used uniquely in: built environment' + range: build_docs_enum + slot_uri: MIXS:0000787 + door_size: + is_a: environment field + aliases: + - door area or size + description: The size of the door + pattern: '{float} {unit}' + examples: + - value: 2.5 square meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 51' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000158 + door_cond: + is_a: environment field + aliases: + - door condition + description: The phsical condition of the door + pattern: '[damaged|needs repair|new|rupture|visible wear]' + examples: + - value: new + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 52' + - 'This field is used uniquely in: built environment' + range: door_cond_enum + slot_uri: MIXS:0000788 + door_direct: + is_a: environment field + aliases: + - door direction of opening + description: The direction the door opens + pattern: '[inward|outward|sideways]' + examples: + - value: inward + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 53' + - 'This field is used uniquely in: built environment' + range: door_direct_enum + slot_uri: MIXS:0000789 + door_loc: + is_a: environment field + aliases: + - door location + description: The relative location of the door in the room + pattern: '[north|south|east|west]' + examples: + - value: north + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 54' + - 'This field is used uniquely in: built environment' + range: door_loc_enum + slot_uri: MIXS:0000790 + door_mat: + is_a: environment field + aliases: + - door material + description: The material the door is composed of + pattern: '[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic + alloy|vinyl|wood|wood/plastic composite]' + examples: + - value: wood + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 55' + - 'This field is used uniquely in: built environment' + range: door_mat_enum + slot_uri: MIXS:0000791 + door_move: + is_a: environment field + aliases: + - door movement + description: The type of movement of the door + pattern: '[collapsible|folding|revolving|rolling shutter|sliding|swinging]' + examples: + - value: swinging + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 56' + - 'This field is used uniquely in: built environment' + range: door_move_enum + slot_uri: MIXS:0000792 + door_water_mold: + is_a: environment field + aliases: + - door signs of water/mold + description: Signs of the presence of mold or mildew on a door + pattern: '[presence of mold visible|no presence of mold visible]' + examples: + - value: presence of mold visible + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 57' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000793 + door_type: + is_a: environment field + aliases: + - door type + description: The type of door material + pattern: '[composite|metal|wooden]' + examples: + - value: wooden + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 58' + - 'This field is used uniquely in: built environment' + range: door_type_enum + slot_uri: MIXS:0000794 + door_comp_type: + is_a: environment field + aliases: + - door type, composite + description: The composite type of the door + pattern: '[metal covered|revolving|sliding|telescopic]' + examples: + - value: revolving + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 59' + - 'This field is used uniquely in: built environment' + range: door_comp_type_enum + slot_uri: MIXS:0000795 + door_type_metal: + is_a: environment field + aliases: + - door type, metal + description: The type of metal door + pattern: '[collapsible|corrugated steel|hollow|rolling shutters|steel plate]' + examples: + - value: hollow + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 60' + - 'This field is used uniquely in: built environment' + range: door_type_metal_enum + slot_uri: MIXS:0000796 + door_type_wood: + is_a: environment field + aliases: + - door type, wood + description: The type of wood door + pattern: '[bettened and ledged|battened|ledged and braced|battened|ledged and + framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire + gauged]' + examples: + - value: battened + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 61' + - 'This field is used uniquely in: built environment' + range: door_type_wood_enum + slot_uri: MIXS:0000797 + drawings: + is_a: environment field + aliases: + - drawings + description: The buildings architectural drawings; if design is chosen, indicate + phase-conceptual, schematic, design development, and construction documents + pattern: '[operation|as built|construction|bid|design|building navigation map|diagram|sketch]' + examples: + - value: sketch + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 62' + - 'This field is used uniquely in: built environment' + range: drawings_enum + slot_uri: MIXS:0000798 + elevator: + is_a: environment field + aliases: + - elevator count + description: The number of elevators within the built structure + pattern: '{integer}' + examples: + - value: '2' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 63' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000799 + escalator: + is_a: environment field + aliases: + - escalator count + description: The number of escalators within the built structure + pattern: '{integer}' + examples: + - value: '4' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 64' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000800 + exp_duct: + is_a: environment field + aliases: + - exposed ductwork + description: The amount of exposed ductwork in the room + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 65' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000144 + exp_pipe: + is_a: environment field + aliases: + - exposed pipes + description: The number of exposed pipes in the room + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 66' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000220 + ext_door: + is_a: environment field + aliases: + - exterior door count + description: The number of exterior doors in the built structure + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 67' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000170 + fireplace_type: + is_a: environment field + aliases: + - fireplace type + description: A firebox with chimney + pattern: '[gas burning|wood burning]' + examples: + - value: wood burning + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 68' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000802 + floor_age: + is_a: environment field + aliases: + - floor age + description: The time period since installment of the carpet or flooring + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: years, weeks, days' + - 'Occurrence: 1' + - 'Position: 69' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000164 + floor_area: + is_a: environment field + aliases: + - floor area + description: The area of the floor space within the room + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 70' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000165 + floor_cond: + is_a: environment field + aliases: + - floor condition + description: The physical condition of the floor at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + pattern: '[new|visible wear|needs repair|damaged|rupture]' + examples: + - value: new + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 71' + - 'This field is used uniquely in: built environment' + range: floor_cond_enum + slot_uri: MIXS:0000803 + floor_count: + is_a: environment field + aliases: + - floor count + description: The number of floors in the building, including basements and mechanical + penthouse + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 72' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000225 + floor_finish_mat: + is_a: environment field + aliases: + - floor finish material + description: The floor covering type; the finished surface that is walked on + pattern: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl + composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify + unfinished|sealed|clear finish|paint]' + examples: + - value: carpet + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 73' + - 'This field is used uniquely in: built environment' + range: floor_finish_mat_enum + slot_uri: MIXS:0000804 + floor_water_mold: + is_a: environment field + aliases: + - floor signs of water/mold + description: Signs of the presence of mold or mildew in a room + pattern: '[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling + discoloration|peeling paint or wallpaper|bulging walls|condensation]' + examples: + - value: ceiling discoloration + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 74' + - 'This field is used uniquely in: built environment' + range: floor_water_mold_enum + slot_uri: MIXS:0000805 + floor_struc: + is_a: environment field + aliases: + - floor structure + description: Refers to the structural elements and subfloor upon which the finish + flooring is installed + pattern: '[balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete]' + examples: + - value: concrete + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 75' + - 'This field is used uniquely in: built environment' + range: floor_struc_enum + slot_uri: MIXS:0000806 + floor_thermal_mass: + is_a: environment field + aliases: + - floor thermal mass + description: The ability of the floor to provide inertia against temperature fluctuations + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: joule per degree Celsius' + - 'Occurrence: 1' + - 'Position: 76' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000166 + freq_clean: + is_a: environment field + aliases: + - frequency of cleaning + description: The number of times the building is cleaned per week + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 77' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000226 + freq_cook: + is_a: environment field + aliases: + - frequency of cooking + description: The number of times a meal is cooked per week + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 78' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000227 + furniture: + is_a: environment field + aliases: + - furniture + description: The types of furniture present in the sampled room + pattern: '[cabinet|chair|desks]' + examples: + - value: chair + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 79' + - 'This field is used uniquely in: built environment' + range: furniture_enum + slot_uri: MIXS:0000807 + gender_restroom: + is_a: environment field + aliases: + - gender of restroom + description: The gender type of the restroom + pattern: '[male|female]' + examples: + - value: male + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 80' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000808 + hall_count: + is_a: environment field + aliases: + - hallway/corridor count + description: The total count of hallways and cooridors in the built structure + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 81' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000228 + handidness: + is_a: environment field + aliases: + - handidness + description: The handidness of the individual sampled + pattern: '[ambidexterity|left handedness|mixed-handedness|right handedness]' + examples: + - value: right handedness + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 82' + - 'This field is used uniquely in: built environment' + range: handidness_enum + slot_uri: MIXS:0000809 + heat_deliv_loc: + is_a: environment field + aliases: + - heating delivery locations + description: The location of heat delivery within the room + pattern: '[north|south|east|west]' + examples: + - value: north + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 83' + - 'This field is used uniquely in: built environment' + range: heat_deliv_loc_enum + slot_uri: MIXS:0000810 + heat_system_deliv_meth: + is_a: environment field + aliases: + - heating system delivery method + description: The method by which the heat is delivered through the system + pattern: '[conductive|radiant]' + examples: + - value: radiant + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 84' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000812 + heat_system_id: + is_a: environment field + aliases: + - heating system identifier + description: The heating system identifier + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: unique identifier' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 85' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000833 + height_carper_fiber: + is_a: environment field + aliases: + - height carpet fiber mat + description: The average carpet fiber height in the indoor environment + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: centimeter' + - 'Occurrence: 1' + - 'Position: 86' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000167 + inside_lux: + is_a: environment field + aliases: + - inside lux light + description: The recorded value at sampling time (power density) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilowatt per square metre' + - 'Occurrence: 1' + - 'Position: 87' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000168 + int_wall_cond: + is_a: environment field + aliases: + - interior wall condition + description: The physical condition of the wall at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + pattern: '[new|visible wear|needs repair|damaged|rupture]' + examples: + - value: damaged + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 88' + - 'This field is used uniquely in: built environment' + range: int_wall_cond_enum + slot_uri: MIXS:0000813 + last_clean: + is_a: environment field + aliases: + - last time swept/mopped/vacuumed + description: The last time the floor was cleaned (swept, mopped, vacuumed) + pattern: '{timestamp}' + examples: + - value: 2018-05-11:T14:30Z + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 89' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000814 + max_occup: + is_a: environment field + aliases: + - maximum occupancy + description: The maximum amount of people allowed in the indoor environment + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 90' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000229 + mech_struc: + is_a: environment field + aliases: + - mechanical structure + description: 'mechanical structure: a moving structure' + pattern: '[subway|coach|carriage|elevator|escalator|boat|train|car|bus]' + examples: + - value: elevator + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 91' + - 'This field is used uniquely in: built environment' + range: mech_struc_enum + slot_uri: MIXS:0000815 + number_plants: + is_a: environment field + aliases: + - number of houseplants + description: The number of plant(s) in the sampling space + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 92' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000230 + number_pets: + is_a: environment field + aliases: + - number of pets + description: The number of pets residing in the sampled space + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 93' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000231 + number_resident: + is_a: environment field + aliases: + - number of residents + description: The number of individuals currently occupying in the sampling location + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 94' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000232 + occup_document: + is_a: environment field + aliases: + - occupancy documentation + description: The type of documentation of occupancy + pattern: '[automated count|estimate|manual count|videos]' + examples: + - value: estimate + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 95' + - 'This field is used uniquely in: built environment' + range: occup_document_enum + slot_uri: MIXS:0000816 + ext_wall_orient: + is_a: environment field + aliases: + - orientations of exterior wall + description: The orientation of the exterior wall + pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' + examples: + - value: northwest + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 96' + - 'This field is used uniquely in: built environment' + range: ext_wall_orient_enum + slot_uri: MIXS:0000817 + ext_window_orient: + is_a: environment field + aliases: + - orientations of exterior window + description: The compass direction the exterior window of the room is facing + pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' + examples: + - value: southwest + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 97' + - 'This field is used uniquely in: built environment' + range: ext_window_orient_enum + slot_uri: MIXS:0000818 + rel_humidity_out: + is_a: environment field + aliases: + - outside relative humidity + description: The recorded outside relative humidity value at the time of sampling + pattern: '{float} {unit}' + examples: + - value: 12 per kilogram of air + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram of air, kilogram of air' + - 'Occurrence: 1' + - 'Position: 98' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000188 + pres_animal: + is_a: environment field + aliases: + - presence of pets, animals, or insects + description: The number and type of animals present in the sampling space + pattern: '[cat|dog|rodent|snake|other];{integer}' + examples: + - value: cat;5 + comments: + - 'Expected value: enumeration;count' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 99' + - 'This field is used uniquely in: built environment' + range: pres_animal_enum + slot_uri: MIXS:0000819 + quad_pos: + is_a: environment field + aliases: + - quadrant position + description: The quadrant position of the sampling room within the building + pattern: '[North side|West side|South side|East side]' + examples: + - value: West side + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 100' + - 'This field is used uniquely in: built environment' + range: quad_pos_enum + slot_uri: MIXS:0000820 + rel_samp_loc: + is_a: environment field + aliases: + - relative sampling location + description: The sampling location within the train car + pattern: '[edge of car|center of car|under a seat]' + examples: + - value: center of car + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 101' + - 'This field is used uniquely in: built environment' + range: rel_samp_loc_enum + slot_uri: MIXS:0000821 + room_air_exch_rate: + is_a: environment field + aliases: + - room air exchange rate + description: The rate at which outside air replaces indoor air in a given space + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: liter per hour' + - 'Occurrence: 1' + - 'Position: 102' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000169 + room_architec_element: + is_a: environment field + aliases: + - room architectural elements + description: The unique details and component parts that, together, form the architecture + of a distinguisahable space within a built structure + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 103' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000233 + room_condt: + is_a: environment field + aliases: + - room condition + description: The condition of the room at the time of sampling + pattern: '[new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew]' + examples: + - value: new + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 104' + - 'This field is used uniquely in: built environment' + range: room_condt_enum + slot_uri: MIXS:0000822 + room_count: + is_a: environment field + aliases: + - room count + description: The total count of rooms in the built structure including all room + types + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 105' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000234 + room_dim: + is_a: environment field + aliases: + - room dimensions + description: The length, width and height of sampling room + pattern: '{integer} {unit} x {integer} {unit} x {integer} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 106' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000192 + room_door_dist: + is_a: environment field + aliases: + - room door distance + description: Distance between doors (meters) in the hallway between the sampling + room and adjacent rooms + pattern: '{integer} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 107' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000193 + room_loc: + is_a: environment field + aliases: + - room location in building + description: The position of the room within the building + pattern: '[corner room|interior room|exterior wall]' + examples: + - value: interior room + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 108' + - 'This field is used uniquely in: built environment' + range: room_loc_enum + slot_uri: MIXS:0000823 + room_moist_damage_hist: + is_a: environment field + aliases: + - room moisture damage or mold history + description: The history of moisture damage or mold in the past 12 months. Number + of events of moisture damage or mold observed + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 109' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000235 + room_net_area: + is_a: environment field + aliases: + - room net area + description: The net floor area of sampling room. Net area excludes wall thicknesses + pattern: '{integer} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square feet, square meter' + - 'Occurrence: 1' + - 'Position: 110' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000194 + room_occup: + is_a: environment field + aliases: + - room occupancy + description: Count of room occupancy at time of sampling + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 111' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000236 + room_samp_pos: + is_a: environment field + aliases: + - room sampling position + description: The horizontal sampling position in the room relative to architectural + elements + pattern: '[north corner|south corner|west corner|east corner|northeast corner|northwest + corner|southeast corner|southwest corner|center]' + examples: + - value: south corner + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 112' + - 'This field is used uniquely in: built environment' + range: room_samp_pos_enum + slot_uri: MIXS:0000824 + room_type: + is_a: environment field + aliases: + - room type + description: The main purpose or activity of the sampling room. A room is any + distinguishable space within a structure + pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail + room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical + or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' + examples: + - value: bathroom + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 113' + - 'This field is used uniquely in: built environment' + range: room_type_enum + slot_uri: MIXS:0000825 + room_vol: + is_a: environment field + aliases: + - room volume + description: Volume of sampling room + pattern: '{integer} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: cubic feet, cubic meter' + - 'Occurrence: 1' + - 'Position: 114' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000195 + room_window_count: + is_a: environment field + aliases: + - room window count + description: Number of windows in the room + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 115' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000237 + room_connected: + is_a: environment field + aliases: + - rooms connected by a doorway + description: List of rooms connected to the sampling room by a doorway + pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail + room|office|stairwell]' + examples: + - value: office + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 116' + - 'This field is used uniquely in: built environment' + range: room_connected_enum + slot_uri: MIXS:0000826 + room_hallway: + is_a: environment field + aliases: + - rooms that are on the same hallway + description: List of room(s) (room number, room name) located in the same hallway + as sampling room + pattern: '{text};{integer}' + examples: + - value: '' + comments: + - 'Expected value: room name;room number' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 117' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000238 + room_door_share: + is_a: environment field + aliases: + - rooms that share a door with sampling room + description: List of room(s) (room number, room name) sharing a door with the + sampling room + pattern: '{text};{integer}' + examples: + - value: '' + comments: + - 'Expected value: room name;room number' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 118' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000242 + room_wall_share: + is_a: environment field + aliases: + - rooms that share a wall with sampling room + description: List of room(s) (room number, room name) sharing a wall with the + sampling room + pattern: '{text};{integer}' + examples: + - value: '' + comments: + - 'Expected value: room name;room number' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 119' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000243 + samp_weather: + is_a: environment field + aliases: + - sampling day weather + description: The weather on the sampling day + pattern: '[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]' + examples: + - value: foggy + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 120' + - 'This field is used uniquely in: built environment' + range: samp_weather_enum + slot_uri: MIXS:0000827 + samp_floor: + is_a: environment field + aliases: + - sampling floor + description: The floor of the building, where the sampling room is located + pattern: '[1st floor|2nd floor|{integer} floor|basement|lobby]' + examples: + - value: 4th floor + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 121' + - 'This field is used uniquely in: built environment' + range: samp_floor_enum + slot_uri: MIXS:0000828 + samp_room_id: + is_a: environment field + aliases: + - sampling room ID or name + description: Sampling room number. This ID should be consistent with the designations + on the building floor plans + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 122' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000244 + samp_time_out: + is_a: environment field + aliases: + - sampling time outside + description: The recent and long term history of outside sampling + pattern: '{float}' + examples: + - value: '' + comments: + - 'Expected value: time' + - 'Preferred unit: hour' + - 'Occurrence: 1' + - 'Position: 123' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000196 + season: + is_a: environment field + aliases: + - season + description: The season when sampling occurred. Any of the four periods into which + the year is divided by the equinoxes and solstices. This field accepts terms + listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + pattern: '{termLabel} {[termID]}' + examples: + - value: autumn [NCIT:C94733] + comments: + - 'Expected value: NCIT:C94729' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 124' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000829 + season_use: + is_a: environment field + aliases: + - seasonal use + description: The seasons the space is occupied + pattern: '[Spring|Summer|Fall|Winter]' + examples: + - value: Winter + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 125' + - 'This field is used uniquely in: built environment' + range: season_use_enum + slot_uri: MIXS:0000830 + shading_device_cond: + is_a: environment field + aliases: + - shading device condition + description: The physical condition of the shading device at the time of sampling + pattern: '[damaged|needs repair|new|rupture|visible wear]' + examples: + - value: new + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 126' + - 'This field is used uniquely in: built environment' + range: shading_device_cond_enum + slot_uri: MIXS:0000831 + shading_device_loc: + is_a: environment field + aliases: + - shading device location + description: The location of the shading device in relation to the built structure + pattern: '[exterior|interior]' + examples: + - value: exterior + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 127' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000832 + shading_device_mat: + is_a: environment field + aliases: + - shading device material + description: The material the shading device is composed of + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: material name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 128' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000245 + shading_device_water_mold: + is_a: environment field + aliases: + - shading device signs of water/mold + description: Signs of the presence of mold or mildew on the shading device + pattern: '[presence of mold visible|no presence of mold visible]' + examples: + - value: no presence of mold visible + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 129' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000834 + shading_device_type: + is_a: environment field + aliases: + - shading device type + description: The type of shading device + pattern: '[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller + awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian + awning]' + examples: + - value: slatted aluminum awning + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 130' + - 'This field is used uniquely in: built environment' + range: shading_device_type_enum + slot_uri: MIXS:0000835 + specific_humidity: + is_a: environment field + aliases: + - specific humidity + description: The mass of water vapour in a unit mass of moist air, usually expressed + as grams of vapour per kilogram of air, or, in air conditioning, as grains per + pound. + pattern: '{float} {unit}' + examples: + - value: 15 per kilogram of air + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram of air, kilogram of air' + - 'Occurrence: 1' + - 'Position: 131' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000214 + specific: + is_a: environment field + aliases: + - specifications + description: 'The building specifications. If design is chosen, indicate phase: + conceptual, schematic, design development, construction documents' + pattern: '[operation|as built|construction|bid|design|photos]' + examples: + - value: construction + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 132' + - 'This field is used uniquely in: built environment' + range: specific_enum + slot_uri: MIXS:0000836 + temp_out: + is_a: environment field + aliases: + - temperature outside house + description: The recorded temperature value at sampling time outside + pattern: '{float} {unit}' + examples: + - value: 5 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 133' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000197 + train_line: + is_a: environment field + aliases: + - train line + description: The subway line name + pattern: '[red|green|orange]' + examples: + - value: red + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 134' + - 'This field is used uniquely in: built environment' + range: train_line_enum + slot_uri: MIXS:0000837 + train_stat_loc: + is_a: environment field + aliases: + - train station collection location + description: The train station collection location + pattern: '[south station above ground|south station underground|south station + amtrak|forest hills|riverside]' + examples: + - value: forest hills + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 135' + - 'This field is used uniquely in: built environment' + range: train_stat_loc_enum + slot_uri: MIXS:0000838 + train_stop_loc: + is_a: environment field + aliases: + - train stop collection location + description: The train stop collection location + pattern: '[end|mid|downtown]' + examples: + - value: end + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 136' + - 'This field is used uniquely in: built environment' + range: train_stop_loc_enum + slot_uri: MIXS:0000839 + vis_media: + is_a: environment field + aliases: + - visual media + description: The building visual media + pattern: '[photos|videos|commonly of the building|site context (adjacent buildings, + vegetation, terrain, streets)|interiors|equipment|3D scans]' + examples: + - value: 3D scans + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 137' + - 'This field is used uniquely in: built environment' + range: vis_media_enum + slot_uri: MIXS:0000840 + wall_area: + is_a: environment field + aliases: + - wall area + description: The total area of the sampled room's walls + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 138' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000198 + wall_const_type: + is_a: environment field + aliases: + - wall construction type + description: The building class of the wall defined by the composition of the + building elements and fire-resistance rating. + pattern: '[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified + fire resistive|fire resistive]' + examples: + - value: fire resistive + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 139' + - 'This field is used uniquely in: built environment' + range: wall_const_type_enum + slot_uri: MIXS:0000841 + wall_finish_mat: + is_a: environment field + aliases: + - wall finish material + description: The material utilized to finish the outer most layer of the wall + pattern: '[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone + facing|acoustical treatment|wood|metal|masonry]' + examples: + - value: wood + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 140' + - 'This field is used uniquely in: built environment' + range: wall_finish_mat_enum + slot_uri: MIXS:0000842 + wall_height: + is_a: environment field + aliases: + - wall height + description: The average height of the walls in the sampled room + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: centimeter' + - 'Occurrence: 1' + - 'Position: 141' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000221 + wall_loc: + is_a: environment field + aliases: + - wall location + description: The relative location of the wall within the room + pattern: '[north|south|east|west]' + examples: + - value: north + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 142' + - 'This field is used uniquely in: built environment' + range: wall_loc_enum + slot_uri: MIXS:0000843 + wall_water_mold: + is_a: environment field + aliases: + - wall signs of water/mold + description: Signs of the presence of mold or mildew on a wall + pattern: '[presence of mold visible|no presence of mold visible]' + examples: + - value: no presence of mold visible + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 143' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000844 + wall_surf_treatment: + is_a: environment field + aliases: + - wall surface treatment + description: The surface treatment of interior wall + pattern: '[painted|wall paper|no treatment|paneling|stucco|fabric]' + examples: + - value: paneling + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 144' + - 'This field is used uniquely in: built environment' + range: wall_surf_treatment_enum + slot_uri: MIXS:0000845 + wall_texture: + is_a: environment field + aliases: + - wall texture + description: The feel, appearance, or consistency of a wall surface + pattern: '[crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange + peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' + examples: + - value: popcorn + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 145' + - 'This field is used uniquely in: built environment' + range: wall_texture_enum + slot_uri: MIXS:0000846 + wall_thermal_mass: + is_a: environment field + aliases: + - wall thermal mass + description: The ability of the wall to provide inertia against temperature fluctuations. + Generally this means concrete or concrete block that is either exposed or covered + only with paint + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: joule per degree Celsius' + - 'Occurrence: 1' + - 'Position: 146' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000222 + water_feat_size: + is_a: environment field + aliases: + - water feature size + description: The size of the water feature + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: square meter' + - 'Occurrence: 1' + - 'Position: 147' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000223 + water_feat_type: + is_a: environment field + aliases: + - water feature type + description: The type of water feature present within the building being sampled + pattern: '[fountain|pool|standing feature|stream|waterfall]' + examples: + - value: stream + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 148' + - 'This field is used uniquely in: built environment' + range: water_feat_type_enum + slot_uri: MIXS:0000847 + weekday: + is_a: environment field + aliases: + - weekday + description: The day of the week when sampling occurred + pattern: '[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]' + examples: + - value: Sunday + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 149' + - 'This field is used uniquely in: built environment' + range: weekday_enum + slot_uri: MIXS:0000848 + window_size: + is_a: environment field + aliases: + - window area/size + description: The window's length and width + pattern: '{float} {unit} x {float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: inch, meter' + - 'Occurrence: 1' + - 'Position: 150' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000224 + window_cond: + is_a: environment field + aliases: + - window condition + description: The physical condition of the window at the time of sampling + pattern: '[damaged|needs repair|new|rupture|visible wear]' + examples: + - value: rupture + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 151' + - 'This field is used uniquely in: built environment' + range: window_cond_enum + slot_uri: MIXS:0000849 + window_cover: + is_a: environment field + aliases: + - window covering + description: The type of window covering + pattern: '[blinds|curtains|none]' + examples: + - value: curtains + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 152' + - 'This field is used uniquely in: built environment' + range: window_cover_enum + slot_uri: MIXS:0000850 + window_horiz_pos: + is_a: environment field + aliases: + - window horizontal position + description: The horizontal position of the window on the wall + pattern: '[left|middle|right]' + examples: + - value: middle + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 153' + - 'This field is used uniquely in: built environment' + range: window_horiz_pos_enum + slot_uri: MIXS:0000851 + window_loc: + is_a: environment field + aliases: + - window location + description: The relative location of the window within the room + pattern: '[north|south|east|west]' + examples: + - value: west + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 154' + - 'This field is used uniquely in: built environment' + range: window_loc_enum + slot_uri: MIXS:0000852 + window_mat: + is_a: environment field + aliases: + - window material + description: The type of material used to finish a window + pattern: '[clad|fiberglass|metal|vinyl|wood]' + examples: + - value: wood + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 155' + - 'This field is used uniquely in: built environment' + range: window_mat_enum + slot_uri: MIXS:0000853 + window_open_freq: + is_a: environment field + aliases: + - window open frequency + description: The number of times windows are opened per week + pattern: '{integer}' + examples: + - value: '' + comments: + - 'Expected value: value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 156' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000246 + window_water_mold: + is_a: environment field + aliases: + - window signs of water/mold + description: Signs of the presence of mold or mildew on the window. + pattern: '[presence of mold visible|no presence of mold visible]' + examples: + - value: no presence of mold visible + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 157' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000854 + window_status: + is_a: environment field + aliases: + - window status + description: Defines whether the windows were open or closed during environmental + testing + pattern: '[closed|open]' + examples: + - value: open + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 158' + - 'This field is used uniquely in: built environment' + slot_uri: MIXS:0000855 + window_type: + is_a: environment field + aliases: + - window type + description: The type of windows + pattern: '[single-hung sash window|horizontal sash window|fixed window]' + examples: + - value: fixed window + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 159' + - 'This field is used uniquely in: built environment' + range: window_type_enum + slot_uri: MIXS:0000856 + window_vert_pos: + is_a: environment field + aliases: + - window vertical position + description: The vertical position of the window on the wall + pattern: '[bottom|middle|top|low|middle|high]' + examples: + - value: middle + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 160' + - 'This field is used uniquely in: built environment' + range: window_vert_pos_enum + slot_uri: MIXS:0000857 + ances_data: + is_a: environment field + aliases: + - ancestral data + description: Information about either pedigree or other ancestral information + description (e.g. parental variety in case of mutant or selection), e.g. A/3*B + (meaning [(A x B) x B] x B) + pattern: '{text}' + examples: + - value: A/3*B + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000247 + biol_stat: + is_a: environment field + aliases: + - biological status + description: The level of genome modification + pattern: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal + selection|mutant]' + examples: + - value: natural + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used in: 2 packages: host-associated, plant-associated' + range: biol_stat_enum + slot_uri: MIXS:0000858 + genetic_mod: + is_a: environment field + aliases: + - genetic modification + description: Genetic modifications of the genome of an organism, which may occur + naturally by spontaneous mutation, or be introduced by some experimental means, + e.g. specification of a transgene or the gene knocked-out or details of transient + transfection + pattern: '{PMID}|{DOI}|{URL}|{text}' + examples: + - value: aox1A transgenic + comments: + - 'Expected value: PMID,DOI,url or free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000859 + host_common_name: + is_a: environment field + aliases: + - host common name + description: Common name of the host, e.g. Human + pattern: '{text}' + examples: + - value: mussel + comments: + - 'Expected value: common name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 4' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000248 + samp_capt_status: + is_a: environment field + aliases: + - sample capture status + description: Reason for the sample + pattern: '[active surveillance in response to an outbreak|active surveillance + not initiated by an outbreak|farm sample|market sample|other]' + examples: + - value: farm sample + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 5' + - 'This field is used in: 2 packages: host-associated, plant-associated' + range: samp_capt_status_enum + slot_uri: MIXS:0000860 + samp_dis_stage: + is_a: environment field + aliases: + - sample disease stage + description: Stage of the disease at the time of sample collection, e.g. inoculation, + penetration, infection, growth and reproduction, dissemination of pathogen. + pattern: '{text}' + examples: + - value: infection + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 6' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000249 + host_taxid: + is_a: environment field + aliases: + - host taxid + description: NCBI taxon id of the host, e.g. 9606 + pattern: '{NCBI taxid}' + examples: + - value: '7955' + comments: + - 'Expected value: NCBI taxon identifier' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 7' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000250 + host_subject_id: + is_a: environment field + aliases: + - host subject id + description: 'A unique identifier by which each subject can be referred to, de-identified, + e.g. #131' + pattern: '{text}' + examples: + - value: MPI123 + comments: + - 'Expected value: unique identifier' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 8' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000861 + host_age: + is_a: environment field + aliases: + - host age + description: Age of host at the time of sampling; relevant scale depends on species + and study, e.g. Could be seconds for amoebae or centuries for trees + pattern: '{float} {unit}' + examples: + - value: 10 days + comments: + - 'Expected value: value' + - 'Preferred unit: year, day, hour' + - 'Occurrence: 1' + - 'Position: 9' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000255 + host_life_stage: + is_a: environment field + aliases: + - host life stage + description: Description of life stage of host + pattern: '{text}' + examples: + - value: adult + comments: + - 'Expected value: stage' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 10' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000251 + host_sex: + is_a: environment field + aliases: + - host sex + description: Physical sex of the host + pattern: '[male|female|neuter|hermaphrodite|not determined]' + examples: + - value: female + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 11' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + range: host_sex_enum + slot_uri: MIXS:0000811 + host_disease_stat: + is_a: environment field + aliases: + - host disease status + description: List of diseases with which the host has been diagnosed; can include + multiple diagnoses. The value of the field depends on host; for humans the terms + should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, + non-human host diseases are free text + pattern: '{termLabel} {[termID]}|{text}' + examples: + - value: rabies [DOID:11260] + comments: + - 'Expected value: disease name or DO' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 12' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000031 + host_body_habitat: + is_a: environment field + aliases: + - host body habitat + description: Original body habitat where the sample was obtained from + pattern: '{text}' + examples: + - value: nasopharynx + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 14' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000866 + host_body_site: + is_a: environment field + aliases: + - host body site + description: Name of body site where the sample was obtained from, such as a specific + organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology + (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, + please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + pattern: '{termLabel} {[termID]}' + examples: + - value: gill [UBERON:0002535] + comments: + - 'Expected value: FMA or UBERON' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 15' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000867 + host_body_product: + is_a: environment field + aliases: + - host body product + description: Substance produced by the body, e.g. Stool, mucus, where the sample + was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy + ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma + or https://www.ebi.ac.uk/ols/ontologies/uberon + pattern: '{termLabel} {[termID]}' + examples: + - value: Portion of mucus [fma66938] + comments: + - 'Expected value: FMA or UBERON' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 16' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000888 + host_tot_mass: + is_a: environment field + aliases: + - host total mass + description: Total mass of the host at collection, the unit depends on host + pattern: '{float} {unit}' + examples: + - value: 2500 gram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilogram, gram' + - 'Occurrence: 1' + - 'Position: 17' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000263 + host_height: + is_a: environment field + aliases: + - host height + description: The height of subject + pattern: '{float} {unit}' + examples: + - value: 0.1 meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: centimeter, millimeter, meter' + - 'Occurrence: 1' + - 'Position: 18' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000264 + host_length: + is_a: environment field + aliases: + - host length + description: The length of subject + pattern: '{float} {unit}' + examples: + - value: 1 meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: centimeter, millimeter, meter' + - 'Occurrence: 1' + - 'Position: 19' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000256 + host_diet: + is_a: environment field + aliases: + - host diet + description: Type of diet depending on the host, for animals omnivore, herbivore + etc., for humans high-fat, meditteranean etc.; can include multiple diet types + pattern: '{text}' + examples: + - value: herbivore + comments: + - 'Expected value: diet type' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 20' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000869 + host_last_meal: + is_a: environment field + aliases: + - host last meal + description: Content of last meal and time since feeding; can include multiple + values + pattern: '{text};{duration}' + examples: + - value: corn feed;P2H + comments: + - 'Expected value: content;duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 21' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000870 + host_growth_cond: + is_a: environment field + aliases: + - host growth conditions + description: Literature reference giving growth conditions of the host + pattern: '{PMID}|{DOI}|{URL}|{text}' + examples: + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 + comments: + - 'Expected value: PMID,DOI,url or free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 22' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000871 + host_substrate: + is_a: environment field + aliases: + - host substrate + description: The growth substrate of the host + pattern: '{text}' + examples: + - value: rock + comments: + - 'Expected value: substrate name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 23' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000252 + host_family_relationship: + is_a: environment field + aliases: + - host family relationship + description: Relationships to other hosts in the same study; can include multiple + relationships + pattern: '{text};{text}' + examples: + - value: offspring;Mussel25 + comments: + - 'Expected value: relationship type;arbitrary identifier' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 24' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000872 + host_infra_specific_name: + is_a: environment field + aliases: + - host infra-specific name + description: Taxonomic information about the host below subspecies level + pattern: '{text}' + examples: + - value: borealis + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 25' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000253 + host_infra_specific_rank: + is_a: environment field + aliases: + - host infra-specific rank + description: Taxonomic rank information about the host below subspecies level, + such as variety, form, rank etc. + pattern: '{text}' + examples: + - value: subspecies + comments: + - 'Expected value: rank' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 26' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000254 + host_genotype: + is_a: environment field + aliases: + - host genotype + description: Observed genotype + pattern: '{text}' + examples: + - value: C57BL/6 + comments: + - 'Expected value: genotype' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 27' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000365 + host_phenotype: + is_a: environment field + aliases: + - host phenotype + description: Phenotype of human or other host. For phenotypic quality ontology + (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. + For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + pattern: '{termLabel} {[termID]}' + examples: + - value: elongated [PATO:0001154] + comments: + - 'Expected value: PATO or HP' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 28' + - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal, plant-associated' + slot_uri: MIXS:0000874 + host_body_temp: + is_a: environment field + aliases: + - host body temperature + description: Core body temperature of the host when sample was collected + pattern: '{float} {unit}' + examples: + - value: 15 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 29' + - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, + human-oral, human-skin, human-vaginal' + slot_uri: MIXS:0000274 + host_dry_mass: + is_a: environment field + aliases: + - host dry mass + description: Measurement of dry mass + pattern: '{float} {unit}' + examples: + - value: 500 gram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilogram, gram' + - 'Occurrence: 1' + - 'Position: 30' + - 'This field is used in: 2 packages: host-associated, plant-associated' + slot_uri: MIXS:0000257 + host_blood_press_diast: + is_a: environment field + aliases: + - host blood pressure diastolic + description: Resting diastolic blood pressure, measured as mm mercury + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millimeter mercury' + - 'Occurrence: 1' + - 'Position: 31' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000258 + host_blood_press_syst: + is_a: environment field + aliases: + - host blood pressure systolic + description: Resting systolic blood pressure, measured as mm mercury + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millimeter mercury' + - 'Occurrence: 1' + - 'Position: 32' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000259 + host_color: + is_a: environment field + aliases: + - host color + description: The color of host + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: color' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 33' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000260 + host_shape: + is_a: environment field + aliases: + - host shape + description: Morphological shape of host + pattern: '{text}' + examples: + - value: round + comments: + - 'Expected value: shape' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 34' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000261 + gravidity: + is_a: environment field + aliases: + - gravidity + description: Whether or not subject is gravid, and if yes date due or date post-conception, + specifying which is used + pattern: '{boolean};{timestamp}' + examples: + - value: yes;due date:2018-05-11 + comments: + - 'Expected value: gravidity status;timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 35' + - 'This field is used uniquely in: host-associated' + slot_uri: MIXS:0000875 + ihmc_medication_code: + is_a: environment field + aliases: + - IHMC medication code + description: Can include multiple medication codes + pattern: '{integer}' + examples: + - value: '810' + comments: + - 'Expected value: IHMC code' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 5' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000884 + smoker: + is_a: environment field + aliases: + - smoker + description: Specification of smoking status + pattern: '{boolean}' + examples: + - value: 'yes' + comments: + - 'Expected value: smoking status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 17' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000262 + host_hiv_stat: + is_a: environment field + aliases: + - host HIV status + description: HIV status of subject, if yes HAART initiation status should also + be indicated as [YES or NO] + pattern: '{boolean};{boolean}' + examples: + - value: yes;yes + comments: + - 'Expected value: HIV status;HAART initiation status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 18' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000265 + drug_usage: + is_a: environment field + aliases: + - drug usage + description: Any drug used by subject and the frequency of usage; can include + multiple drugs used + pattern: '{text};{integer}/[year|month|week|day|hour]' + examples: + - value: Lipitor;2/day + comments: + - 'Expected value: drug name;frequency' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 19' + - 'This field is used uniquely in: human-associated' + range: drug_usage_enum + slot_uri: MIXS:0000894 + host_body_mass_index: + is_a: environment field + aliases: + - host body-mass index + description: Body mass index, calculated as weight/(height)squared + pattern: '{float} {unit}' + examples: + - value: 22 kilogram per square meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilogram per square meter' + - 'Occurrence: 1' + - 'Position: 20' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000317 + diet_last_six_month: + is_a: environment field + aliases: + - major diet change in last six months + description: Specification of major diet changes in the last six months, if yes + the change should be specified + pattern: '{boolean};{text}' + examples: + - value: yes;vegetarian diet + comments: + - 'Expected value: diet change;current diet' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 21' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000266 + weight_loss_3_month: + is_a: environment field + aliases: + - weight loss in last three months + description: Specification of weight loss in the last three months, if yes should + be further specified to include amount of weight loss + pattern: '{boolean};{float} {unit}' + examples: + - value: yes;5 kilogram + comments: + - 'Expected value: weight loss specification;measurement value' + - 'Preferred unit: kilogram, gram' + - 'Occurrence: 1' + - 'Position: 22' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000295 + ihmc_ethnicity: + is_a: environment field + aliases: + - IHMC ethnicity + description: Ethnicity of the subject + pattern: '{integer}|{text}' + examples: + - value: caucasian + comments: + - 'Expected value: IHMC code or free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 23' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000895 + host_occupation: + is_a: environment field + aliases: + - host occupation + description: Most frequent job performed by subject + pattern: '{integer}' + examples: + - value: veterinary + comments: + - 'Expected value: IHMC code' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 24' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000896 + pet_farm_animal: + is_a: environment field + aliases: + - presence of pets or farm animals + description: Specification of presence of pets or farm animals in the environment + of subject, if yes the animals should be specified; can include multiple animals + present + pattern: '{boolean};{text}' + examples: + - value: yes; 5 cats + comments: + - 'Expected value: presence status;type of animal or pet' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 25' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000267 + travel_out_six_month: + is_a: environment field + aliases: + - travel outside the country in last six months + description: Specification of the countries travelled in the last six months; + can include multiple travels + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: country name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 26' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000268 + twin_sibling: + is_a: environment field + aliases: + - twin sibling presence + description: Specification of twin sibling presence + pattern: '{boolean}' + examples: + - value: 'yes' + comments: + - 'Expected value: presence status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 27' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000326 + medic_hist_perform: + is_a: environment field + aliases: + - medical history performed + description: Whether full medical history was collected + pattern: '{boolean}' + examples: + - value: 'TRUE' + comments: + - 'Expected value: true or false' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 28' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000897 + study_complt_stat: + is_a: environment field + aliases: + - study completion status + description: Specification of study completion status, if no the reason should + be specified + pattern: '{boolean};[adverse event|non-compliance|lost to follow up|other-specify]' + examples: + - value: no;non-compliance + comments: + - 'Expected value: YES or NO due to (1)adverse event (2) non-compliance (3) lost + to follow up (4)other-specify' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 29' + - 'This field is used uniquely in: human-associated' + range: study_complt_stat_enum + slot_uri: MIXS:0000898 + pulmonary_disord: + is_a: environment field + aliases: + - lung/pulmonary disorder + description: History of pulmonary disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + lung disease (https://disease-ontology.org/?id=DOID:850). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 30' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000269 + nose_throat_disord: + is_a: environment field + aliases: + - lung/nose-throat disorder + description: History of nose-throat disorders; can include multiple disorders, The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory + tract disease (https://disease-ontology.org/?id=DOID:974). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 31' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000270 + blood_blood_disord: + is_a: environment field + aliases: + - blood/blood disorder + description: History of blood disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 32' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000271 + host_pulse: + is_a: environment field + aliases: + - host pulse + description: Resting pulse, measured as beats per minute + pattern: '{float} {unit}' + examples: + - value: 65 beats per minute + comments: + - 'Expected value: measurement value' + - 'Preferred unit: beats per minute' + - 'Occurrence: 1' + - 'Position: 35' + - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, + human-skin, human-vaginal' + slot_uri: MIXS:0000333 + gestation_state: + is_a: environment field + aliases: + - amniotic fluid/gestation state + description: Specification of the gestation state + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: gestation state' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 36' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000272 + maternal_health_stat: + is_a: environment field + aliases: + - amniotic fluid/maternal health status + description: Specification of the maternal health status + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: health status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 37' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000273 + foetal_health_stat: + is_a: environment field + aliases: + - amniotic fluid/foetal health status + description: Specification of foetal health status, should also include abortion + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: health status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 38' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000275 + amniotic_fluid_color: + is_a: environment field + aliases: + - amniotic fluid/color + description: Specification of the color of the amniotic fluid sample + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: color' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 39' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000276 + urogenit_tract_disor: + is_a: environment field + aliases: + - urine/urogenital tract disorder + description: 'History of urogenital tract disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + urinary system disease (https://disease-ontology.org/?id=DOID:18). ' + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 41' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000278 + urine_collect_meth: + is_a: environment field + aliases: + - urine/collection method + description: Specification of urine collection method + pattern: '[clean catch|catheter]' + examples: + - value: catheter + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 43' + - 'This field is used uniquely in: human-associated' + slot_uri: MIXS:0000899 + gastrointest_disord: + is_a: environment field + aliases: + - gastrointestinal tract disorder + description: History of gastrointestinal tract disorders; can include multiple + disorders. History of blood disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: human-gut' + slot_uri: MIXS:0000280 + liver_disord: + is_a: environment field + aliases: + - liver disorder + description: History of liver disorders; can include multiple disorders. The terms + should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + liver disease (https://disease-ontology.org/?id=DOID:409). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 2' + - 'This field is used uniquely in: human-gut' + slot_uri: MIXS:0000282 + special_diet: + is_a: environment field + aliases: + - special diet + description: Specification of special diet; can include multiple special diets + pattern: '[low carb|reduced calorie|vegetarian|other(to be specified)]' + examples: + - value: other:vegan + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 3' + - 'This field is used uniquely in: human-gut' + range: special_diet_enum + slot_uri: MIXS:0000905 + nose_mouth_teeth_throat_disord: + is_a: environment field + aliases: + - nose/mouth/teeth/throat disorder + description: History of nose/mouth/teeth/throat disorders; can include multiple + disorders. The terms should be chosen from the DO (Human Disease Ontology) at + http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), + mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), + or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: human-oral' + slot_uri: MIXS:0000283 + time_last_toothbrush: + is_a: environment field + aliases: + - time since last toothbrushing + description: Specification of the time since last toothbrushing + pattern: '{duration}' + examples: + - value: P2H45M + comments: + - 'Expected value: duration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used uniquely in: human-oral' + slot_uri: MIXS:0000924 + dermatology_disord: + is_a: environment field + aliases: + - dermatology disorder + description: History of dermatology disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + skin disease (https://disease-ontology.org/?id=DOID:37). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: human-skin' + slot_uri: MIXS:0000284 + time_since_last_wash: + is_a: environment field + aliases: + - time since last wash + description: Specification of the time since last wash + pattern: '{duration}' + examples: + - value: P1D + comments: + - 'Expected value: duration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used uniquely in: human-skin' + slot_uri: MIXS:0000943 + dominant_hand: + is_a: environment field + aliases: + - dominant hand + description: Dominant hand of the subject + pattern: '[left|right|ambidextrous]' + examples: + - value: right + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used uniquely in: human-skin' + range: dominant_hand_enum + slot_uri: MIXS:0000944 + menarche: + is_a: environment field + aliases: + - menarche + description: Date of most recent menstruation + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000965 + sexual_act: + is_a: environment field + aliases: + - sexual activity + description: Current sexual partner and frequency of sex + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: partner sex;frequency' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000285 + pregnancy: + is_a: environment field + aliases: + - pregnancy + description: Date due of pregnancy + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000966 + douche: + is_a: environment field + aliases: + - douche + description: Date of most recent douche + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 4' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000967 + birth_control: + is_a: environment field + aliases: + - birth control + description: Specification of birth control medication used + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: medication name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 5' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000286 + menopause: + is_a: environment field + aliases: + - menopause + description: Date of onset of menopause + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 6' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000968 + hrt: + is_a: environment field + aliases: + - HRT + description: Whether subject had hormone replacement theraphy, and if yes start + date + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 7' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000969 + hysterectomy: + is_a: environment field + aliases: + - hysterectomy + description: Specification of whether hysterectomy was performed + pattern: '{boolean}' + examples: + - value: 'no' + comments: + - 'Expected value: hysterectomy status' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 8' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000287 + gynecologic_disord: + is_a: environment field + aliases: + - gynecological disorder + description: History of gynecological disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: gynecological disorder' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 9' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000288 + urogenit_disord: + is_a: environment field + aliases: + - urogenital disorder + description: 'History of urogenital disorders, can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary + system disease (https://disease-ontology.org/?id=DOID:18). ' + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: disorder name' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 10' + - 'This field is used uniquely in: human-vaginal' + slot_uri: MIXS:0000289 + hcr: + is_a: environment field + aliases: + - hydrocarbon resource type + description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR + defined as a natural environmental feature containing large amounts of hydrocarbons + at high concentrations potentially suitable for commercial exploitation. This + term should not be confused with the Hydrocarbon Occurrence term which also + includes hydrocarbon-rich environments with currently limited commercial interest + such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose + entry in "additional info" field + pattern: '[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight + Gas Reservoir|other]' + examples: + - value: Oil Sand + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: hcr_enum + slot_uri: MIXS:0000988 + hc_produced: + is_a: environment field + aliases: + - hydrocarbon type produced + description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, + etc). If "other" is specified, please propose entry in "additional info" field + pattern: '[Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other]' + examples: + - value: Gas + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: hc_produced_enum + slot_uri: MIXS:0000989 + basin: + is_a: environment field + aliases: + - basin name + description: Name of the basin (e.g. Campos) + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000290 + field: + is_a: environment field + aliases: + - field name + description: Name of the hydrocarbon field (e.g. Albacora) + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 4' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000291 + reservoir: + is_a: environment field + aliases: + - reservoir name + description: Name of the reservoir (e.g. Carapebus) + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 5' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000303 + hcr_temp: + is_a: environment field + aliases: + - hydrocarbon resource original temperature + description: Original temperature of the hydrocarbon resource + pattern: '{float} - {float} {unit}' + examples: + - value: 150-295 degree Celsius + comments: + - 'Expected value: measurement value range' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 6' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000393 + tvdss_of_hcr_temp: + is_a: environment field + aliases: + - depth (TVDSS) of hydrocarbon resource temperature + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where + the original temperature was measured (e.g. 1345 m) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 7' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000394 + hcr_pressure: + is_a: environment field + aliases: + - hydrocarbon resource original pressure + description: Original pressure of the hydrocarbon resource + pattern: '{float} - {float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value range' + - 'Preferred unit: atmosphere, kilopascal' + - 'Occurrence: 1' + - 'Position: 8' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000395 + tvdss_of_hcr_pressure: + is_a: environment field + aliases: + - depth (TVDSS) of hydrocarbon resource pressure + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where + the original pressure was measured (e.g. 1578 m ) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 9' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000397 + permeability: + is_a: environment field + aliases: + - permeability + description: 'Measure of the ability of a hydrocarbon resource to allow fluids + to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' + pattern: '{integer} - {integer} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value range' + - 'Preferred unit: mD' + - 'Occurrence: 1' + - 'Position: 10' + - 'This field is used uniquely in: hydrocarbon resources-cores' + slot_uri: MIXS:0000404 + porosity: + is_a: environment field + aliases: + - porosity + description: Porosity of deposited sediment is volume of voids divided by the + total volume of sample + pattern: '{float} - {float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value or range' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 11' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, sediment' + slot_uri: MIXS:0000211 + lithology: + is_a: environment field + aliases: + - lithology + description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). + If "other" is specified, please propose entry in "additional info" field' + pattern: '[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]' + examples: + - value: Volcanic + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 12' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: lithology_enum + slot_uri: MIXS:0000990 + depos_env: + is_a: environment field + aliases: + - depositional environment + description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). + If "other" is specified, please propose entry in "additional info" field + pattern: '[Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|Continental + - Lacustrine|Transitional - Deltaic|Transitional - Tidal|Transitional - Lagoonal|Transitional + - Beach|Transitional - Lake|Marine - Shallow|Marine - Deep|Marine - Reef|Other + - Evaporite|Other - Glacial|Other - Volcanic|other]' + examples: + - value: Continental - Alluvial + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 13' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: depos_env_enum + slot_uri: MIXS:0000992 + hcr_geol_age: + is_a: environment field + aliases: + - hydrocarbon resource geological age + description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). + If "other" is specified, please propose entry in "additional info" field' + pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' + examples: + - value: Silurian + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 14' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: hcr_geol_age_enum + slot_uri: MIXS:0000993 + owc_tvdss: + is_a: environment field + aliases: + - oil water contact depth + description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 15' + - 'This field is used uniquely in: hydrocarbon resources-cores' + slot_uri: MIXS:0000405 + hcr_fw_salinity: + is_a: environment field + aliases: + - formation water salinity + description: Original formation water salinity (prior to secondary recovery e.g. + Waterflooding) expressed as TDS + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 16' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000406 + sulfate_fw: + is_a: environment field + aliases: + - sulfate in formation water + description: Original sulfate concentration in the hydrocarbon resource + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 17' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000407 + vfa_fw: + is_a: environment field + aliases: + - vfa in formation water + description: Original volatile fatty acid concentration in the hydrocarbon resource + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 18' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000408 + sr_kerog_type: + is_a: environment field + aliases: + - source rock kerogen type + description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic + and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ + fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris + (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). + If "other" is specified, please propose entry in "additional info" field' + pattern: '[Type I|Type II|Type III|Type IV|other]' + examples: + - value: Type IV + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 19' + - 'This field is used uniquely in: hydrocarbon resources-cores' + range: sr_kerog_type_enum + slot_uri: MIXS:0000994 + sr_lithology: + is_a: environment field + aliases: + - source rock lithology + description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). + If "other" is specified, please propose entry in "additional info" field + pattern: '[Clastic|Carbonate|Coal|Biosilicieous|other]' + examples: + - value: Coal + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 20' + - 'This field is used uniquely in: hydrocarbon resources-cores' + range: sr_lithology_enum + slot_uri: MIXS:0000995 + sr_dep_env: + is_a: environment field + aliases: + - source rock depositional environment + description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). + If "other" is specified, please propose entry in "additional info" field + pattern: '[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]' + examples: + - value: Marine + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 21' + - 'This field is used uniquely in: hydrocarbon resources-cores' + range: sr_dep_env_enum + slot_uri: MIXS:0000996 + sr_geol_age: + is_a: environment field + aliases: + - source rock geological age + description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). + If "other" is specified, please propose entry in "additional info" field' + pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' + examples: + - value: Silurian + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 22' + - 'This field is used uniquely in: hydrocarbon resources-cores' + range: sr_geol_age_enum + slot_uri: MIXS:0000997 + samp_well_name: + is_a: environment field + aliases: + - sample well name + description: Name of the well (e.g. BXA1123) where sample was taken + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 35' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000296 + win: + is_a: environment field + aliases: + - well identification number + description: 'A unique identifier of a well or wellbore. This is part of the Global + Framework for Well Identification initiative which is compiled by the Professional + Petroleum Data Management Association (PPDM) in an effort to improve well identification + systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 36' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000297 + samp_type: + is_a: environment field + aliases: + - sample type + description: Type of material (i.e. sample) collected. Includes types like core, + rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid + deposit, produced fluid, produced water, injected water, swabs, etc. If "other" + is specified, please propose entry in "additional info" field + pattern: '[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid + deposit|produced fluid|produced water|injected water|water from treatment plant|fresh + water|sea water|drilling fluid|procedural blank|positive control|negative control|other]' + examples: + - value: solid deposit + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 37' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: samp_type_enum + slot_uri: MIXS:0000998 + samp_subtype: + is_a: environment field + aliases: + - sample subtype + description: Name of sample sub-type. For example if "sample type" is "Produced + Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, + please propose entry in "additional info" field + pattern: '[oil phase|water phase|biofilm|not applicable|other]' + examples: + - value: biofilm + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 38' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + range: samp_subtype_enum + slot_uri: MIXS:0000999 + pressure: + is_a: environment field + aliases: + - pressure + description: Pressure to which the sample is subject to, in atmospheres + pattern: '{float} {unit}' + examples: + - value: 50 atmosphere + comments: + - 'Expected value: measurement value' + - 'Preferred unit: atmosphere' + - 'Occurrence: 1' + - 'Position: 41' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000412 + samp_tvdss: + is_a: environment field + aliases: + - sample true vertical depth subsea + description: Depth of the sample i.e. The vertical distance between the sea level + and the sampled position in the subsurface. Depth can be reported as an interval + for subsurface samples e.g. 1325.75-1362.25 m + pattern: '{float}-{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value or measurement value range' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 42' + - 'This field is used uniquely in: hydrocarbon resources-cores' + slot_uri: MIXS:0000409 + samp_md: + is_a: environment field + aliases: + - sample measured depth + description: In non deviated well, measured depth is equal to the true vertical + depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated + wells, the MD is the length of trajectory of the borehole measured from the + same reference or datum. Common datums used are ground level (GL), drilling + rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). + If "other" is specified, please propose entry in "additional info" field + pattern: '{float} {unit};[GL|DF|RT|KB|MSL|other]' + examples: + - value: 1534 meter;MSL + comments: + - 'Expected value: measurement value;enumeration' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 43' + - 'This field is used uniquely in: hydrocarbon resources-cores' + range: samp_md_enum + slot_uri: MIXS:0000413 + samp_transport_cond: + is_a: environment field + aliases: + - sample transport conditions + description: "Sample transport duration (in days or hrs) and temperature the sample\ + \ was exposed to (e.g. 5.5 days; 20 \xAC\u221EC)" + pattern: '{float} {unit};{float} {unit}' + examples: + - value: 5 days;-20 degree Celsius + comments: + - 'Expected value: measurement value;measurement value' + - 'Preferred unit: days;degree Celsius' + - 'Occurrence: 1' + - 'Position: 47' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000410 + organism_count_qpcr_info: + is_a: environment field + aliases: + - organism count qPCR information + description: 'If qpcr was used for the cell count, the target gene name, the primer + sequence and the cycling conditions should also be provided. (Example: 16S rrna; + FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; + annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; + 30 cycles)' + pattern: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes; total cycles' + examples: + - value: '' + comments: + - 'Expected value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial + denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes; total cycles' + - 'Preferred unit: number of cells per gram (or ml or cm^2)' + - 'Occurrence: 1' + - 'Position: 53' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000099 + ph: + is_a: environment field + aliases: + - pH + description: Ph measurement of the sample, or liquid portion of sample, or aqueous + phase of the fluid + pattern: '{float}' + examples: + - value: '7.2' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 54' + - 'This field is used in: 8 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, soil, wastewater_sludge, water' + slot_uri: MIXS:0001001 + alkalinity: + is_a: environment field + aliases: + - alkalinity + description: Alkalinity, the ability of a solution to neutralize acids to the + equivalence point of carbonate or bicarbonate + pattern: '{float} {unit}' + examples: + - value: 50 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milliequivalent per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 56' + - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000421 + alkalinity_method: + is_a: environment field + aliases: + - alkalinity method + description: Method used for alkalinity measurement + pattern: '{text}' + examples: + - value: titration + comments: + - 'Expected value: description of method' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 57' + - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, water' + slot_uri: MIXS:0000298 + sulfate: + is_a: environment field + aliases: + - sulfate + description: Concentration of sulfate in the sample + pattern: '{float} {unit}' + examples: + - value: 5 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 58' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000423 + sulfide: + is_a: environment field + aliases: + - sulfide + description: Concentration of sulfide in the sample + pattern: '{float} {unit}' + examples: + - value: 2 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 59' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000424 + tot_sulfur: + is_a: environment field + aliases: + - total sulfur + description: Concentration of total sulfur in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 60' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000419 + nitrate: + is_a: environment field + aliases: + - nitrate + description: Concentration of nitrate in the sample + pattern: '{float} {unit}' + examples: + - value: 65 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 61' + - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000425 + nitrite: + is_a: environment field + aliases: + - nitrite + description: Concentration of nitrite in the sample + pattern: '{float} {unit}' + examples: + - value: 0.5 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 62' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000426 + ammonium: + is_a: environment field + aliases: + - ammonium + description: Concentration of ammonium in the sample + pattern: '{float} {unit}' + examples: + - value: 1.5 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 63' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000427 + tot_nitro: + is_a: environment field + aliases: + - total nitrogen concentration + description: 'Total nitrogen concentration of water samples, calculated by: total + nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured + without filtering, reported as nitrogen' + pattern: '{float} {unit}' + examples: + - value: 50 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 64' + - 'This field is used in: 4 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, wastewater_sludge, water' + slot_uri: MIXS:0000102 + diss_iron: + is_a: environment field + aliases: + - dissolved iron + description: Concentration of dissolved iron in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 65' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000139 + sodium: + is_a: environment field + aliases: + - sodium + description: Sodium concentration in the sample + pattern: '{float} {unit}' + examples: + - value: 10.5 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 66' + - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000428 + chloride: + is_a: environment field + aliases: + - chloride + description: Concentration of chloride in the sample + pattern: '{float} {unit}' + examples: + - value: 5000 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 67' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000429 + potassium: + is_a: environment field + aliases: + - potassium + description: Concentration of potassium in the sample + pattern: '{float} {unit}' + examples: + - value: 463 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 68' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000430 + magnesium: + is_a: environment field + aliases: + - magnesium + description: Concentration of magnesium in the sample + pattern: '{float} {unit}' + examples: + - value: 52.8 micromole per kilogram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: mole per liter, milligram per liter, parts per million, micromole + per kilogram' + - 'Occurrence: 1' + - 'Position: 69' + - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000431 + calcium: + is_a: environment field + aliases: + - calcium + description: Concentration of calcium in the sample + pattern: '{float} {unit}' + examples: + - value: 0.2 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, micromole per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 70' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000432 + tot_iron: + is_a: environment field + aliases: + - total iron + description: Concentration of total iron in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, milligram per kilogram' + - 'Occurrence: 1' + - 'Position: 71' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000105 + diss_org_carb: + is_a: environment field + aliases: + - dissolved organic carbon + description: Concentration of dissolved organic carbon in the sample, liquid portion + of the sample, or aqueous phase of the fluid + pattern: '{float} {unit}' + examples: + - value: 197 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 72' + - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000433 + diss_inorg_carb: + is_a: environment field + aliases: + - dissolved inorganic carbon + description: Dissolved inorganic carbon concentration in the sample, typically + measured after filtering the sample using a 0.45 micrometer filter + pattern: '{float} {unit}' + examples: + - value: 2059 micromole per kilogram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 73' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000434 + diss_inorg_phosp: + is_a: environment field + aliases: + - dissolved inorganic phosphorus + description: Concentration of dissolved inorganic phosphorus in the sample + pattern: '{float} {unit}' + examples: + - value: 56.5 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 74' + - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, water' + slot_uri: MIXS:0000106 + tot_phosp: + is_a: environment field + aliases: + - total phosphorus + description: 'Total phosphorus concentration in the sample, calculated by: total + phosphorus = total dissolved phosphorus + particulate phosphorus' + pattern: '{float} {unit}' + examples: + - value: 0.03 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 75' + - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, water' + slot_uri: MIXS:0000117 + suspend_solids: + is_a: environment field + aliases: + - suspended solids + description: Concentration of substances including a wide variety of material, + such as silt, decaying plant and animal matter; can include multiple substances + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: suspended solid name;measurement value' + - 'Preferred unit: gram, microgram, milligram per liter, mole per liter, gram + per liter, part per million' + - 'Occurrence: m' + - 'Position: 76' + - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, wastewater_sludge' + slot_uri: MIXS:0000150 + density: + is_a: environment field + aliases: + - density + description: Density of the sample, which is its mass per unit volume (aka volumetric + mass density) + pattern: '{float} {unit}' + examples: + - value: 1000 kilogram per cubic meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram per cubic meter, gram per cubic centimeter' + - 'Occurrence: 1' + - 'Position: 77' + - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, miscellaneous natural or artificial environment, sediment, + water' + slot_uri: MIXS:0000435 + diss_carb_dioxide: + is_a: environment field + aliases: + - dissolved carbon dioxide + description: Concentration of dissolved carbon dioxide in the sample or liquid + portion of the sample + pattern: '{float} {unit}' + examples: + - value: 5 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 78' + - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial + environment, sediment, water' + slot_uri: MIXS:0000436 + diss_oxygen_fluid: + is_a: environment field + aliases: + - dissolved oxygen in fluids + description: Concentration of dissolved oxygen in the oil field produced fluids + as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per kilogram, milligram per liter' + - 'Occurrence: 1' + - 'Position: 79' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000438 + vfa: + is_a: environment field + aliases: + - volatile fatty acids + description: Concentration of Volatile Fatty Acids in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 80' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000152 + benzene: + is_a: environment field + aliases: + - benzene + description: Concentration of benzene in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 81' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000153 + toluene: + is_a: environment field + aliases: + - toluene + description: Concentration of toluene in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 82' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000154 + ethylbenzene: + is_a: environment field + aliases: + - ethylbenzene + description: Concentration of ethylbenzene in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 83' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000155 + xylene: + is_a: environment field + aliases: + - xylene + description: Concentration of xylene in the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 84' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000156 + api: + is_a: environment field + aliases: + - API gravity + description: "API gravity is a measure of how heavy or light a petroleum liquid\ + \ is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\ + \ 31.1\xAC\u221E API)" + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degrees API' + - 'Occurrence: 1' + - 'Position: 85' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000157 + tan: + is_a: environment field + aliases: + - total acid number + description: "Total Acid Number\xAC\u2020(TAN) is a measurement of acidity that\ + \ is determined by the amount of\xAC\u2020potassium hydroxide\xAC\u2020in milligrams\ + \ that is needed to neutralize the acids in one gram of oil.\xAC\u2020It is\ + \ an important quality measurement of\xAC\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 86' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000120 + viscosity: + is_a: environment field + aliases: + - viscosity + description: "A measure of oil's resistance\xAC\u2020to gradual deformation by\xAC\ + \u2020shear stress\xAC\u2020or\xAC\u2020tensile stress (e.g. 3.5 cp; 100 \xAC\ + \u221EC)" + pattern: '{float} {unit};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value;measurement value' + - 'Preferred unit: cP at degree Celsius' + - 'Occurrence: 1' + - 'Position: 87' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000126 + pour_point: + is_a: environment field + aliases: + - pour point + description: "Temperature at which a liquid becomes semi solid and loses its flow\ + \ characteristics. In crude oil a high\xAC\u2020pour point\xAC\u2020is generally\ + \ associated with a high paraffin content, typically found in crude deriving\ + \ from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 88' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000127 + saturates_pc: + is_a: environment field + aliases: + - saturates wt% + description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ + \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ + \ polarizability and polarity. There are three main methods to obtain SARA results.\ + \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ + \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: name;measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 89' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000131 + aromatics_pc: + is_a: environment field + aliases: + - aromatics wt% + description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ + \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ + \ polarizability and polarity. There are three main methods to obtain SARA results.\ + \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ + \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: name;measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 90' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000133 + resins_pc: + is_a: environment field + aliases: + - resins wt% + description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ + \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ + \ polarizability and polarity. There are three main methods to obtain SARA results.\ + \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ + \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: name;measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 91' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000134 + asphaltenes_pc: + is_a: environment field + aliases: + - asphaltenes wt% + description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ + \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ + \ polarizability and polarity. There are three main methods to obtain SARA results.\ + \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ + \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: name;measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 92' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000135 + additional_info: + is_a: environment field + aliases: + - additional info + description: Information that doesn't fit anywhere else. Can also be used to propose + new entries for fields with controlled vocabulary + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 94' + - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon + resources-fluids_swabs' + slot_uri: MIXS:0000300 + prod_start_date: + is_a: environment field + aliases: + - production start date + description: Date of field's first production + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 23' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0001008 + prod_rate: + is_a: environment field + aliases: + - production rate + description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: cubic meter per day' + - 'Occurrence: 1' + - 'Position: 24' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000452 + water_production_rate: + is_a: environment field + aliases: + - water production rate + description: Water production rates per well (e.g. 987 m3 / day) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: cubic meter per day' + - 'Occurrence: 1' + - 'Position: 25' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000453 + water_cut: + is_a: environment field + aliases: + - water cut + description: Current amount of water (%) in a produced fluid stream; or the average + of the combined streams + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 26' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000454 + iwf: + is_a: environment field + aliases: + - injection water fraction + description: Proportion of the produced fluids derived from injected water at + the time of sampling. (e.g. 87%) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percent' + - 'Occurrence: 1' + - 'Position: 27' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000455 + add_recov_method: + is_a: environment field + aliases: + - secondary and tertiary recovery methods and start date + description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed + for increase of hydrocarbon recovery from resource and start date for each one + of them. If "other" is specified, please propose entry in "additional info" + field + pattern: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer + Addition|Surfactant Addition|Not Applicable|other];{timestamp}' + examples: + - value: Polymer Addition;2018-06-21T14:30Z + comments: + - 'Expected value: enumeration;timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 28' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + range: add_recov_method_enum + slot_uri: MIXS:0001009 + iw_bt_date_well: + is_a: environment field + aliases: + - injection water breakthrough date of specific well + description: Injection water breakthrough date per well following a secondary + and/or tertiary recovery + pattern: '{timestamp}' + examples: + - value: '2018-05-11' + comments: + - 'Expected value: timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 29' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0001010 + biocide: + is_a: environment field + aliases: + - biocide administration + description: List of biocides (commercial name of product and supplier) and date + of administration + pattern: '{text};{text};{timestamp}' + examples: + - value: ALPHA 1427;Baker Hughes;2008-01-23 + comments: + - 'Expected value: name;name;timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 30' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0001011 + biocide_admin_method: + is_a: environment field + aliases: + - biocide administration method + description: Method of biocide administration (dose, frequency, duration, time + elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 + days) + pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' + examples: + - value: '' + comments: + - 'Expected value: measurement value;frequency;duration;duration' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 31' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000456 + chem_treatment: + is_a: environment field + aliases: + - chemical treatment + description: List of chemical compounds administered upstream the sampling location + where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, + demulsifiers, and other production chemicals etc.). The commercial name of the + product and name of the supplier should be provided. The date of administration + should also be included + pattern: '{text};{text};{timestamp}' + examples: + - value: ACCENT 1125;DOW;2010-11-17 + comments: + - 'Expected value: name;name;timestamp' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 32' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0001012 + chem_treatment_method: + is_a: environment field + aliases: + - chemical treatment method + description: Method of chemical administration(dose, frequency, duration, time + elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 + hr; 0 days) + pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' + examples: + - value: '' + comments: + - 'Expected value: measurement value;frequency;duration;duration' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 33' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000457 + samp_loc_corr_rate: + is_a: environment field + aliases: + - corrosion rate at sample location + description: Metal corrosion rate is the speed of metal deterioration due to environmental + conditions. As environmental conditions change corrosion rates change accordingly. + Therefore, long term corrosion rates are generally more informative than short + term rates and for that reason they are preferred during reporting. In the case + of suspected MIC, corrosion rate measurements at the time of sampling might + provide insights into the involvement of certain microbial community members + in MIC as well as potential microbial interplays + pattern: '{float} - {float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value range' + - 'Preferred unit: millimeter per year' + - 'Occurrence: 1' + - 'Position: 34' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000136 + samp_collection_point: + is_a: environment field + aliases: + - sample collection point + description: Sampling point on the asset were sample was collected (e.g. Wellhead, + storage tank, separator, etc). If "other" is specified, please propose entry + in "additional info" field + pattern: '[well|test well|drilling rig|wellhead|separator|storage tank|other]' + examples: + - value: well + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 39' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + range: samp_collection_point_enum + slot_uri: MIXS:0001015 + samp_preserv: + is_a: environment field + aliases: + - preservative added to sample + description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, + etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: name;measurement value' + - 'Preferred unit: milliliter' + - 'Occurrence: 1' + - 'Position: 46' + - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + slot_uri: MIXS:0000463 + alkyl_diethers: + is_a: environment field + aliases: + - alkyl diethers + description: Concentration of alkyl diethers + pattern: '{float} {unit}' + examples: + - value: 0.005 mole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: mole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000490 + aminopept_act: + is_a: environment field + aliases: + - aminopeptidase activity + description: Measurement of aminopeptidase activity + pattern: '{float} {unit}' + examples: + - value: 0.269 mole per liter per hour + comments: + - 'Expected value: measurement value' + - 'Preferred unit: mole per liter per hour' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000172 + bacteria_carb_prod: + is_a: environment field + aliases: + - bacterial carbon production + description: Measurement of bacterial carbon production + pattern: '{float} {unit}' + examples: + - value: 2.53 microgram per liter per hour + comments: + - 'Expected value: measurement value' + - 'Preferred unit: nanogram per hour' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000173 + biomass: + is_a: environment field + aliases: + - biomass + description: Amount of biomass; should include the name for the part of biomass + measured, e.g. Microbial, total. Can include multiple measurements + pattern: '{text};{float} {unit}' + examples: + - value: total;20 gram + comments: + - 'Expected value: biomass type;measurement value' + - 'Preferred unit: ton, kilogram, gram' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000174 + bishomohopanol: + is_a: environment field + aliases: + - bishomohopanol + description: Concentration of bishomohopanol + pattern: '{float} {unit}' + examples: + - value: 14 microgram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, microgram per gram' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000175 + bromide: + is_a: environment field + aliases: + - bromide + description: Concentration of bromide + pattern: '{float} {unit}' + examples: + - value: 0.05 parts per million + comments: + - 'Expected value: measurement value' + - 'Preferred unit: parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000176 + carb_nitro_ratio: + is_a: environment field + aliases: + - carbon/nitrogen ratio + description: Ratio of amount or concentrations of carbon to nitrogen + pattern: '{float} {unit}' + examples: + - value: '0.417361111' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000310 + chlorophyll: + is_a: environment field + aliases: + - chlorophyll + description: Concentration of chlorophyll + pattern: '{float} {unit}' + examples: + - value: 5 milligram per cubic meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per cubic meter, microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000177 + diether_lipids: + is_a: environment field + aliases: + - diether lipids + description: Concentration of diether lipids; can include multiple types of diether + lipids + pattern: '{text};{float} {unit}' + examples: + - value: 0.2 nanogram per liter + comments: + - 'Expected value: diether lipid name;measurement value' + - 'Preferred unit: nanogram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000178 + diss_hydrogen: + is_a: environment field + aliases: + - dissolved hydrogen + description: Concentration of dissolved hydrogen + pattern: '{float} {unit}' + examples: + - value: 0.3 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000179 + diss_org_nitro: + is_a: environment field + aliases: + - dissolved organic nitrogen + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 + pattern: '{float} {unit}' + examples: + - value: 0.05 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000162 + diss_oxygen: + is_a: environment field + aliases: + - dissolved oxygen + description: Concentration of dissolved oxygen + pattern: '{float} {unit}' + examples: + - value: 175 micromole per kilogram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per kilogram, milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000119 + glucosidase_act: + is_a: environment field + aliases: + - glucosidase activity + description: Measurement of glucosidase activity + pattern: '{float} {unit}' + examples: + - value: 5 mol per liter per hour + comments: + - 'Expected value: measurement value' + - 'Preferred unit: mol per liter per hour' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000137 + mean_frict_vel: + is_a: environment field + aliases: + - mean friction velocity + description: Measurement of mean friction velocity + pattern: '{float} {unit}' + examples: + - value: 0.5 meter per second + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter per second' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000498 + mean_peak_frict_vel: + is_a: environment field + aliases: + - mean peak friction velocity + description: Measurement of mean peak friction velocity + pattern: '{float} {unit}' + examples: + - value: 1 meter per second + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter per second' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000502 + n_alkanes: + is_a: environment field + aliases: + - n-alkanes + description: Concentration of n-alkanes; can include multiple n-alkanes + pattern: '{text};{float} {unit}' + examples: + - value: n-hexadecane;100 milligram per liter + comments: + - 'Expected value: n-alkane name;measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000503 + nitro: + is_a: environment field + aliases: + - nitrogen + description: Concentration of nitrogen (total) + pattern: '{float} {unit}' + examples: + - value: 4.2 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000504 + org_carb: + is_a: environment field + aliases: + - organic carbon + description: Concentration of organic carbon + pattern: '{float} {unit}' + examples: + - value: 1.5 microgram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000508 + org_matter: + is_a: environment field + aliases: + - organic matter + description: Concentration of organic matter + pattern: '{float} {unit}' + examples: + - value: 1.75 milligram per cubic meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000204 + org_nitro: + is_a: environment field + aliases: + - organic nitrogen + description: Concentration of organic nitrogen + pattern: '{float} {unit}' + examples: + - value: 4 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000205 + part_org_carb: + is_a: environment field + aliases: + - particulate organic carbon + description: Concentration of particulate organic carbon + pattern: '{float} {unit}' + examples: + - value: 1.92 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000515 + petroleum_hydrocarb: + is_a: environment field + aliases: + - petroleum hydrocarbon + description: Concentration of petroleum hydrocarbon + pattern: '{float} {unit}' + examples: + - value: 0.05 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000516 + phaeopigments: + is_a: environment field + aliases: + - phaeopigments + description: Concentration of phaeopigments; can include multiple phaeopigments + pattern: '{text};{float} {unit}' + examples: + - value: 2.5 milligram per cubic meter + comments: + - 'Expected value: phaeopigment name;measurement value' + - 'Preferred unit: milligram per cubic meter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000180 + phosphate: + is_a: environment field + aliases: + - phosphate + description: Concentration of phosphate + pattern: '{float} {unit}' + examples: + - value: 0.7 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 5 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, wastewater_sludge, water' + slot_uri: MIXS:0000505 + phosplipid_fatt_acid: + is_a: environment field + aliases: + - phospholipid fatty acid + description: Concentration of phospholipid fatty acids; can include multiple values + pattern: '{text};{float} {unit}' + examples: + - value: 2.98 milligram per liter + comments: + - 'Expected value: phospholipid fatty acid name;measurement value' + - 'Preferred unit: mole per gram, mole per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000181 + redox_potential: + is_a: environment field + aliases: + - redox potential + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential + pattern: '{float} {unit}' + examples: + - value: 300 millivolt + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millivolt' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000182 + salinity: + is_a: environment field + aliases: + - salinity + description: Salinity is the total concentration of all dissolved salts in a water + sample. While salinity can be measured by a complete chemical analysis, this + method is difficult and time consuming. More often, it is instead derived from + the conductivity measurement. This is known as practical salinity. These derivations + compare the specific conductance of the sample to a salinity standard such as + seawater + pattern: '{float} {unit}' + examples: + - value: 25 practical salinity unit + comments: + - 'Expected value: measurement value' + - 'Preferred unit: practical salinity unit, percentage' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000183 + silicate: + is_a: environment field + aliases: + - silicate + description: Concentration of silicate + pattern: '{float} {unit}' + examples: + - value: 0.05 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural + or artificial environment, sediment, water' + slot_uri: MIXS:0000184 + tot_carb: + is_a: environment field + aliases: + - total carbon + description: Total carbon content + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: microbial mat_biofilm, sediment' + slot_uri: MIXS:0000525 + tot_nitro_content: + is_a: environment field + aliases: + - total nitrogen content + description: Total nitrogen content of the sample + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter, milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' + slot_uri: MIXS:0000530 + tot_org_carb: + is_a: environment field + aliases: + - total organic carbon + description: 'Definition for soil: total organic carbon content of the soil, definition + otherwise: total organic carbon content' + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram Carbon per kilogram sample material' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' + slot_uri: MIXS:0000533 + turbidity: + is_a: environment field + aliases: + - turbidity + description: Measure of the amount of cloudiness or haziness in water caused by + individual particles + pattern: '{float} {unit}' + examples: + - value: 0.3 nephelometric turbidity units + comments: + - 'Expected value: measurement value' + - 'Preferred unit: formazin turbidity unit, formazin nephelometric units' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + slot_uri: MIXS:0000191 + water_content: + is_a: environment field + aliases: + - water content + description: Water content measurement + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: gram per gram or cubic centimeter per cubic centimeter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' + slot_uri: MIXS:0000185 + water_current: + is_a: environment field + aliases: + - water current + description: Measurement of magnitude and direction of flow within a fluid + pattern: '{float} {unit}' + examples: + - value: 10 cubic meter per second + comments: + - 'Expected value: measurement value' + - 'Preferred unit: cubic meter per second, knots' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: miscellaneous natural or artificial environment, + water' + slot_uri: MIXS:0000203 + air_temp_regm: + is_a: environment field + aliases: + - air temperature regimen + description: Information about treatment involving an exposure to varying temperatures; + should include the temperature, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include different temperature regimens + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: temperature value;treatment interval and duration' + - 'Preferred unit: degree Celsius' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000551 + antibiotic_regm: + is_a: environment field + aliases: + - antibiotic regimen + description: Information about treatment involving antibiotic administration; + should include the name of antibiotic, amount administered, treatment regimen + including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + antibiotic regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: antibiotic name;antibiotic amount;treatment interval and duration' + - 'Preferred unit: milligram' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000553 + biotic_regm: + is_a: environment field + aliases: + - biotic regimen + description: Information about treatment(s) involving use of biotic factors, such + as bacteria, viruses or fungi. + pattern: '{text}' + examples: + - value: sample inoculated with Rhizobium spp. Culture + comments: + - 'Expected value: free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001038 + chem_mutagen: + is_a: environment field + aliases: + - chemical mutagen + description: Treatment involving use of mutagens; should include the name of mutagen, + amount administered, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple mutagen regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: mutagen name;mutagen amount;treatment interval and duration' + - 'Preferred unit: milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000555 + climate_environment: + is_a: environment field + aliases: + - climate environment + description: Treatment involving an exposure to a particular climate; treatment + regimen including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + climates + pattern: '{text};{Rn/start_time/end_time/duration}' + examples: + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: climate name;treatment interval and duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001040 + cult_root_med: + is_a: environment field + aliases: + - culture rooting medium + description: Name or reference for the hydroponic or in vitro culture rooting + medium; can be the name of a commonly used medium or reference to a specific + medium, e.g. Murashige and Skoog medium. If the medium has not been formally + published, use the rooting medium descriptors. + pattern: '{text}|{PMID}|{DOI}|{URL}' + examples: + - value: http://himedialabs.com/TD/PT158.pdf + comments: + - 'Expected value: name, PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001041 + fertilizer_regm: + is_a: environment field + aliases: + - fertilizer regimen + description: Information about treatment involving the use of fertilizers; should + include the name of fertilizer, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple fertilizer + regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: fertilizer name;fertilizer amount;treatment interval and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000556 + fungicide_regm: + is_a: environment field + aliases: + - fungicide regimen + description: Information about treatment involving use of fungicides; should include + the name of fungicide, amount administered, treatment regimen including how + many times the treatment was repeated, how long each treatment lasted, and the + start and end time of the entire treatment; can include multiple fungicide regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: fungicide name;fungicide amount;treatment interval and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000557 + gaseous_environment: + is_a: environment field + aliases: + - gaseous environment + description: Use of conditions with differing gaseous environments; should include + the name of gaseous compound, amount administered, treatment duration, interval + and total experimental duration; can include multiple gaseous environment regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: gaseous compound name;gaseous compound amount;treatment interval + and duration' + - 'Preferred unit: micromole per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000558 + gravity: + is_a: environment field + aliases: + - gravity + description: Information about treatment involving use of gravity factor to study + various types of responses in presence, absence or modified levels of gravity; + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple treatments + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: gravity factor value;treatment interval and duration' + - 'Preferred unit: meter per square second, g' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000559 + growth_facil: + is_a: environment field + aliases: + - growth facility + description: 'Type of facility where the sampled plant was grown; controlled vocabulary: + growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively + use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' + pattern: '{text}|{termLabel} {[termID]}' + examples: + - value: Growth chamber [CO_715:0000189] + comments: + - 'Expected value: free text or CO' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001043 + growth_habit: + is_a: environment field + aliases: + - growth habit + description: Characteristic shape, appearance or growth form of a plant species + pattern: '[erect|semi-erect|spreading|prostrate]' + examples: + - value: spreading + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + range: growth_habit_enum + slot_uri: MIXS:0001044 + growth_hormone_regm: + is_a: environment field + aliases: + - growth hormone regimen + description: Information about treatment involving use of growth hormones; should + include the name of growth hormone, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple growth + hormone regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: growth hormone name;growth hormone amount;treatment interval + and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000560 + herbicide_regm: + is_a: environment field + aliases: + - herbicide regimen + description: Information about treatment involving use of herbicides; information + about treatment involving use of growth hormones; should include the name of + herbicide, amount administered, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include multiple regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: herbicide name;herbicide amount;treatment interval and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000561 + host_wet_mass: + is_a: environment field + aliases: + - host wet mass + description: Measurement of wet mass + pattern: '{float} {unit}' + examples: + - value: 1500 gram + comments: + - 'Expected value: measurement value' + - 'Preferred unit: kilogram, gram' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000567 + humidity_regm: + is_a: environment field + aliases: + - humidity regimen + description: Information about treatment involving an exposure to varying degree + of humidity; information about treatment involving use of growth hormones; should + include amount of humidity administered, treatment regimen including how many + times the treatment was repeated, how long each treatment lasted, and the start + and end time of the entire treatment; can include multiple regimens + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: humidity value;treatment interval and duration' + - 'Preferred unit: gram per cubic meter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000568 + light_regm: + is_a: environment field + aliases: + - light regimen + description: Information about treatment(s) involving exposure to light, including + both light intensity and quality. + pattern: '{text};{float} {unit};{float} {unit}' + examples: + - value: incandescant light;10 lux;450 nanometer + comments: + - 'Expected value: exposure type;light intensity;light quality' + - 'Preferred unit: lux; micrometer, nanometer, angstrom' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000569 + mechanical_damage: + is_a: environment field + aliases: + - mechanical damage + description: Information about any mechanical damage exerted on the plant; can + include multiple damages and sites + pattern: '{text};{text}' + examples: + - value: pruning;bark + comments: + - 'Expected value: damage type;body site' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001052 + mineral_nutr_regm: + is_a: environment field + aliases: + - mineral nutrient regimen + description: Information about treatment involving the use of mineral supplements; + should include the name of mineral nutrient, amount administered, treatment + regimen including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + mineral nutrient regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: mineral nutrient name;mineral nutrient amount;treatment interval + and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000570 + non_mineral_nutr_regm: + is_a: environment field + aliases: + - non-mineral nutrient regimen + description: Information about treatment involving the exposure of plant to non-mineral + nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral + nutrient, amount administered, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include multiple non-mineral nutrient regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: non-mineral nutrient name;non-mineral nutrient amount;treatment + interval and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000571 + ph_regm: + is_a: environment field + aliases: + - pH regimen + description: Information about treatment involving exposure of plants to varying + levels of ph of the growth media, treatment regimen including how many times + the treatment was repeated, how long each treatment lasted, and the start and + end time of the entire treatment; can include multiple regimen + pattern: '{float};{Rn/start_time/end_time/duration}' + examples: + - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: measurement value;treatment interval and duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001056 + pesticide_regm: + is_a: environment field + aliases: + - pesticide regimen + description: Information about treatment involving use of insecticides; should + include the name of pesticide, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple pesticide + regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: pesticide name;pesticide amount;treatment interval and duration' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000573 + plant_growth_med: + is_a: environment field + aliases: + - plant growth medium + description: Specification of the media for growing the plants or tissue cultured + samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in + vitro liquid culture medium. Recommended value is a specific value from EO:plant + growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) + or other controlled vocabulary + pattern: '{termLabel} {[termID]} or [husk|other artificial liquid medium|other + artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' + examples: + - value: hydroponic plant culture media [EO:0007067] + comments: + - 'Expected value: EO or enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + range: plant_growth_med_enum + slot_uri: MIXS:0001057 + plant_product: + is_a: environment field + aliases: + - plant product + description: Substance produced by the plant, where the sample was obtained from + pattern: '{text}' + examples: + - value: xylem sap [PO:0025539] + comments: + - 'Expected value: product name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001058 + plant_sex: + is_a: environment field + aliases: + - plant sex + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, + staminate, monoecieous, hermaphrodite. + pattern: '[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]' + examples: + - value: Hermaphroditic + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + range: plant_sex_enum + slot_uri: MIXS:0001059 + plant_struc: + is_a: environment field + aliases: + - plant structure + description: Name of plant structure the sample was obtained from; for Plant Ontology + (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, + e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the + sex of it can be recorded here. + pattern: '{termLabel} {[termID]}' + examples: + - value: epidermis [PO:0005679] + comments: + - 'Expected value: PO' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001060 + radiation_regm: + is_a: environment field + aliases: + - radiation regimen + description: Information about treatment involving exposure of plant or a plant + part to a particular radiation regimen; should include the radiation type, amount + or intensity administered, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple radiation regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: radiation type name;radiation amount;treatment interval and + duration' + - 'Preferred unit: rad, gray' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000575 + rainfall_regm: + is_a: environment field + aliases: + - rainfall regimen + description: Information about treatment involving an exposure to a given amount + of rainfall, treatment regimen including how many times the treatment was repeated, + how long each treatment lasted, and the start and end time of the entire treatment; + can include multiple regimens + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: measurement value;treatment interval and duration' + - 'Preferred unit: millimeter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000576 + root_cond: + is_a: environment field + aliases: + - rooting conditions + description: Relevant rooting conditions such as field plot size, sowing density, + container dimensions, number of plants per container. + pattern: '{PMID}|{DOI}|{URL}|{text}' + examples: + - value: http://himedialabs.com/TD/PT158.pdf + comments: + - 'Expected value: PMID,DOI,url or free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001061 + root_med_carbon: + is_a: environment field + aliases: + - rooting medium carbon + description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + pattern: '{text};{float} {unit}' + examples: + - value: sucrose + comments: + - 'Expected value: carbon source name;measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000577 + root_med_macronutr: + is_a: environment field + aliases: + - rooting medium macronutrients + description: "Measurement of the culture rooting medium macronutrients (N,P, K,\ + \ Ca, Mg, S); e.g. KH2PO4 (170\xAC\u2020mg/L)." + pattern: '{text};{float} {unit}' + examples: + - value: "KH2PO4;170\xAC\u2020milligram per liter" + comments: + - 'Expected value: macronutrient name;measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000578 + root_med_micronutr: + is_a: environment field + aliases: + - rooting medium micronutrients + description: "Measurement of the culture rooting medium micronutrients (Fe, Mn,\ + \ Zn, B, Cu, Mo); e.g. H3BO3 (6.2\xAC\u2020mg/L)." + pattern: '{text};{float} {unit}' + examples: + - value: "H3BO3;6.2\xAC\u2020milligram per liter" + comments: + - 'Expected value: micronutrient name;measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000579 + root_med_suppl: + is_a: environment field + aliases: + - rooting medium organic supplements + description: "Organic supplements of the culture rooting medium, such as vitamins,\ + \ amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic\ + \ acid (0.5\xAC\u2020mg/L)." + pattern: '{text};{float} {unit}' + examples: + - value: nicotinic acid;0.5 milligram per liter + comments: + - 'Expected value: supplement name;measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000580 + root_med_ph: + is_a: environment field + aliases: + - rooting medium pH + description: pH measurement of the culture rooting medium; e.g. 5.5. + pattern: '{float}' + examples: + - value: '7.5' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001062 + root_med_regl: + is_a: environment field + aliases: + - rooting medium regulators + description: "Growth regulators in the culture rooting medium such as cytokinins,\ + \ auxins, gybberellins, abscisic acid; e.g. 0.5\xAC\u2020mg/L NAA." + pattern: '{text};{float} {unit}' + examples: + - value: abscisic acid;0.75 milligram per liter + comments: + - 'Expected value: regulator name;measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000581 + root_med_solid: + is_a: environment field + aliases: + - rooting medium solidifier + description: Specification of the solidifying agent in the culture rooting medium; + e.g. agar. + pattern: '{text}' + examples: + - value: agar + comments: + - 'Expected value: name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001063 + salt_regm: + is_a: environment field + aliases: + - salt regimen + description: Information about treatment involving use of salts as supplement + to liquid and soil growth media; should include the name of salt, amount administered, + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple salt regimens + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: salt name;salt amount;treatment interval and duration' + - 'Preferred unit: gram, microgram, mole per liter, gram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000582 + season_environment: + is_a: environment field + aliases: + - seasonal environment + description: Treatment involving an exposure to a particular season (e.g. Winter, + summer, rabi, rainy etc.), treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment + pattern: '{text};{Rn/start_time/end_time/duration}' + examples: + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: seasonal environment name;treatment interval and duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001068 + standing_water_regm: + is_a: environment field + aliases: + - standing water regimen + description: Treatment involving an exposure to standing water during a plant's + life span, types can be flood water or standing water, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple regimens + pattern: '{text};{Rn/start_time/end_time/duration}' + examples: + - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: standing water type;treatment interval and duration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001069 + tiss_cult_growth_med: + is_a: environment field + aliases: + - tissue culture growth media + description: Description of plant tissue culture growth media used + pattern: '{PMID}|{DOI}|{URL}|{text}' + examples: + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf + comments: + - 'Expected value: PMID,DOI,url or free text' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0001070 + water_temp_regm: + is_a: environment field + aliases: + - water temperature regimen + description: Information about treatment involving an exposure to water with varying + degree of temperature, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple regimens + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: measurement value;treatment interval and duration' + - 'Preferred unit: degree Celsius' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000590 + watering_regm: + is_a: environment field + aliases: + - watering regimen + description: Information about treatment involving an exposure to watering frequencies, + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple regimens + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + examples: + - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + comments: + - 'Expected value: measurement value;treatment interval and duration' + - 'Preferred unit: milliliter, liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: plant-associated' + slot_uri: MIXS:0000591 + particle_class: + is_a: environment field + aliases: + - particle classification + description: Particles are classified, based on their size, into six general categories:clay, + silt, sand, gravel, cobbles, and boulders; should include amount of particle + preceded by the name of the particle type; can include multiple values + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: particle name;measurement value' + - 'Preferred unit: micrometer' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: sediment' + slot_uri: MIXS:0000206 + sediment_type: + is_a: environment field + aliases: + - sediment type + description: Information about the sediment type based on major constituents + pattern: '[biogenous|cosmogenous|hydrogenous|lithogenous]' + examples: + - value: biogenous + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: sediment' + range: sediment_type_enum + slot_uri: MIXS:0001078 + tidal_stage: + is_a: environment field + aliases: + - tidal stage + description: Stage of tide + pattern: '[low tide|ebb tide|flood tide|high tide]' + examples: + - value: high tide + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: sediment, water' + range: tidal_stage_enum + slot_uri: MIXS:0000750 + tot_depth_water_col: + is_a: environment field + aliases: + - total depth of water column + description: Measurement of total depth of water column + pattern: '{float} {unit}' + examples: + - value: 500 meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: meter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used in: 2 packages: sediment, water' + slot_uri: MIXS:0000634 + cur_land_use: + is_a: environment field + aliases: + - current land use + description: Present state of sample site + pattern: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt + flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small + grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands + (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands + used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub + land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional + shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub + crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers + (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed + hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest + receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water + body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery + trees)]' + examples: + - value: conifers + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: soil' + range: cur_land_use_enum + slot_uri: MIXS:0001080 + cur_vegetation: + is_a: environment field + aliases: + - current vegetation + description: Vegetation classification from one or more standard classification + systems, or agricultural crop + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: current vegetation type' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 2' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000312 + cur_vegetation_meth: + is_a: environment field + aliases: + - current vegetation method + description: Reference or method used in vegetation classification + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 3' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000314 + previous_land_use: + is_a: environment field + aliases: + - history/previous land use + description: Previous land use and dates + pattern: '{text};{timestamp}' + examples: + - value: '' + comments: + - 'Expected value: land use name;date' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 4' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000315 + previous_land_use_meth: + is_a: environment field + aliases: + - history/previous land use method + description: Reference or method used in determining previous land use and dates + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 5' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000316 + crop_rotation: + is_a: environment field + aliases: + - history/crop rotation + description: Whether or not crop is rotated, and if yes, rotation schedule + pattern: '{boolean};{Rn/start_time/end_time/duration}' + examples: + - value: yes;R2/2017-01-01/2018-12-31/P6M + comments: + - 'Expected value: crop rotation status;schedule' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 6' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000318 + agrochem_addition: + is_a: environment field + aliases: + - history/agrochemical additions + description: Addition of fertilizers, pesticides, etc. - amount and time of applications + pattern: '{text};{float} {unit};{timestamp}' + examples: + - value: roundup;5 milligram per liter;2018-06-21 + comments: + - 'Expected value: agrochemical name;agrochemical amount;timestamp' + - 'Preferred unit: gram, mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 7' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000639 + tillage: + is_a: environment field + aliases: + - history/tillage + description: Note method(s) used for tilling + pattern: '[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc + plough]' + examples: + - value: chisel + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 8' + - 'This field is used uniquely in: soil' + range: tillage_enum + slot_uri: MIXS:0001081 + fire: + is_a: environment field + aliases: + - history/fire + description: Historical and/or physical evidence of fire + pattern: '{timestamp}' + examples: + - value: '' + comments: + - 'Expected value: date' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 9' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0001086 + flooding: + is_a: environment field + aliases: + - history/flooding + description: Historical and/or physical evidence of flooding + pattern: '{timestamp}' + examples: + - value: '' + comments: + - 'Expected value: date' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 10' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000319 + extreme_event: + is_a: environment field + aliases: + - history/extreme events + description: Unusual physical events that may have affected microbial populations + pattern: '{timestamp}' + examples: + - value: '' + comments: + - 'Expected value: date' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 11' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000320 + horizon: + is_a: environment field + aliases: + - horizon + description: Specific layer in the land area which measures parallel to the soil + surface and possesses physical characteristics which differ from the layers + above and beneath + pattern: '[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]' + examples: + - value: A horizon + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 12' + - 'This field is used uniquely in: soil' + range: horizon_enum + slot_uri: MIXS:0001082 + horizon_meth: + is_a: environment field + aliases: + - horizon method + description: Reference or method used in determining the horizon + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 13' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000321 + sieving: + is_a: environment field + aliases: + - composite design/sieving (if any) + description: Collection design of pooled samples and/or sieve size and amount + of sample sieved + pattern: '{{text}|{float} {unit}};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: design name and/or size;amount' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 14' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000322 + water_content_soil_meth: + is_a: environment field + aliases: + - water content method + description: Reference or method used in determining the water content of soil + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 16' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000323 + pool_dna_extracts: + is_a: environment field + aliases: + - pooling of DNA extracts (if done) + description: Indicate whether multiple DNA extractions were mixed. If the answer + yes, the number of extracts that were pooled should be given + pattern: '{boolean};{integer}' + examples: + - value: yes;5 + comments: + - 'Expected value: pooling status;number of pooled extracts' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 18' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000325 + store_cond: + is_a: environment field + aliases: + - storage conditions (fresh/frozen/other) + description: Explain how and for how long the soil sample was stored before DNA + extraction + pattern: '{text};{duration}' + examples: + - value: -20 degree Celsius freezer;P2Y10D + comments: + - 'Expected value: storage condition type;duration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 19' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000327 + link_climate_info: + is_a: environment field + aliases: + - link to climate information + description: Link to climate resource + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 20' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000328 + annual_temp: + is_a: environment field + aliases: + - mean annual temperature + description: Mean annual temperature + pattern: '{float} {unit}' + examples: + - value: 12.5 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 21' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000642 + season_temp: + is_a: environment field + aliases: + - mean seasonal temperature + description: Mean seasonal temperature + pattern: '{float} {unit}' + examples: + - value: 18 degree Celsius + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree Celsius' + - 'Occurrence: 1' + - 'Position: 22' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000643 + annual_precpt: + is_a: environment field + aliases: + - mean annual precipitation + description: The average of all annual precipitation values known, or an estimated + equivalent value derived by such methods as regional indexes or Isohyetal maps. + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millimeter' + - 'Occurrence: 1' + - 'Position: 23' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000644 + season_precpt: + is_a: environment field + aliases: + - mean seasonal precipitation + description: The average of all seasonal precipitation values known, or an estimated + equivalent value derived by such methods as regional indexes or Isohyetal maps. + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millimeter' + - 'Occurrence: 1' + - 'Position: 24' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000645 + link_class_info: + is_a: environment field + aliases: + - link to classification information + description: Link to digitized soil maps or other soil classification information + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 25' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000329 + fao_class: + is_a: environment field + aliases: + - soil_taxonomic/FAO classification + description: Soil classification from the FAO World Reference Database for Soil + Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + pattern: '[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]' + examples: + - value: Luvisols + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 26' + - 'This field is used uniquely in: soil' + range: fao_class_enum + slot_uri: MIXS:0001083 + local_class: + is_a: environment field + aliases: + - soil_taxonomic/local classification + description: Soil classification based on local soil classification system + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: local classification name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 27' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000330 + local_class_meth: + is_a: environment field + aliases: + - soil_taxonomic/local classification method + description: Reference or method used in determining the local soil classification + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 28' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000331 + soil_type: + is_a: environment field + aliases: + - soil type + description: Soil series name or other lower-level classification + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: soil type name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 29' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000332 + soil_type_meth: + is_a: environment field + aliases: + - soil type method + description: Reference or method used in determining soil series name or other + lower-level classification + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 30' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000334 + slope_gradient: + is_a: environment field + aliases: + - slope gradient + description: Commonly called 'slope'. The angle between ground surface and a horizontal + line (in percent). This is the direction that overland water would flow. This + measure is usually taken with a hand level meter or clinometer + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 31' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000646 + slope_aspect: + is_a: environment field + aliases: + - slope aspect + description: The direction a slope faces. While looking down a slope use a compass + to record the direction you are facing (direction or degrees); e.g., nw or 315 + degrees. This measure provides an indication of sun and wind exposure that will + influence soil temperature and evapotranspiration. + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: degree' + - 'Occurrence: 1' + - 'Position: 32' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000647 + profile_position: + is_a: environment field + aliases: + - profile position + description: Cross-sectional position in the hillslope where sample was collected.sample + area position in relation to surrounding areas + pattern: '[summit|shoulder|backslope|footslope|toeslope]' + examples: + - value: summit + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 33' + - 'This field is used uniquely in: soil' + range: profile_position_enum + slot_uri: MIXS:0001084 + drainage_class: + is_a: environment field + aliases: + - drainage classification + description: Drainage classification from a standard system such as the USDA system + pattern: '[very poorly|poorly|somewhat poorly|moderately well|well|excessively + drained]' + examples: + - value: well + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 34' + - 'This field is used uniquely in: soil' + range: drainage_class_enum + slot_uri: MIXS:0001085 + texture: + is_a: environment field + aliases: + - texture + description: The relative proportion of different grain sizes of mineral particles + in a soil, as described using a standard system; express as % sand (50 um to + 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty + clay loam) optional. + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 35' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000335 + texture_meth: + is_a: environment field + aliases: + - texture method + description: Reference or method used in determining soil texture + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 36' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000336 + ph_meth: + is_a: environment field + aliases: + - pH method + description: Reference or method used in determining ph + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 38' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0001106 + tot_org_c_meth: + is_a: environment field + aliases: + - total organic carbon method + description: Reference or method used in determining total organic carbon + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 40' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000337 + tot_nitro_content_meth: + is_a: environment field + aliases: + - total nitrogen content method + description: Reference or method used in determining the total nitrogen + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 42' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000338 + microbial_biomass: + is_a: environment field + aliases: + - microbial biomass + description: The part of the organic matter in the soil that constitutes living + microorganisms smaller than 5-10 micrometer. If you keep this, you would need + to have correction factors used for conversion to the final units + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: ton, kilogram, gram per kilogram soil' + - 'Occurrence: 1' + - 'Position: 43' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000650 + microbial_biomass_meth: + is_a: environment field + aliases: + - microbial biomass method + description: Reference or method used in determining microbial biomass + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 44' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000339 + link_addit_analys: + is_a: environment field + aliases: + - links to additional analysis + description: Link to additional analysis results performed on the sample + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 45' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000340 + extreme_salinity: + is_a: environment field + aliases: + - extreme_unusual_properties/salinity + description: Measured salinity + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: millisiemens per meter' + - 'Occurrence: 1' + - 'Position: 46' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000651 + salinity_meth: + is_a: environment field + aliases: + - extreme_unusual_properties/salinity method + description: Reference or method used in determining salinity + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 47' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000341 + heavy_metals: + is_a: environment field + aliases: + - extreme_unusual_properties/heavy metals + description: Heavy metals present and concentrationsany drug used by subject and + the frequency of usage; can include multiple heavy metals and concentrations + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: heavy metal name;measurement value' + - 'Preferred unit: microgram per gram' + - 'Occurrence: m' + - 'Position: 48' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000652 + heavy_metals_meth: + is_a: environment field + aliases: + - extreme_unusual_properties/heavy metals method + description: Reference or method used in determining heavy metals + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or url' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 49' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000343 + al_sat: + is_a: environment field + aliases: + - extreme_unusual_properties/Al saturation + description: Aluminum saturation (esp. For tropical soils) + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 50' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000607 + al_sat_meth: + is_a: environment field + aliases: + - extreme_unusual_properties/Al saturation method + description: Reference or method used in determining Al saturation + pattern: '{PMID}|{DOI}|{URL}' + examples: + - value: '' + comments: + - 'Expected value: PMID,DOI or URL' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 51' + - 'This field is used uniquely in: soil' + slot_uri: MIXS:0000324 + biochem_oxygen_dem: + is_a: environment field + aliases: + - biochemical oxygen demand + description: Amount of dissolved oxygen needed by aerobic biological organisms + in a body of water to break down organic material present in a given water sample + at certain temperature over a specific time period + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000653 + chem_oxygen_dem: + is_a: environment field + aliases: + - chemical oxygen demand + description: A measure of the capacity of water to consume oxygen during the decomposition + of organic matter and the oxidation of inorganic chemicals such as ammonia and + nitrite + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000656 + efficiency_percent: + is_a: environment field + aliases: + - efficiency percent + description: Percentage of volatile solids removed from the anaerobic digestor + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000657 + emulsions: + is_a: environment field + aliases: + - emulsions + description: Amount or concentration of substances such as paints, adhesives, + mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion + types + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: emulsion name;measurement value' + - 'Preferred unit: gram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000660 + gaseous_substances: + is_a: environment field + aliases: + - gaseous substances + description: Amount or concentration of substances such as hydrogen sulfide, carbon + dioxide, methane, etc.; can include multiple substances + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: gaseous substance name;measurement value' + - 'Preferred unit: micromole per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000661 + indust_eff_percent: + is_a: environment field + aliases: + - industrial effluent percent + description: Percentage of industrial effluents received by wastewater treatment + plant + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: percentage' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000662 + inorg_particles: + is_a: environment field + aliases: + - inorganic particles + description: Concentration of particles such as sand, grit, metal particles, ceramics, + etc.; can include multiple particles + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: inorganic particle name;measurement value' + - 'Preferred unit: mole per liter, milligram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000664 + org_particles: + is_a: environment field + aliases: + - organic particles + description: Concentration of particles such as faeces, hairs, food, vomit, paper + fibers, plant material, humus, etc. + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: particle name;measurement value' + - 'Preferred unit: gram per liter' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000665 + pre_treatment: + is_a: environment field + aliases: + - pre-treatment + description: The process of pre-treatment removes materials that can be easily + collected from the raw wastewater + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: pre-treatment type' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000348 + primary_treatment: + is_a: environment field + aliases: + - primary treatment + description: The process to produce both a generally homogeneous liquid capable + of being treated biologically and a sludge that can be separately treated or + processed + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: primary treatment type' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000349 + reactor_type: + is_a: environment field + aliases: + - reactor type + description: Anaerobic digesters can be designed and engineered to operate using + a number of different process configurations, as batch or continuous, mesophilic, + high solid or low solid, and single stage or multistage + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: reactor type name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000350 + secondary_treatment: + is_a: environment field + aliases: + - secondary treatment + description: The process for substantially degrading the biological content of + the sewage + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: secondary treatment type' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000351 + sewage_type: + is_a: environment field + aliases: + - sewage type + description: Type of wastewater treatment plant as municipial or industrial + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: sewage type name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000215 + sludge_retent_time: + is_a: environment field + aliases: + - sludge retention time + description: The time activated sludge remains in reactor + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: hours' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000669 + soluble_inorg_mat: + is_a: environment field + aliases: + - soluble inorganic material + description: Concentration of substances such as ammonia, road-salt, sea-salt, + cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: soluble inorganic material name;measurement value' + - 'Preferred unit: gram, microgram, mole per liter, gram per liter, parts per + million' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000672 + soluble_org_mat: + is_a: environment field + aliases: + - soluble organic material + description: Concentration of substances such as urea, fruit sugars, soluble proteins, + drugs, pharmaceuticals, etc. + pattern: '{text};{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: soluble organic material name;measurement value' + - 'Preferred unit: gram, microgram, mole per liter, gram per liter, parts per + million' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000673 + tertiary_treatment: + is_a: environment field + aliases: + - tertiary treatment + description: The process providing a final treatment stage to raise the effluent + quality before it is discharged to the receiving environment + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: tertiary treatment type' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000352 + tot_phosphate: + is_a: environment field + aliases: + - total phosphate + description: Total amount or concentration of phosphate + pattern: '{float} {unit}' + examples: + - value: '' + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000689 + wastewater_type: + is_a: environment field + aliases: + - wastewater type + description: The origin of wastewater such as human waste, rainfall, storm drains, + etc. + pattern: '{text}' + examples: + - value: '' + comments: + - 'Expected value: wastewater type name' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: wastewater_sludge' + slot_uri: MIXS:0000353 + atmospheric_data: + is_a: environment field + aliases: + - atmospheric data + description: Measurement of atmospheric data; can include multiple data + pattern: '{text};{float} {unit}' + examples: + - value: wind speed;9 knots + comments: + - 'Expected value: atmospheric data name;measurement value' + - 'Preferred unit: ' + - 'Occurrence: m' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0001097 + bac_prod: + is_a: environment field + aliases: + - bacterial production + description: Bacterial production in the water column measured by isotope uptake + pattern: '{float} {unit}' + examples: + - value: 5 milligram per cubic meter per day + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per cubic meter per day' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000683 + bac_resp: + is_a: environment field + aliases: + - bacterial respiration + description: Measurement of bacterial respiration in the water column + pattern: '{float} {unit}' + examples: + - value: 300 micromole oxygen per liter per hour + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per cubic meter per day, micromole oxygen per liter + per hour' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000684 + conduc: + is_a: environment field + aliases: + - conductivity + description: Electrical conductivity of water + pattern: '{float} {unit}' + examples: + - value: 10 milliSiemens per centimeter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milliSiemens per centimeter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000692 + diss_inorg_nitro: + is_a: environment field + aliases: + - dissolved inorganic nitrogen + description: Concentration of dissolved inorganic nitrogen + pattern: '{float} {unit}' + examples: + - value: 761 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000698 + down_par: + is_a: environment field + aliases: + - downward PAR + description: Visible waveband radiance and irradiance measurements in the water + column + pattern: '{float} {unit}' + examples: + - value: 28.71 microEinstein per square meter per second + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microEinstein per square meter per second, microEinstein per + square centimeter per second' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000703 + fluor: + is_a: environment field + aliases: + - fluorescence + description: Raw or converted fluorescence of water + pattern: '{float} {unit}' + examples: + - value: 2.5 volts + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram chlorophyll a per cubic meter, volts' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000704 + light_intensity: + is_a: environment field + aliases: + - light intensity + description: Measurement of light intensity + pattern: '{float} {unit}' + examples: + - value: 0.3 lux + comments: + - 'Expected value: measurement value' + - 'Preferred unit: lux' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000706 + part_org_nitro: + is_a: environment field + aliases: + - particulate organic nitrogen + description: Concentration of particulate organic nitrogen + pattern: '{float} {unit}' + examples: + - value: 0.3 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000719 + photon_flux: + is_a: environment field + aliases: + - photon flux + description: Measurement of photon flux + pattern: '{float} {unit}' + examples: + - value: 3.926 micromole photons per second per square meter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: number of photons per second per unit area' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000725 + primary_prod: + is_a: environment field + aliases: + - primary production + description: Measurement of primary production, generally measured as isotope + uptake + pattern: '{float} {unit}' + examples: + - value: 100 milligram per cubic meter per day + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per cubic meter per day, gram per square meter per + day' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000728 + size_frac_low: + is_a: environment field + aliases: + - size-fraction lower threshold + description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. + Materials larger than the size threshold are excluded from the sample + pattern: '{float} {unit}' + examples: + - value: 0.2 micrometer + comments: + - 'Expected value: value' + - 'Preferred unit: micrometer' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000735 + size_frac_up: + is_a: environment field + aliases: + - size-fraction upper threshold + description: Refers to the mesh/pore size used to retain the sample. Materials + smaller than the size threshold are excluded from the sample + pattern: '{float} {unit}' + examples: + - value: 20 micrometer + comments: + - 'Expected value: value' + - 'Preferred unit: micrometer' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000736 + soluble_react_phosp: + is_a: environment field + aliases: + - soluble reactive phosphorus + description: Concentration of soluble reactive phosphorus + pattern: '{float} {unit}' + examples: + - value: 0.1 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: micromole per liter, milligram per liter, parts per million' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000738 + suspend_part_matter: + is_a: environment field + aliases: + - suspended particulate matter + description: Concentration of suspended particulate matter + pattern: '{float} {unit}' + examples: + - value: 0.5 milligram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: milligram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000741 + tot_diss_nitro: + is_a: environment field + aliases: + - total dissolved nitrogen + description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured + by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' + pattern: '{float} {unit}' + examples: + - value: 40 microgram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000744 + tot_inorg_nitro: + is_a: environment field + aliases: + - total inorganic nitrogen + description: Total inorganic nitrogen content + pattern: '{float} {unit}' + examples: + - value: 40 microgram per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000745 + tot_part_carb: + is_a: environment field + aliases: + - total particulate carbon + description: Total particulate carbon content + pattern: '{float} {unit}' + examples: + - value: 35 micromole per liter + comments: + - 'Expected value: measurement value' + - 'Preferred unit: microgram per liter, micromole per liter' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: water' + slot_uri: MIXS:0000747 +classes: + core: + description: core package + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - ploidy + - num_replicons + - extrachrom_elements + - estimated_size + - ref_biomaterial + - source_mat_id + - pathogenicity + - biotic_relationship + - specific_host + - host_spec_range + - health_disease_stat + - trophic_level + - propagation + - encoded_traits + - rel_to_oxygen + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - source_uvig + - virus_enrich_appr + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - target_gene + - target_subfragment + - pcr_primers + - mid + - adapters + - pcr_cond + - seq_meth + - seq_quality_check + - chimera_check + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - x_16s_recover + - x_16s_recover_software + - trnas + - trna_ext_software + - compl_score + - compl_software + - compl_appr + - contam_score + - contam_screen_input + - contam_screen_param + - decontam_software + - sort_tech + - single_cell_lysis_appr + - single_cell_lysis_prot + - wga_amp_appr + - wga_amp_kit + - bin_param + - bin_software + - reassembly_bin + - mag_cov_software + - vir_ident_software + - pred_genome_type + - pred_genome_struc + - detec_type + - votu_class_appr + - votu_seq_comp_appr + - votu_db + - host_pred_appr + - host_pred_est_acc + - url + - sop + air: + description: air + mappings: [] + slots: + - barometric_press + - carb_dioxide + - carb_monoxide + - chem_administration + - humidity + - methane + - misc_param + - organism_count + - oxygen + - oxy_stat_samp + - perturbation + - pollutants + - resp_part_matter + - samp_salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - solar_irradiance + - temp + - ventilation_rate + - ventilation_type + - volatile_org_comp + - wind_direction + - wind_speed + slot_usage: {} + built environment: + description: built environment + mappings: [] + slots: + - surf_material + - surf_air_cont + - rel_air_humidity + - abs_air_humidity + - surf_humidity + - air_temp + - surf_temp + - surf_moisture_ph + - build_occup_type + - surf_moisture + - dew_point + - carb_dioxide + - ventilation_type + - organism_count + - indoor_space + - indoor_surf + - filter_type + - heat_cool_type + - substructure_type + - building_setting + - light_type + - samp_sort_meth + - space_typ_state + - typ_occup_density + - occup_samp + - occup_density_samp + - address + - adj_room + - aero_struc + - amount_light + - arch_struc + - avg_occup + - avg_dew_point + - avg_temp + - bathroom_count + - bedroom_count + - built_struc_age + - built_struc_set + - built_struc_type + - ceil_area + - ceil_cond + - ceil_finish_mat + - ceil_water_mold + - ceil_struc + - ceil_texture + - ceil_thermal_mass + - ceil_type + - cool_syst_id + - date_last_rain + - build_docs + - door_size + - door_cond + - door_direct + - door_loc + - door_mat + - door_move + - door_water_mold + - door_type + - door_comp_type + - door_type_metal + - door_type_wood + - drawings + - elevator + - escalator + - exp_duct + - exp_pipe + - ext_door + - fireplace_type + - floor_age + - floor_area + - floor_cond + - floor_count + - floor_finish_mat + - floor_water_mold + - floor_struc + - floor_thermal_mass + - freq_clean + - freq_cook + - furniture + - gender_restroom + - hall_count + - handidness + - heat_deliv_loc + - heat_system_deliv_meth + - heat_system_id + - height_carper_fiber + - inside_lux + - int_wall_cond + - last_clean + - max_occup + - mech_struc + - number_plants + - number_pets + - number_resident + - occup_document + - ext_wall_orient + - ext_window_orient + - rel_humidity_out + - pres_animal + - quad_pos + - rel_samp_loc + - room_air_exch_rate + - room_architec_element + - room_condt + - room_count + - room_dim + - room_door_dist + - room_loc + - room_moist_damage_hist + - room_net_area + - room_occup + - room_samp_pos + - room_type + - room_vol + - room_window_count + - room_connected + - room_hallway + - room_door_share + - room_wall_share + - samp_weather + - samp_floor + - samp_room_id + - samp_time_out + - season + - season_use + - shading_device_cond + - shading_device_loc + - shading_device_mat + - shading_device_water_mold + - shading_device_type + - specific_humidity + - specific + - temp_out + - train_line + - train_stat_loc + - train_stop_loc + - vis_media + - wall_area + - wall_const_type + - wall_finish_mat + - wall_height + - wall_loc + - wall_water_mold + - wall_surf_treatment + - wall_texture + - wall_thermal_mass + - water_feat_size + - water_feat_type + - weekday + - window_size + - window_cond + - window_cover + - window_horiz_pos + - window_loc + - window_mat + - window_open_freq + - window_water_mold + - window_status + - window_type + - window_vert_pos + slot_usage: {} + host-associated: + description: host-associated + mappings: [] + slots: + - ances_data + - biol_stat + - genetic_mod + - host_common_name + - samp_capt_status + - samp_dis_stage + - host_taxid + - host_subject_id + - host_age + - host_life_stage + - host_sex + - host_disease_stat + - chem_administration + - host_body_habitat + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_length + - host_diet + - host_last_meal + - host_growth_cond + - host_substrate + - host_family_relationship + - host_infra_specific_name + - host_infra_specific_rank + - host_genotype + - host_phenotype + - host_body_temp + - host_dry_mass + - host_blood_press_diast + - host_blood_press_syst + - host_color + - host_shape + - gravidity + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - misc_param + slot_usage: {} + human-associated: + description: human-associated + mappings: [] + slots: + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_family_relationship + - host_genotype + - host_phenotype + - host_body_temp + - smoker + - host_hiv_stat + - drug_usage + - host_body_mass_index + - diet_last_six_month + - weight_loss_3_month + - ihmc_ethnicity + - host_occupation + - pet_farm_animal + - travel_out_six_month + - twin_sibling + - medic_hist_perform + - study_complt_stat + - pulmonary_disord + - nose_throat_disord + - blood_blood_disord + - host_pulse + - gestation_state + - maternal_health_stat + - foetal_health_stat + - amniotic_fluid_color + - urogenit_tract_disor + - urine_collect_meth + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - misc_param + slot_usage: {} + human-gut: + description: human-gut + mappings: [] + slots: + - gastrointest_disord + - liver_disord + - special_diet + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_family_relationship + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ihmc_ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_store_temp + - samp_vol_we_dna_ext + - samp_store_dur + - samp_store_loc + - misc_param + slot_usage: {} + human-oral: + description: human-oral + mappings: [] + slots: + - nose_mouth_teeth_throat_disord + - time_last_toothbrush + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_family_relationship + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ihmc_ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - misc_param + slot_usage: {} + human-skin: + description: human-skin + mappings: [] + slots: + - dermatology_disord + - time_since_last_wash + - dominant_hand + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_family_relationship + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ihmc_ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - misc_param + slot_usage: {} + human-vaginal: + description: human-vaginal + mappings: [] + slots: + - menarche + - sexual_act + - pregnancy + - douche + - birth_control + - menopause + - hrt + - hysterectomy + - gynecologic_disord + - urogenit_disord + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_family_relationship + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ihmc_ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - samp_salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_loc + - samp_store_dur + - misc_param + slot_usage: {} + hydrocarbon resources-cores: + description: hydrocarbon resources-cores + mappings: [] + slots: + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_pressure + - permeability + - porosity + - lithology + - depos_env + - hcr_geol_age + - owc_tvdss + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - sr_kerog_type + - sr_lithology + - sr_dep_env + - sr_geol_age + - samp_well_name + - win + - samp_type + - samp_subtype + - temp + - pressure + - samp_tvdss + - samp_md + - oxy_stat_samp + - samp_transport_cond + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - organism_count_qpcr_info + - ph + - samp_salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc + - misc_param + - additional_info + slot_usage: {} + hydrocarbon resources-fluids_swabs: + description: hydrocarbon resources-fluids/swabs + mappings: [] + slots: + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_pressure + - lithology + - depos_env + - hcr_geol_age + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - prod_start_date + - prod_rate + - water_production_rate + - water_cut + - iwf + - add_recov_method + - iw_bt_date_well + - biocide + - biocide_admin_method + - chem_treatment + - chem_treatment_method + - samp_loc_corr_rate + - samp_well_name + - win + - samp_type + - samp_subtype + - samp_collection_point + - temp + - pressure + - oxy_stat_samp + - samp_preserv + - samp_transport_cond + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - organism_count_qpcr_info + - ph + - samp_salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc + - misc_param + - additional_info + slot_usage: {} + microbial mat_biofilm: + description: microbial mat/biofilm + mappings: [] + slots: + - alkalinity + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - part_org_carb + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - tot_carb + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content + slot_usage: {} + miscellaneous natural or artificial environment: + description: miscellaneous natural or artificial environment + mappings: [] + slots: + - alkalinity + - ammonium + - biomass + - bromide + - calcium + - chem_administration + - chloride + - chlorophyll + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_nitro + - diss_oxygen + - misc_param + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - perturbation + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - water_current + slot_usage: {} + plant-associated: + description: plant-associated + mappings: [] + slots: + - air_temp_regm + - ances_data + - antibiotic_regm + - biol_stat + - biotic_regm + - chem_administration + - chem_mutagen + - climate_environment + - cult_root_med + - fertilizer_regm + - fungicide_regm + - gaseous_environment + - genetic_mod + - gravity + - growth_facil + - growth_habit + - growth_hormone_regm + - herbicide_regm + - host_age + - host_common_name + - host_disease_stat + - host_dry_mass + - host_genotype + - host_height + - host_infra_specific_name + - host_infra_specific_rank + - host_length + - host_life_stage + - host_phenotype + - host_taxid + - host_tot_mass + - host_wet_mass + - humidity_regm + - light_regm + - mechanical_damage + - mineral_nutr_regm + - misc_param + - non_mineral_nutr_regm + - organism_count + - oxy_stat_samp + - ph_regm + - perturbation + - pesticide_regm + - plant_growth_med + - plant_product + - plant_sex + - plant_struc + - radiation_regm + - rainfall_regm + - root_cond + - root_med_carbon + - root_med_macronutr + - root_med_micronutr + - root_med_suppl + - root_med_ph + - root_med_regl + - root_med_solid + - salt_regm + - samp_capt_status + - samp_dis_stage + - samp_salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - season_environment + - standing_water_regm + - temp + - tiss_cult_growth_med + - water_temp_regm + - watering_regm + slot_usage: {} + sediment: + description: sediment + mappings: [] + slots: + - alkalinity + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - particle_class + - part_org_carb + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - porosity + - potassium + - pressure + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - sediment_type + - silicate + - sodium + - sulfate + - sulfide + - temp + - tidal_stage + - tot_carb + - tot_depth_water_col + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content + slot_usage: {} + soil: + description: soil + mappings: [] + slots: + - cur_land_use + - cur_vegetation + - cur_vegetation_meth + - previous_land_use + - previous_land_use_meth + - crop_rotation + - agrochem_addition + - tillage + - fire + - flooding + - extreme_event + - horizon + - horizon_meth + - sieving + - water_content + - water_content_soil_meth + - samp_vol_we_dna_ext + - pool_dna_extracts + - store_cond + - link_climate_info + - annual_temp + - season_temp + - annual_precpt + - season_precpt + - link_class_info + - fao_class + - local_class + - local_class_meth + - soil_type + - soil_type_meth + - slope_gradient + - slope_aspect + - profile_position + - drainage_class + - texture + - texture_meth + - ph + - ph_meth + - tot_org_carb + - tot_org_c_meth + - tot_nitro_content + - tot_nitro_content_meth + - microbial_biomass + - microbial_biomass_meth + - link_addit_analys + - extreme_salinity + - salinity_meth + - heavy_metals + - heavy_metals_meth + - al_sat + - al_sat_meth + - misc_param + slot_usage: {} + wastewater_sludge: + description: wastewater/sludge + mappings: [] + slots: + - alkalinity + - biochem_oxygen_dem + - chem_administration + - chem_oxygen_dem + - efficiency_percent + - emulsions + - gaseous_substances + - indust_eff_percent + - inorg_particles + - misc_param + - nitrate + - org_particles + - organism_count + - oxy_stat_samp + - ph + - perturbation + - phosphate + - pre_treatment + - primary_treatment + - reactor_type + - samp_salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - secondary_treatment + - sewage_type + - sludge_retent_time + - sodium + - soluble_inorg_mat + - soluble_org_mat + - suspend_solids + - temp + - tertiary_treatment + - tot_nitro + - tot_phosphate + - wastewater_type + slot_usage: {} + water: + description: water + mappings: [] + slots: + - alkalinity + - alkalinity_method + - alkyl_diethers + - aminopept_act + - ammonium + - atmospheric_data + - bacteria_carb_prod + - bac_prod + - bac_resp + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - conduc + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_inorg_nitro + - diss_inorg_phosp + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - down_par + - fluor + - glucosidase_act + - light_intensity + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - part_org_carb + - part_org_nitro + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - photon_flux + - potassium + - pressure + - primary_prod + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - size_frac_low + - size_frac_up + - sodium + - soluble_react_phosp + - sulfate + - sulfide + - suspend_part_matter + - temp + - tidal_stage + - tot_depth_water_col + - tot_diss_nitro + - tot_inorg_nitro + - tot_nitro + - tot_part_carb + - tot_phosp + - turbidity + - water_current + slot_usage: {} + migs_eu: + mixin: true + description: migs_eu Checklist + todos: + - add details here + migs_ba: + mixin: true + description: migs_ba Checklist + todos: + - add details here + migs_pl: + mixin: true + description: migs_pl Checklist + todos: + - add details here + migs_vi: + mixin: true + description: migs_vi Checklist + todos: + - add details here + migs_org: + mixin: true + description: migs_org Checklist + todos: + - add details here + me: + mixin: true + description: me Checklist + todos: + - add details here + mimarks_s: + mixin: true + description: mimarks_s Checklist + todos: + - add details here + mimarks_c: + mixin: true + description: mimarks_c Checklist + todos: + - add details here + misag: + mixin: true + description: misag Checklist + todos: + - add details here + mimag: + mixin: true + description: mimag Checklist + todos: + - add details here + miuvig: + mixin: true + description: miuvig Checklist + todos: + - add details here + core migs_eu: + is_a: core + mixins: + - migs_eu + description: Combinatorial checklist for core with migs_eu + core migs_ba: + is_a: core + mixins: + - migs_ba + description: Combinatorial checklist for core with migs_ba + core migs_pl: + is_a: core + mixins: + - migs_pl + description: Combinatorial checklist for core with migs_pl + core migs_vi: + is_a: core + mixins: + - migs_vi + description: Combinatorial checklist for core with migs_vi + core migs_org: + is_a: core + mixins: + - migs_org + description: Combinatorial checklist for core with migs_org + core me: + is_a: core + mixins: + - me + description: Combinatorial checklist for core with me + core mimarks_s: + is_a: core + mixins: + - mimarks_s + description: Combinatorial checklist for core with mimarks_s + core mimarks_c: + is_a: core + mixins: + - mimarks_c + description: Combinatorial checklist for core with mimarks_c + core misag: + is_a: core + mixins: + - misag + description: Combinatorial checklist for core with misag + core mimag: + is_a: core + mixins: + - mimag + description: Combinatorial checklist for core with mimag + core miuvig: + is_a: core + mixins: + - miuvig + description: Combinatorial checklist for core with miuvig + air migs_eu: + is_a: air + mixins: + - migs_eu + description: Combinatorial checklist for air with migs_eu + air migs_ba: + is_a: air + mixins: + - migs_ba + description: Combinatorial checklist for air with migs_ba + air migs_pl: + is_a: air + mixins: + - migs_pl + description: Combinatorial checklist for air with migs_pl + air migs_vi: + is_a: air + mixins: + - migs_vi + description: Combinatorial checklist for air with migs_vi + air migs_org: + is_a: air + mixins: + - migs_org + description: Combinatorial checklist for air with migs_org + air me: + is_a: air + mixins: + - me + description: Combinatorial checklist for air with me + air mimarks_s: + is_a: air + mixins: + - mimarks_s + description: Combinatorial checklist for air with mimarks_s + air mimarks_c: + is_a: air + mixins: + - mimarks_c + description: Combinatorial checklist for air with mimarks_c + air misag: + is_a: air + mixins: + - misag + description: Combinatorial checklist for air with misag + air mimag: + is_a: air + mixins: + - mimag + description: Combinatorial checklist for air with mimag + air miuvig: + is_a: air + mixins: + - miuvig + description: Combinatorial checklist for air with miuvig + built environment migs_eu: + is_a: built environment + mixins: + - migs_eu + description: Combinatorial checklist for built environment with migs_eu + built environment migs_ba: + is_a: built environment + mixins: + - migs_ba + description: Combinatorial checklist for built environment with migs_ba + built environment migs_pl: + is_a: built environment + mixins: + - migs_pl + description: Combinatorial checklist for built environment with migs_pl + built environment migs_vi: + is_a: built environment + mixins: + - migs_vi + description: Combinatorial checklist for built environment with migs_vi + built environment migs_org: + is_a: built environment + mixins: + - migs_org + description: Combinatorial checklist for built environment with migs_org + built environment me: + is_a: built environment + mixins: + - me + description: Combinatorial checklist for built environment with me + built environment mimarks_s: + is_a: built environment + mixins: + - mimarks_s + description: Combinatorial checklist for built environment with mimarks_s + built environment mimarks_c: + is_a: built environment + mixins: + - mimarks_c + description: Combinatorial checklist for built environment with mimarks_c + built environment misag: + is_a: built environment + mixins: + - misag + description: Combinatorial checklist for built environment with misag + built environment mimag: + is_a: built environment + mixins: + - mimag + description: Combinatorial checklist for built environment with mimag + built environment miuvig: + is_a: built environment + mixins: + - miuvig + description: Combinatorial checklist for built environment with miuvig + host-associated migs_eu: + is_a: host-associated + mixins: + - migs_eu + description: Combinatorial checklist for host-associated with migs_eu + host-associated migs_ba: + is_a: host-associated + mixins: + - migs_ba + description: Combinatorial checklist for host-associated with migs_ba + host-associated migs_pl: + is_a: host-associated + mixins: + - migs_pl + description: Combinatorial checklist for host-associated with migs_pl + host-associated migs_vi: + is_a: host-associated + mixins: + - migs_vi + description: Combinatorial checklist for host-associated with migs_vi + host-associated migs_org: + is_a: host-associated + mixins: + - migs_org + description: Combinatorial checklist for host-associated with migs_org + host-associated me: + is_a: host-associated + mixins: + - me + description: Combinatorial checklist for host-associated with me + host-associated mimarks_s: + is_a: host-associated + mixins: + - mimarks_s + description: Combinatorial checklist for host-associated with mimarks_s + host-associated mimarks_c: + is_a: host-associated + mixins: + - mimarks_c + description: Combinatorial checklist for host-associated with mimarks_c + host-associated misag: + is_a: host-associated + mixins: + - misag + description: Combinatorial checklist for host-associated with misag + host-associated mimag: + is_a: host-associated + mixins: + - mimag + description: Combinatorial checklist for host-associated with mimag + host-associated miuvig: + is_a: host-associated + mixins: + - miuvig + description: Combinatorial checklist for host-associated with miuvig + human-associated migs_eu: + is_a: human-associated + mixins: + - migs_eu + description: Combinatorial checklist for human-associated with migs_eu + human-associated migs_ba: + is_a: human-associated + mixins: + - migs_ba + description: Combinatorial checklist for human-associated with migs_ba + human-associated migs_pl: + is_a: human-associated + mixins: + - migs_pl + description: Combinatorial checklist for human-associated with migs_pl + human-associated migs_vi: + is_a: human-associated + mixins: + - migs_vi + description: Combinatorial checklist for human-associated with migs_vi + human-associated migs_org: + is_a: human-associated + mixins: + - migs_org + description: Combinatorial checklist for human-associated with migs_org + human-associated me: + is_a: human-associated + mixins: + - me + description: Combinatorial checklist for human-associated with me + human-associated mimarks_s: + is_a: human-associated + mixins: + - mimarks_s + description: Combinatorial checklist for human-associated with mimarks_s + human-associated mimarks_c: + is_a: human-associated + mixins: + - mimarks_c + description: Combinatorial checklist for human-associated with mimarks_c + human-associated misag: + is_a: human-associated + mixins: + - misag + description: Combinatorial checklist for human-associated with misag + human-associated mimag: + is_a: human-associated + mixins: + - mimag + description: Combinatorial checklist for human-associated with mimag + human-associated miuvig: + is_a: human-associated + mixins: + - miuvig + description: Combinatorial checklist for human-associated with miuvig + human-gut migs_eu: + is_a: human-gut + mixins: + - migs_eu + description: Combinatorial checklist for human-gut with migs_eu + human-gut migs_ba: + is_a: human-gut + mixins: + - migs_ba + description: Combinatorial checklist for human-gut with migs_ba + human-gut migs_pl: + is_a: human-gut + mixins: + - migs_pl + description: Combinatorial checklist for human-gut with migs_pl + human-gut migs_vi: + is_a: human-gut + mixins: + - migs_vi + description: Combinatorial checklist for human-gut with migs_vi + human-gut migs_org: + is_a: human-gut + mixins: + - migs_org + description: Combinatorial checklist for human-gut with migs_org + human-gut me: + is_a: human-gut + mixins: + - me + description: Combinatorial checklist for human-gut with me + human-gut mimarks_s: + is_a: human-gut + mixins: + - mimarks_s + description: Combinatorial checklist for human-gut with mimarks_s + human-gut mimarks_c: + is_a: human-gut + mixins: + - mimarks_c + description: Combinatorial checklist for human-gut with mimarks_c + human-gut misag: + is_a: human-gut + mixins: + - misag + description: Combinatorial checklist for human-gut with misag + human-gut mimag: + is_a: human-gut + mixins: + - mimag + description: Combinatorial checklist for human-gut with mimag + human-gut miuvig: + is_a: human-gut + mixins: + - miuvig + description: Combinatorial checklist for human-gut with miuvig + human-oral migs_eu: + is_a: human-oral + mixins: + - migs_eu + description: Combinatorial checklist for human-oral with migs_eu + human-oral migs_ba: + is_a: human-oral + mixins: + - migs_ba + description: Combinatorial checklist for human-oral with migs_ba + human-oral migs_pl: + is_a: human-oral + mixins: + - migs_pl + description: Combinatorial checklist for human-oral with migs_pl + human-oral migs_vi: + is_a: human-oral + mixins: + - migs_vi + description: Combinatorial checklist for human-oral with migs_vi + human-oral migs_org: + is_a: human-oral + mixins: + - migs_org + description: Combinatorial checklist for human-oral with migs_org + human-oral me: + is_a: human-oral + mixins: + - me + description: Combinatorial checklist for human-oral with me + human-oral mimarks_s: + is_a: human-oral + mixins: + - mimarks_s + description: Combinatorial checklist for human-oral with mimarks_s + human-oral mimarks_c: + is_a: human-oral + mixins: + - mimarks_c + description: Combinatorial checklist for human-oral with mimarks_c + human-oral misag: + is_a: human-oral + mixins: + - misag + description: Combinatorial checklist for human-oral with misag + human-oral mimag: + is_a: human-oral + mixins: + - mimag + description: Combinatorial checklist for human-oral with mimag + human-oral miuvig: + is_a: human-oral + mixins: + - miuvig + description: Combinatorial checklist for human-oral with miuvig + human-skin migs_eu: + is_a: human-skin + mixins: + - migs_eu + description: Combinatorial checklist for human-skin with migs_eu + human-skin migs_ba: + is_a: human-skin + mixins: + - migs_ba + description: Combinatorial checklist for human-skin with migs_ba + human-skin migs_pl: + is_a: human-skin + mixins: + - migs_pl + description: Combinatorial checklist for human-skin with migs_pl + human-skin migs_vi: + is_a: human-skin + mixins: + - migs_vi + description: Combinatorial checklist for human-skin with migs_vi + human-skin migs_org: + is_a: human-skin + mixins: + - migs_org + description: Combinatorial checklist for human-skin with migs_org + human-skin me: + is_a: human-skin + mixins: + - me + description: Combinatorial checklist for human-skin with me + human-skin mimarks_s: + is_a: human-skin + mixins: + - mimarks_s + description: Combinatorial checklist for human-skin with mimarks_s + human-skin mimarks_c: + is_a: human-skin + mixins: + - mimarks_c + description: Combinatorial checklist for human-skin with mimarks_c + human-skin misag: + is_a: human-skin + mixins: + - misag + description: Combinatorial checklist for human-skin with misag + human-skin mimag: + is_a: human-skin + mixins: + - mimag + description: Combinatorial checklist for human-skin with mimag + human-skin miuvig: + is_a: human-skin + mixins: + - miuvig + description: Combinatorial checklist for human-skin with miuvig + human-vaginal migs_eu: + is_a: human-vaginal + mixins: + - migs_eu + description: Combinatorial checklist for human-vaginal with migs_eu + human-vaginal migs_ba: + is_a: human-vaginal + mixins: + - migs_ba + description: Combinatorial checklist for human-vaginal with migs_ba + human-vaginal migs_pl: + is_a: human-vaginal + mixins: + - migs_pl + description: Combinatorial checklist for human-vaginal with migs_pl + human-vaginal migs_vi: + is_a: human-vaginal + mixins: + - migs_vi + description: Combinatorial checklist for human-vaginal with migs_vi + human-vaginal migs_org: + is_a: human-vaginal + mixins: + - migs_org + description: Combinatorial checklist for human-vaginal with migs_org + human-vaginal me: + is_a: human-vaginal + mixins: + - me + description: Combinatorial checklist for human-vaginal with me + human-vaginal mimarks_s: + is_a: human-vaginal + mixins: + - mimarks_s + description: Combinatorial checklist for human-vaginal with mimarks_s + human-vaginal mimarks_c: + is_a: human-vaginal + mixins: + - mimarks_c + description: Combinatorial checklist for human-vaginal with mimarks_c + human-vaginal misag: + is_a: human-vaginal + mixins: + - misag + description: Combinatorial checklist for human-vaginal with misag + human-vaginal mimag: + is_a: human-vaginal + mixins: + - mimag + description: Combinatorial checklist for human-vaginal with mimag + human-vaginal miuvig: + is_a: human-vaginal + mixins: + - miuvig + description: Combinatorial checklist for human-vaginal with miuvig + hydrocarbon resources-cores migs_eu: + is_a: hydrocarbon resources-cores + mixins: + - migs_eu + description: Combinatorial checklist for hydrocarbon resources-cores with migs_eu + hydrocarbon resources-cores migs_ba: + is_a: hydrocarbon resources-cores + mixins: + - migs_ba + description: Combinatorial checklist for hydrocarbon resources-cores with migs_ba + hydrocarbon resources-cores migs_pl: + is_a: hydrocarbon resources-cores + mixins: + - migs_pl + description: Combinatorial checklist for hydrocarbon resources-cores with migs_pl + hydrocarbon resources-cores migs_vi: + is_a: hydrocarbon resources-cores + mixins: + - migs_vi + description: Combinatorial checklist for hydrocarbon resources-cores with migs_vi + hydrocarbon resources-cores migs_org: + is_a: hydrocarbon resources-cores + mixins: + - migs_org + description: Combinatorial checklist for hydrocarbon resources-cores with migs_org + hydrocarbon resources-cores me: + is_a: hydrocarbon resources-cores + mixins: + - me + description: Combinatorial checklist for hydrocarbon resources-cores with me + hydrocarbon resources-cores mimarks_s: + is_a: hydrocarbon resources-cores + mixins: + - mimarks_s + description: Combinatorial checklist for hydrocarbon resources-cores with mimarks_s + hydrocarbon resources-cores mimarks_c: + is_a: hydrocarbon resources-cores + mixins: + - mimarks_c + description: Combinatorial checklist for hydrocarbon resources-cores with mimarks_c + hydrocarbon resources-cores misag: + is_a: hydrocarbon resources-cores + mixins: + - misag + description: Combinatorial checklist for hydrocarbon resources-cores with misag + hydrocarbon resources-cores mimag: + is_a: hydrocarbon resources-cores + mixins: + - mimag + description: Combinatorial checklist for hydrocarbon resources-cores with mimag + hydrocarbon resources-cores miuvig: + is_a: hydrocarbon resources-cores + mixins: + - miuvig + description: Combinatorial checklist for hydrocarbon resources-cores with miuvig + hydrocarbon resources-fluids_swabs migs_eu: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - migs_eu + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + migs_eu + hydrocarbon resources-fluids_swabs migs_ba: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - migs_ba + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + migs_ba + hydrocarbon resources-fluids_swabs migs_pl: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - migs_pl + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + migs_pl + hydrocarbon resources-fluids_swabs migs_vi: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - migs_vi + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + migs_vi + hydrocarbon resources-fluids_swabs migs_org: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - migs_org + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + migs_org + hydrocarbon resources-fluids_swabs me: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - me + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + me + hydrocarbon resources-fluids_swabs mimarks_s: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - mimarks_s + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + mimarks_s + hydrocarbon resources-fluids_swabs mimarks_c: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - mimarks_c + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + mimarks_c + hydrocarbon resources-fluids_swabs misag: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - misag + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + misag + hydrocarbon resources-fluids_swabs mimag: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - mimag + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + mimag + hydrocarbon resources-fluids_swabs miuvig: + is_a: hydrocarbon resources-fluids_swabs + mixins: + - miuvig + description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with + miuvig + microbial mat_biofilm migs_eu: + is_a: microbial mat_biofilm + mixins: + - migs_eu + description: Combinatorial checklist for microbial mat_biofilm with migs_eu + microbial mat_biofilm migs_ba: + is_a: microbial mat_biofilm + mixins: + - migs_ba + description: Combinatorial checklist for microbial mat_biofilm with migs_ba + microbial mat_biofilm migs_pl: + is_a: microbial mat_biofilm + mixins: + - migs_pl + description: Combinatorial checklist for microbial mat_biofilm with migs_pl + microbial mat_biofilm migs_vi: + is_a: microbial mat_biofilm + mixins: + - migs_vi + description: Combinatorial checklist for microbial mat_biofilm with migs_vi + microbial mat_biofilm migs_org: + is_a: microbial mat_biofilm + mixins: + - migs_org + description: Combinatorial checklist for microbial mat_biofilm with migs_org + microbial mat_biofilm me: + is_a: microbial mat_biofilm + mixins: + - me + description: Combinatorial checklist for microbial mat_biofilm with me + microbial mat_biofilm mimarks_s: + is_a: microbial mat_biofilm + mixins: + - mimarks_s + description: Combinatorial checklist for microbial mat_biofilm with mimarks_s + microbial mat_biofilm mimarks_c: + is_a: microbial mat_biofilm + mixins: + - mimarks_c + description: Combinatorial checklist for microbial mat_biofilm with mimarks_c + microbial mat_biofilm misag: + is_a: microbial mat_biofilm + mixins: + - misag + description: Combinatorial checklist for microbial mat_biofilm with misag + microbial mat_biofilm mimag: + is_a: microbial mat_biofilm + mixins: + - mimag + description: Combinatorial checklist for microbial mat_biofilm with mimag + microbial mat_biofilm miuvig: + is_a: microbial mat_biofilm + mixins: + - miuvig + description: Combinatorial checklist for microbial mat_biofilm with miuvig + miscellaneous natural or artificial environment migs_eu: + is_a: miscellaneous natural or artificial environment + mixins: + - migs_eu + description: Combinatorial checklist for miscellaneous natural or artificial environment + with migs_eu + miscellaneous natural or artificial environment migs_ba: + is_a: miscellaneous natural or artificial environment + mixins: + - migs_ba + description: Combinatorial checklist for miscellaneous natural or artificial environment + with migs_ba + miscellaneous natural or artificial environment migs_pl: + is_a: miscellaneous natural or artificial environment + mixins: + - migs_pl + description: Combinatorial checklist for miscellaneous natural or artificial environment + with migs_pl + miscellaneous natural or artificial environment migs_vi: + is_a: miscellaneous natural or artificial environment + mixins: + - migs_vi + description: Combinatorial checklist for miscellaneous natural or artificial environment + with migs_vi + miscellaneous natural or artificial environment migs_org: + is_a: miscellaneous natural or artificial environment + mixins: + - migs_org + description: Combinatorial checklist for miscellaneous natural or artificial environment + with migs_org + miscellaneous natural or artificial environment me: + is_a: miscellaneous natural or artificial environment + mixins: + - me + description: Combinatorial checklist for miscellaneous natural or artificial environment + with me + miscellaneous natural or artificial environment mimarks_s: + is_a: miscellaneous natural or artificial environment + mixins: + - mimarks_s + description: Combinatorial checklist for miscellaneous natural or artificial environment + with mimarks_s + miscellaneous natural or artificial environment mimarks_c: + is_a: miscellaneous natural or artificial environment + mixins: + - mimarks_c + description: Combinatorial checklist for miscellaneous natural or artificial environment + with mimarks_c + miscellaneous natural or artificial environment misag: + is_a: miscellaneous natural or artificial environment + mixins: + - misag + description: Combinatorial checklist for miscellaneous natural or artificial environment + with misag + miscellaneous natural or artificial environment mimag: + is_a: miscellaneous natural or artificial environment + mixins: + - mimag + description: Combinatorial checklist for miscellaneous natural or artificial environment + with mimag + miscellaneous natural or artificial environment miuvig: + is_a: miscellaneous natural or artificial environment + mixins: + - miuvig + description: Combinatorial checklist for miscellaneous natural or artificial environment + with miuvig + plant-associated migs_eu: + is_a: plant-associated + mixins: + - migs_eu + description: Combinatorial checklist for plant-associated with migs_eu + plant-associated migs_ba: + is_a: plant-associated + mixins: + - migs_ba + description: Combinatorial checklist for plant-associated with migs_ba + plant-associated migs_pl: + is_a: plant-associated + mixins: + - migs_pl + description: Combinatorial checklist for plant-associated with migs_pl + plant-associated migs_vi: + is_a: plant-associated + mixins: + - migs_vi + description: Combinatorial checklist for plant-associated with migs_vi + plant-associated migs_org: + is_a: plant-associated + mixins: + - migs_org + description: Combinatorial checklist for plant-associated with migs_org + plant-associated me: + is_a: plant-associated + mixins: + - me + description: Combinatorial checklist for plant-associated with me + plant-associated mimarks_s: + is_a: plant-associated + mixins: + - mimarks_s + description: Combinatorial checklist for plant-associated with mimarks_s + plant-associated mimarks_c: + is_a: plant-associated + mixins: + - mimarks_c + description: Combinatorial checklist for plant-associated with mimarks_c + plant-associated misag: + is_a: plant-associated + mixins: + - misag + description: Combinatorial checklist for plant-associated with misag + plant-associated mimag: + is_a: plant-associated + mixins: + - mimag + description: Combinatorial checklist for plant-associated with mimag + plant-associated miuvig: + is_a: plant-associated + mixins: + - miuvig + description: Combinatorial checklist for plant-associated with miuvig + sediment migs_eu: + is_a: sediment + mixins: + - migs_eu + description: Combinatorial checklist for sediment with migs_eu + sediment migs_ba: + is_a: sediment + mixins: + - migs_ba + description: Combinatorial checklist for sediment with migs_ba + sediment migs_pl: + is_a: sediment + mixins: + - migs_pl + description: Combinatorial checklist for sediment with migs_pl + sediment migs_vi: + is_a: sediment + mixins: + - migs_vi + description: Combinatorial checklist for sediment with migs_vi + sediment migs_org: + is_a: sediment + mixins: + - migs_org + description: Combinatorial checklist for sediment with migs_org + sediment me: + is_a: sediment + mixins: + - me + description: Combinatorial checklist for sediment with me + sediment mimarks_s: + is_a: sediment + mixins: + - mimarks_s + description: Combinatorial checklist for sediment with mimarks_s + sediment mimarks_c: + is_a: sediment + mixins: + - mimarks_c + description: Combinatorial checklist for sediment with mimarks_c + sediment misag: + is_a: sediment + mixins: + - misag + description: Combinatorial checklist for sediment with misag + sediment mimag: + is_a: sediment + mixins: + - mimag + description: Combinatorial checklist for sediment with mimag + sediment miuvig: + is_a: sediment + mixins: + - miuvig + description: Combinatorial checklist for sediment with miuvig + soil migs_eu: + is_a: soil + mixins: + - migs_eu + description: Combinatorial checklist for soil with migs_eu + soil migs_ba: + is_a: soil + mixins: + - migs_ba + description: Combinatorial checklist for soil with migs_ba + soil migs_pl: + is_a: soil + mixins: + - migs_pl + description: Combinatorial checklist for soil with migs_pl + soil migs_vi: + is_a: soil + mixins: + - migs_vi + description: Combinatorial checklist for soil with migs_vi + soil migs_org: + is_a: soil + mixins: + - migs_org + description: Combinatorial checklist for soil with migs_org + soil me: + is_a: soil + mixins: + - me + description: Combinatorial checklist for soil with me + soil mimarks_s: + is_a: soil + mixins: + - mimarks_s + description: Combinatorial checklist for soil with mimarks_s + soil mimarks_c: + is_a: soil + mixins: + - mimarks_c + description: Combinatorial checklist for soil with mimarks_c + soil misag: + is_a: soil + mixins: + - misag + description: Combinatorial checklist for soil with misag + soil mimag: + is_a: soil + mixins: + - mimag + description: Combinatorial checklist for soil with mimag + soil miuvig: + is_a: soil + mixins: + - miuvig + description: Combinatorial checklist for soil with miuvig + wastewater_sludge migs_eu: + is_a: wastewater_sludge + mixins: + - migs_eu + description: Combinatorial checklist for wastewater_sludge with migs_eu + wastewater_sludge migs_ba: + is_a: wastewater_sludge + mixins: + - migs_ba + description: Combinatorial checklist for wastewater_sludge with migs_ba + wastewater_sludge migs_pl: + is_a: wastewater_sludge + mixins: + - migs_pl + description: Combinatorial checklist for wastewater_sludge with migs_pl + wastewater_sludge migs_vi: + is_a: wastewater_sludge + mixins: + - migs_vi + description: Combinatorial checklist for wastewater_sludge with migs_vi + wastewater_sludge migs_org: + is_a: wastewater_sludge + mixins: + - migs_org + description: Combinatorial checklist for wastewater_sludge with migs_org + wastewater_sludge me: + is_a: wastewater_sludge + mixins: + - me + description: Combinatorial checklist for wastewater_sludge with me + wastewater_sludge mimarks_s: + is_a: wastewater_sludge + mixins: + - mimarks_s + description: Combinatorial checklist for wastewater_sludge with mimarks_s + wastewater_sludge mimarks_c: + is_a: wastewater_sludge + mixins: + - mimarks_c + description: Combinatorial checklist for wastewater_sludge with mimarks_c + wastewater_sludge misag: + is_a: wastewater_sludge + mixins: + - misag + description: Combinatorial checklist for wastewater_sludge with misag + wastewater_sludge mimag: + is_a: wastewater_sludge + mixins: + - mimag + description: Combinatorial checklist for wastewater_sludge with mimag + wastewater_sludge miuvig: + is_a: wastewater_sludge + mixins: + - miuvig + description: Combinatorial checklist for wastewater_sludge with miuvig + water migs_eu: + is_a: water + mixins: + - migs_eu + description: Combinatorial checklist for water with migs_eu + water migs_ba: + is_a: water + mixins: + - migs_ba + description: Combinatorial checklist for water with migs_ba + water migs_pl: + is_a: water + mixins: + - migs_pl + description: Combinatorial checklist for water with migs_pl + water migs_vi: + is_a: water + mixins: + - migs_vi + description: Combinatorial checklist for water with migs_vi + water migs_org: + is_a: water + mixins: + - migs_org + description: Combinatorial checklist for water with migs_org + water me: + is_a: water + mixins: + - me + description: Combinatorial checklist for water with me + water mimarks_s: + is_a: water + mixins: + - mimarks_s + description: Combinatorial checklist for water with mimarks_s + water mimarks_c: + is_a: water + mixins: + - mimarks_c + description: Combinatorial checklist for water with mimarks_c + water misag: + is_a: water + mixins: + - misag + description: Combinatorial checklist for water with misag + water mimag: + is_a: water + mixins: + - mimag + description: Combinatorial checklist for water with mimag + water miuvig: + is_a: water + mixins: + - miuvig + description: Combinatorial checklist for water with miuvig +subsets: {} +enums: + investigation_type_enum: + permissible_values: + eukaryote: {} + bacteria_archaea: {} + plasmid: {} + virus: {} + organelle: {} + metagenome: {} + metatranscriptome: {} + mimarks-survey: {} + mimarks-specimen: {} + misag: {} + mimag: {} + miuvig: {} + env_package_enum: + permissible_values: + air: {} + built environment: {} + host-associated: {} + human-associated: {} + human-skin: {} + human-oral: {} + human-gut: {} + human-vaginal: {} + hydrocarbon resources-cores: {} + hydrocarbon resources-fluids/swabs: {} + microbial mat/biofilm: {} + misc environment: {} + plant-associated: {} + sediment: {} + soil: {} + wastewater/sludge: {} + water: {} + biotic_relationship_enum: + permissible_values: + free living: {} + parasitism: {} + commensalism: {} + symbiotic: {} + mutualism: {} + health_disease_stat_enum: + permissible_values: + healthy: {} + diseased: {} + dead: {} + disease-free: {} + undetermined: {} + recovering: {} + resolving: {} + pre-existing condition: {} + pathological: {} + life threatening: {} + congenital: {} + trophic_level_enum: + permissible_values: + autotroph: {} + carboxydotroph: {} + chemoautotroph: {} + chemoheterotroph: {} + chemolithoautotroph: {} + chemolithotroph: {} + chemoorganoheterotroph: {} + chemoorganotroph: {} + chemosynthetic: {} + chemotroph: {} + copiotroph: {} + diazotroph: {} + facultative: {} + heterotroph: {} + lithoautotroph: {} + lithoheterotroph: {} + lithotroph: {} + methanotroph: {} + methylotroph: {} + mixotroph: {} + obligate: {} + chemoautolithotroph: {} + oligotroph: {} + organoheterotroph: {} + organotroph: {} + photoautotroph: {} + photoheterotroph: {} + photolithoautotroph: {} + photolithotroph: {} + photosynthetic: {} + phototroph: {} + rel_to_oxygen_enum: + permissible_values: + aerobe: {} + anaerobe: {} + facultative: {} + microaerophilic: {} + microanaerobe: {} + obligate aerobe: {} + obligate anaerobe: {} + source_uvig_enum: + permissible_values: + metagenome (not viral targeted): {} + viral fraction metagenome (virome): {} + sequence-targeted metagenome: {} + metatranscriptome (not viral targeted): {} + viral fraction RNA metagenome (RNA virome): {} + sequence-targeted RNA metagenome: {} + microbial single amplified genome (SAG): {} + viral single amplified genome (vSAG): {} + isolate microbial genome: {} + other: {} + virus_enrich_appr_enum: + permissible_values: + filtration: {} + ultrafiltration: {} + centrifugation: {} + ultracentrifugation: {} + PEG Precipitation: {} + FeCl Precipitation: {} + CsCl density gradient: {} + DNAse: {} + RNAse: {} + targeted sequence capture: {} + other: {} + none: {} + lib_layout_enum: + permissible_values: + paired: {} + single: {} + vector: {} + other: {} + seq_meth_enum: + permissible_values: + 454 GS: {} + 454 GS 20: {} + 454 GS FLX: {} + 454 GS FLX+: {} + 454 GS FLX Titanium: {} + 454 GS Junior: {} + AB 310 Genetic Analyzer: {} + AB 3130 Genetic Analyzer: {} + AB 3130xL Genetic Analyzer: {} + AB 3500 Genetic Analyzer: {} + AB 3500xL Genetic Analyzer: {} + AB 3730 Genetic Analyzer: {} + AB 3730xL Genetic Analyzer: {} + AB 5500 Genetic Analyzer: {} + AB 5500xl Genetic Analyzer: {} + AB 5500xl-W Genetic Analysis System: {} + AB SOLiD System: {} + AB SOLiD System 2.0: {} + AB SOLiD System 3.0: {} + AB SOLiD 3 Plus System: {} + AB SOLiD 4 System: {} + AB SOLiD 4hq System: {} + AB SOLiD PI System: {} + BGISEQ-500: {} + GridION: {} + Illumina Genome Analyzer: {} + Illumina Genome Analyzer II: {} + Illumina Genome Analyzer IIx: {} + Illumina HiSeq 1000: {} + Illumina HiSeq 1500: {} + Illumina HiSeq 2000: {} + Illumina HiSeq 2500: {} + Illumina HiSeq 3000: {} + Illumina HiSeq 4000: {} + Illumina HiScanSQ: {} + Illumina MiSeq: {} + Illumina HiSeq X Five: {} + Illumina HiSeq X Ten: {} + Illumina NextSeq 500: {} + Illumina NextSeq 550: {} + Ion Torrent PGM: {} + Ion Torrent Proton: {} + Ion Torrent S5: {} + Ion Torrent S5 XL: {} + MinION: {} + PacBio RS: {} + PacBio RS II: {} + PromethION: {} + Sequel: {} + tax_ident_enum: + permissible_values: + 16S rRNA gene: {} + multi-marker approach: {} + other: {} + assembly_qual_enum: + permissible_values: + Finished genome: {} + High-quality draft genome: {} + Medium-quality draft genome: {} + Low-quality draft genome: {} + Genome fragment(s): {} + compl_score_enum: + permissible_values: + high: {} + med: {} + low;{percentage}: {} + compl_appr_enum: + permissible_values: + marker gene: {} + reference based: {} + other: {} + contam_screen_param_enum: + permissible_values: + ref db: {} + kmer: {} + coverage: {} + combination;{text: {} + integer}: {} + decontam_software_enum: + permissible_values: + checkm/refinem: {} + anvi'o: {} + prodege: {} + bbtools:decontaminate.sh: {} + acdc: {} + combination: {} + sort_tech_enum: + permissible_values: + flow cytometric cell sorting: {} + microfluidics: {} + lazer-tweezing: {} + optical manipulation: {} + micromanipulation: {} + other: {} + single_cell_lysis_appr_enum: + permissible_values: + chemical: {} + enzymatic: {} + physical: {} + combination: {} + bin_param_enum: + permissible_values: + homology search: {} + kmer: {} + coverage: {} + codon usage: {} + combination: {} + bin_software_enum: + permissible_values: + metabat: {} + maxbin: {} + concoct: {} + groupm: {} + esom: {} + metawatt: {} + combination: {} + other: {} + mag_cov_software_enum: + permissible_values: + bwa: {} + bbmap: {} + bowtie: {} + other: {} + pred_genome_type_enum: + permissible_values: + DNA: {} + dsDNA: {} + ssDNA: {} + RNA: {} + dsRNA: {} + ssRNA: {} + ssRNA (+): {} + ssRNA (-): {} + mixed: {} + uncharacterized: {} + pred_genome_struc_enum: + permissible_values: + segmented: {} + non-segmented: {} + undetermined: {} + host_pred_appr_enum: + permissible_values: + provirus: {} + host sequence similarity: {} + CRISPR spacer match: {} + kmer similarity: {} + co-occurrence: {} + combination: {} + other: {} + organism_count_enum: + permissible_values: + ATP: {} + MPN: {} + other: {} + oxy_stat_samp_enum: + permissible_values: + aerobic: {} + anaerobic: {} + other: {} + surf_material_enum: + permissible_values: + adobe: {} + carpet: {} + cinder blocks: {} + concrete: {} + hay bales: {} + glass: {} + metal: {} + paint: {} + plastic: {} + stainless steel: {} + stone: {} + stucco: {} + tile: {} + vinyl: {} + wood: {} + surf_air_cont_enum: + permissible_values: + dust: {} + organic matter: {} + particulate matter: {} + volatile organic compounds: {} + biological contaminants: {} + radon: {} + nutrients: {} + biocides: {} + build_occup_type_enum: + permissible_values: + office: {} + market: {} + restaurant: {} + residence: {} + school: {} + residential: {} + commercial: {} + low rise: {} + high rise: {} + wood framed: {} + health care: {} + airport: {} + sports complex: {} + indoor_space_enum: + permissible_values: + bedroom: {} + office: {} + bathroom: {} + foyer: {} + kitchen: {} + locker room: {} + hallway: {} + elevator: {} + indoor_surf_enum: + permissible_values: + cabinet: {} + ceiling: {} + counter top: {} + door: {} + shelving: {} + vent cover: {} + window: {} + wall: {} + filter_type_enum: + permissible_values: + particulate air filter: {} + chemical air filter: {} + low-MERV pleated media: {} + HEPA: {} + electrostatic: {} + gas-phase or ultraviolet air treatments: {} + heat_cool_type_enum: + permissible_values: + radiant system: {} + heat pump: {} + forced air system: {} + steam forced heat: {} + wood stove: {} + substructure_type_enum: + permissible_values: + crawlspace: {} + slab on grade: {} + basement: {} + building_setting_enum: + permissible_values: + urban: {} + suburban: {} + exurban: {} + rural: {} + light_type_enum: + permissible_values: + natural light: {} + electric light: {} + desk lamp: {} + flourescent lights: {} + none: {} + arch_struc_enum: + permissible_values: + building: {} + shed: {} + home: {} + ceil_cond_enum: + permissible_values: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + ceil_finish_mat_enum: + permissible_values: + drywall: {} + mineral fibre: {} + tiles: {} + PVC: {} + plasterboard: {} + metal: {} + fiberglass: {} + stucco: {} + mineral wool/calcium silicate: {} + wood: {} + ceil_texture_enum: + permissible_values: + crows feet: {} + crows-foot stomp: {} + double skip: {} + hawk and trowel: {} + knockdown: {} + popcorn: {} + orange peel: {} + rosebud stomp: {} + Santa-Fe texture: {} + skip trowel: {} + smooth: {} + stomp knockdown: {} + swirl: {} + ceil_type_enum: + permissible_values: + cathedral: {} + dropped: {} + concave: {} + barrel-shaped: {} + coffered: {} + cove: {} + stretched: {} + build_docs_enum: + permissible_values: + building information model: {} + commissioning report: {} + complaint logs: {} + contract administration: {} + cost estimate: {} + janitorial schedules or logs: {} + maintenance plans: {} + schedule: {} + sections: {} + shop drawings: {} + submittals: {} + ventilation system: {} + windows: {} + door_cond_enum: + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + door_direct_enum: + permissible_values: + inward: {} + outward: {} + sideways: {} + door_loc_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + door_mat_enum: + permissible_values: + aluminum: {} + cellular PVC: {} + engineered plastic: {} + fiberboard: {} + fiberglass: {} + metal: {} + thermoplastic alloy: {} + vinyl: {} + wood: {} + wood/plastic composite: {} + door_move_enum: + permissible_values: + collapsible: {} + folding: {} + revolving: {} + rolling shutter: {} + sliding: {} + swinging: {} + door_type_enum: + permissible_values: + composite: {} + metal: {} + wooden: {} + door_comp_type_enum: + permissible_values: + metal covered: {} + revolving: {} + sliding: {} + telescopic: {} + door_type_metal_enum: + permissible_values: + collapsible: {} + corrugated steel: {} + hollow: {} + rolling shutters: {} + steel plate: {} + door_type_wood_enum: + permissible_values: + bettened and ledged: {} + battened: {} + ledged and braced: {} + ledged and framed: {} + ledged, braced and frame: {} + framed and paneled: {} + glashed or sash: {} + flush: {} + louvered: {} + wire gauged: {} + drawings_enum: + permissible_values: + operation: {} + as built: {} + construction: {} + bid: {} + design: {} + building navigation map: {} + diagram: {} + sketch: {} + floor_cond_enum: + permissible_values: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + floor_finish_mat_enum: + permissible_values: + tile: {} + wood strip or parquet: {} + carpet: {} + rug: {} + laminate wood: {} + lineoleum: {} + vinyl composition tile: {} + sheet vinyl: {} + stone: {} + bamboo: {} + cork: {} + terrazo: {} + concrete: {} + none;specify unfinished: {} + sealed: {} + clear finish: {} + paint: {} + floor_water_mold_enum: + permissible_values: + mold odor: {} + wet floor: {} + water stains: {} + wall discoloration: {} + floor discoloration: {} + ceiling discoloration: {} + peeling paint or wallpaper: {} + bulging walls: {} + condensation: {} + floor_struc_enum: + permissible_values: + balcony: {} + floating floor: {} + glass floor: {} + raised floor: {} + sprung floor: {} + wood-framed: {} + concrete: {} + furniture_enum: + permissible_values: + cabinet: {} + chair: {} + desks: {} + handidness_enum: + permissible_values: + ambidexterity: {} + left handedness: {} + mixed-handedness: {} + right handedness: {} + heat_deliv_loc_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + int_wall_cond_enum: + permissible_values: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + mech_struc_enum: + permissible_values: + subway: {} + coach: {} + carriage: {} + elevator: {} + escalator: {} + boat: {} + train: {} + car: {} + bus: {} + occup_document_enum: + permissible_values: + automated count: {} + estimate: {} + manual count: {} + videos: {} + ext_wall_orient_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + northeast: {} + southeast: {} + southwest: {} + northwest: {} + ext_window_orient_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + northeast: {} + southeast: {} + southwest: {} + northwest: {} + pres_animal_enum: + permissible_values: + cat: {} + dog: {} + rodent: {} + snake: {} + other;{integer}: {} + quad_pos_enum: + permissible_values: + North side: {} + West side: {} + South side: {} + East side: {} + rel_samp_loc_enum: + permissible_values: + edge of car: {} + center of car: {} + under a seat: {} + room_condt_enum: + permissible_values: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + visible signs of mold/mildew: {} + room_loc_enum: + permissible_values: + corner room: {} + interior room: {} + exterior wall: {} + room_samp_pos_enum: + permissible_values: + north corner: {} + south corner: {} + west corner: {} + east corner: {} + northeast corner: {} + northwest corner: {} + southeast corner: {} + southwest corner: {} + center: {} + room_type_enum: + permissible_values: + attic: {} + bathroom: {} + closet: {} + conference room: {} + elevator: {} + examining room: {} + hallway: {} + kitchen: {} + mail room: {} + private office: {} + open office: {} + stairwell: {} + ',restroom': {} + lobby: {} + vestibule: {} + mechanical or electrical room: {} + data center: {} + laboratory_wet: {} + laboratory_dry: {} + gymnasium: {} + natatorium: {} + auditorium: {} + lockers: {} + cafe: {} + warehouse: {} + room_connected_enum: + permissible_values: + attic: {} + bathroom: {} + closet: {} + conference room: {} + elevator: {} + examining room: {} + hallway: {} + kitchen: {} + mail room: {} + office: {} + stairwell: {} + samp_weather_enum: + permissible_values: + clear sky: {} + cloudy: {} + foggy: {} + hail: {} + rain: {} + snow: {} + sleet: {} + sunny: {} + windy: {} + samp_floor_enum: + permissible_values: + 1st floor: {} + 2nd floor: {} + basement: {} + lobby: {} + season_use_enum: + permissible_values: + Spring: {} + Summer: {} + Fall: {} + Winter: {} + shading_device_cond_enum: + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + shading_device_type_enum: + permissible_values: + bahama shutters: {} + exterior roll blind: {} + gambrel awning: {} + hood awning: {} + porchroller awning: {} + sarasota shutters: {} + slatted aluminum: {} + solid aluminum awning: {} + sun screen: {} + tree: {} + trellis: {} + venetian awning: {} + specific_enum: + permissible_values: + operation: {} + as built: {} + construction: {} + bid: {} + design: {} + photos: {} + train_line_enum: + permissible_values: + red: {} + green: {} + orange: {} + train_stat_loc_enum: + permissible_values: + south station above ground: {} + south station underground: {} + south station amtrak: {} + forest hills: {} + riverside: {} + train_stop_loc_enum: + permissible_values: + end: {} + mid: {} + downtown: {} + vis_media_enum: + permissible_values: + photos: {} + videos: {} + commonly of the building: {} + site context (adjacent buildings, vegetation, terrain, streets): {} + interiors: {} + equipment: {} + 3D scans: {} + wall_const_type_enum: + permissible_values: + frame construction: {} + joisted masonry: {} + light noncombustible: {} + masonry noncombustible: {} + modified fire resistive: {} + fire resistive: {} + wall_finish_mat_enum: + permissible_values: + plaster: {} + gypsum plaster: {} + veneer plaster: {} + gypsum board: {} + tile: {} + terrazzo: {} + stone facing: {} + acoustical treatment: {} + wood: {} + metal: {} + masonry: {} + wall_loc_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + wall_surf_treatment_enum: + permissible_values: + painted: {} + wall paper: {} + no treatment: {} + paneling: {} + stucco: {} + fabric: {} + wall_texture_enum: + permissible_values: + crows feet: {} + crows-foot stomp: {} + ? '' + : {} + double skip: {} + hawk and trowel: {} + knockdown: {} + popcorn: {} + orange peel: {} + rosebud stomp: {} + Santa-Fe texture: {} + skip trowel: {} + smooth: {} + stomp knockdown: {} + swirl: {} + water_feat_type_enum: + permissible_values: + fountain: {} + pool: {} + standing feature: {} + stream: {} + waterfall: {} + weekday_enum: + permissible_values: + Monday: {} + Tuesday: {} + Wednesday: {} + Thursday: {} + Friday: {} + Saturday: {} + Sunday: {} + window_cond_enum: + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + window_cover_enum: + permissible_values: + blinds: {} + curtains: {} + none: {} + window_horiz_pos_enum: + permissible_values: + left: {} + middle: {} + right: {} + window_loc_enum: + permissible_values: + north: {} + south: {} + east: {} + west: {} + window_mat_enum: + permissible_values: + clad: {} + fiberglass: {} + metal: {} + vinyl: {} + wood: {} + window_type_enum: + permissible_values: + single-hung sash window: {} + horizontal sash window: {} + fixed window: {} + window_vert_pos_enum: + permissible_values: + bottom: {} + middle: {} + top: {} + low: {} + high: {} + biol_stat_enum: + permissible_values: + wild: {} + natural: {} + semi-natural: {} + inbred line: {} + breeder's line: {} + hybrid: {} + clonal selection: {} + mutant: {} + samp_capt_status_enum: + permissible_values: + active surveillance in response to an outbreak: {} + active surveillance not initiated by an outbreak: {} + farm sample: {} + market sample: {} + other: {} + host_sex_enum: + permissible_values: + male: {} + female: {} + neuter: {} + hermaphrodite: {} + not determined: {} + drug_usage_enum: + permissible_values: + month: {} + week: {} + day: {} + hour: {} + study_complt_stat_enum: + permissible_values: + non-compliance: {} + lost to follow up: {} + other-specify: {} + special_diet_enum: + permissible_values: + low carb: {} + reduced calorie: {} + vegetarian: {} + other(to be specified): {} + dominant_hand_enum: + permissible_values: + left: {} + right: {} + ambidextrous: {} + hcr_enum: + permissible_values: + Oil Reservoir: {} + Gas Reservoir: {} + Oil Sand: {} + Coalbed: {} + Shale: {} + Tight Oil Reservoir: {} + Tight Gas Reservoir: {} + other: {} + hc_produced_enum: + permissible_values: + Oil: {} + Gas-Condensate: {} + Gas: {} + Bitumen: {} + Coalbed Methane: {} + other: {} + lithology_enum: + permissible_values: + Basement: {} + Chalk: {} + Chert: {} + Coal: {} + Conglomerate: {} + Diatomite: {} + Dolomite: {} + Limestone: {} + Sandstone: {} + Shale: {} + Siltstone: {} + Volcanic: {} + other: {} + depos_env_enum: + permissible_values: + Continental - Alluvial: {} + Continental - Aeolian: {} + Continental - Fluvial: {} + Continental - Lacustrine: {} + Transitional - Deltaic: {} + Transitional - Tidal: {} + Transitional - Lagoonal: {} + Transitional - Beach: {} + Transitional - Lake: {} + Marine - Shallow: {} + Marine - Deep: {} + Marine - Reef: {} + Other - Evaporite: {} + Other - Glacial: {} + Other - Volcanic: {} + other: {} + hcr_geol_age_enum: + permissible_values: + Archean: {} + Cambrian: {} + Carboniferous: {} + Cenozoic: {} + Cretaceous: {} + Devonian: {} + Jurassic: {} + Mesozoic: {} + Neogene: {} + Ordovician: {} + Paleogene: {} + Paleozoic: {} + Permian: {} + Precambrian: {} + Proterozoic: {} + Silurian: {} + Triassic: {} + other: {} + sr_kerog_type_enum: + permissible_values: + Type I: {} + Type II: {} + Type III: {} + Type IV: {} + other: {} + sr_lithology_enum: + permissible_values: + Clastic: {} + Carbonate: {} + Coal: {} + Biosilicieous: {} + other: {} + sr_dep_env_enum: + permissible_values: + Lacustine: {} + Fluvioldeltaic: {} + Fluviomarine: {} + Marine: {} + other: {} + sr_geol_age_enum: + permissible_values: + Archean: {} + Cambrian: {} + Carboniferous: {} + Cenozoic: {} + Cretaceous: {} + Devonian: {} + Jurassic: {} + Mesozoic: {} + Neogene: {} + Ordovician: {} + Paleogene: {} + Paleozoic: {} + Permian: {} + Precambrian: {} + Proterozoic: {} + Silurian: {} + Triassic: {} + other: {} + samp_type_enum: + permissible_values: + core: {} + rock trimmings: {} + drill cuttings: {} + piping section: {} + coupon: {} + pigging debris: {} + solid deposit: {} + produced fluid: {} + produced water: {} + injected water: {} + water from treatment plant: {} + fresh water: {} + sea water: {} + drilling fluid: {} + procedural blank: {} + positive control: {} + negative control: {} + other: {} + samp_subtype_enum: + permissible_values: + oil phase: {} + water phase: {} + biofilm: {} + not applicable: {} + other: {} + samp_md_enum: + permissible_values: + DF: {} + RT: {} + KB: {} + MSL: {} + other: {} + add_recov_method_enum: + permissible_values: + Water Injection: {} + Dump Flood: {} + Gas Injection: {} + Wag Immiscible Injection: {} + Polymer Addition: {} + Surfactant Addition: {} + Not Applicable: {} + other;{timestamp}: {} + samp_collection_point_enum: + permissible_values: + well: {} + test well: {} + drilling rig: {} + wellhead: {} + separator: {} + storage tank: {} + other: {} + growth_habit_enum: + permissible_values: + erect: {} + semi-erect: {} + spreading: {} + prostrate: {} + plant_growth_med_enum: + permissible_values: + other artificial liquid medium: {} + other artificial solid medium: {} + peat moss: {} + perlite: {} + pumice: {} + sand: {} + soil: {} + vermiculite: {} + water: {} + plant_sex_enum: + permissible_values: + Androdioecious: {} + Androecious: {} + Androgynous: {} + Androgynomonoecious: {} + Andromonoecious: {} + Bisexual: {} + Dichogamous: {} + Diclinous: {} + Dioecious: {} + Gynodioecious: {} + Gynoecious: {} + Gynomonoecious: {} + Hermaphroditic: {} + Imperfect: {} + Monoclinous: {} + Monoecious: {} + Perfect: {} + Polygamodioecious: {} + Polygamomonoecious: {} + Polygamous: {} + Protandrous: {} + Protogynous: {} + Subandroecious: {} + Subdioecious: {} + Subgynoecious: {} + Synoecious: {} + Trimonoecious: {} + Trioecious: {} + Unisexual: {} + sediment_type_enum: + permissible_values: + biogenous: {} + cosmogenous: {} + hydrogenous: {} + lithogenous: {} + tidal_stage_enum: + permissible_values: + low tide: {} + ebb tide: {} + flood tide: {} + high tide: {} + cur_land_use_enum: + permissible_values: + cities: {} + farmstead: {} + industrial areas: {} + roads/railroads: {} + rock: {} + sand: {} + gravel: {} + mudflats: {} + salt flats: {} + badlands: {} + permanent snow or ice: {} + saline seeps: {} + mines/quarries: {} + oil waste areas: {} + small grains: {} + row crops: {} + vegetable crops: {} + horticultural plants (e.g. tulips): {} + marshlands (grass,sedges,rushes): {} + tundra (mosses,lichens): {} + rangeland: {} + pastureland (grasslands used for livestock grazing): {} + hayland: {} + meadows (grasses,alfalfa,fescue,bromegrass,timothy): {} + shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus): {} + successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries): {} + shrub crops (blueberries,nursery ornamentals,filberts): {} + vine crops (grapes): {} + conifers (e.g. pine,spruce,fir,cypress): {} + hardwoods (e.g. oak,hickory,elm,aspen): {} + intermixed hardwood and conifers: {} + tropical (e.g. mangrove,palms): {} + rainforest (evergreen forest receiving >406 cm annual rainfall): {} + swamp (permanent or semi-permanent water body dominated by woody plants): {} + crop trees (nuts,fruit,christmas trees,nursery trees): {} + tillage_enum: + permissible_values: + drill: {} + cutting disc: {} + ridge till: {} + strip tillage: {} + zonal tillage: {} + chisel: {} + tined: {} + mouldboard: {} + disc plough: {} + horizon_enum: + permissible_values: + O horizon: {} + A horizon: {} + E horizon: {} + B horizon: {} + C horizon: {} + R layer: {} + Permafrost: {} + fao_class_enum: + permissible_values: + Acrisols: {} + Andosols: {} + Arenosols: {} + Cambisols: {} + Chernozems: {} + Ferralsols: {} + Fluvisols: {} + Gleysols: {} + Greyzems: {} + Gypsisols: {} + Histosols: {} + Kastanozems: {} + Lithosols: {} + Luvisols: {} + Nitosols: {} + Phaeozems: {} + Planosols: {} + Podzols: {} + Podzoluvisols: {} + Rankers: {} + Regosols: {} + Rendzinas: {} + Solonchaks: {} + Solonetz: {} + Vertisols: {} + Yermosols: {} + profile_position_enum: + permissible_values: + summit: {} + shoulder: {} + backslope: {} + footslope: {} + toeslope: {} + drainage_class_enum: + permissible_values: + very poorly: {} + poorly: {} + somewhat poorly: {} + moderately well: {} + well: {} + excessively drained: {} From 60ba2e425ef6036a698a5c9eb007681ceb6493cf Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 15:06:35 -0700 Subject: [PATCH 4/7] update --- mixs6/Air.md | 64 +- mixs6/AirMe.md | 234 +++++++- mixs6/AirMigsBa.md | 299 +++++++++- mixs6/AirMigsEu.md | 299 +++++++++- mixs6/AirMigsOrg.md | 254 +++++++- mixs6/AirMigsPl.md | 269 ++++++++- mixs6/AirMigsVi.md | 294 ++++++++- mixs6/AirMimag.md | 314 +++++++++- mixs6/AirMimarksC.md | 199 ++++++- mixs6/AirMimarksS.md | 219 ++++++- mixs6/AirMisag.md | 319 +++++++++- mixs6/AirMiuvig.md | 384 +++++++++++- mixs6/BuiltEnvironment.md | 106 ++-- mixs6/BuiltEnvironmentMe.md | 276 +++++++-- mixs6/BuiltEnvironmentMigsBa.md | 341 +++++++++-- mixs6/BuiltEnvironmentMigsEu.md | 341 +++++++++-- mixs6/BuiltEnvironmentMigsOrg.md | 296 ++++++++-- mixs6/BuiltEnvironmentMigsPl.md | 311 ++++++++-- mixs6/BuiltEnvironmentMigsVi.md | 336 +++++++++-- mixs6/BuiltEnvironmentMimag.md | 356 +++++++++-- mixs6/BuiltEnvironmentMimarksC.md | 241 ++++++-- mixs6/BuiltEnvironmentMimarksS.md | 261 ++++++-- mixs6/BuiltEnvironmentMisag.md | 361 +++++++++-- mixs6/BuiltEnvironmentMiuvig.md | 426 +++++++++++-- mixs6/Core.md | 27 +- mixs6/Host-associated.md | 62 +- mixs6/Host-associatedMe.md | 232 +++++++- mixs6/Host-associatedMigsBa.md | 297 +++++++++- mixs6/Host-associatedMigsEu.md | 297 +++++++++- mixs6/Host-associatedMigsOrg.md | 252 +++++++- mixs6/Host-associatedMigsPl.md | 267 ++++++++- mixs6/Host-associatedMigsVi.md | 292 ++++++++- mixs6/Host-associatedMimag.md | 312 +++++++++- mixs6/Host-associatedMimarksC.md | 197 +++++- mixs6/Host-associatedMimarksS.md | 217 ++++++- mixs6/Host-associatedMisag.md | 317 +++++++++- mixs6/Host-associatedMiuvig.md | 382 +++++++++++- mixs6/Human-associated.md | 58 +- mixs6/Human-associatedMe.md | 228 ++++++- mixs6/Human-associatedMigsBa.md | 293 ++++++++- mixs6/Human-associatedMigsEu.md | 293 ++++++++- mixs6/Human-associatedMigsOrg.md | 248 +++++++- mixs6/Human-associatedMigsPl.md | 263 +++++++- mixs6/Human-associatedMigsVi.md | 288 ++++++++- mixs6/Human-associatedMimag.md | 308 +++++++++- mixs6/Human-associatedMimarksC.md | 193 +++++- mixs6/Human-associatedMimarksS.md | 213 ++++++- mixs6/Human-associatedMisag.md | 313 +++++++++- mixs6/Human-associatedMiuvig.md | 378 +++++++++++- mixs6/Human-gut.md | 58 +- mixs6/Human-gutMe.md | 228 ++++++- mixs6/Human-gutMigsBa.md | 293 ++++++++- mixs6/Human-gutMigsEu.md | 293 ++++++++- mixs6/Human-gutMigsOrg.md | 248 +++++++- mixs6/Human-gutMigsPl.md | 263 +++++++- mixs6/Human-gutMigsVi.md | 288 ++++++++- mixs6/Human-gutMimag.md | 308 +++++++++- mixs6/Human-gutMimarksC.md | 193 +++++- mixs6/Human-gutMimarksS.md | 213 ++++++- mixs6/Human-gutMisag.md | 313 +++++++++- mixs6/Human-gutMiuvig.md | 378 +++++++++++- mixs6/Human-oral.md | 58 +- mixs6/Human-oralMe.md | 228 ++++++- mixs6/Human-oralMigsBa.md | 293 ++++++++- mixs6/Human-oralMigsEu.md | 293 ++++++++- mixs6/Human-oralMigsOrg.md | 248 +++++++- mixs6/Human-oralMigsPl.md | 263 +++++++- mixs6/Human-oralMigsVi.md | 288 ++++++++- mixs6/Human-oralMimag.md | 308 +++++++++- mixs6/Human-oralMimarksC.md | 193 +++++- mixs6/Human-oralMimarksS.md | 213 ++++++- mixs6/Human-oralMisag.md | 313 +++++++++- mixs6/Human-oralMiuvig.md | 378 +++++++++++- mixs6/Human-skin.md | 58 +- mixs6/Human-skinMe.md | 228 ++++++- mixs6/Human-skinMigsBa.md | 293 ++++++++- mixs6/Human-skinMigsEu.md | 293 ++++++++- mixs6/Human-skinMigsOrg.md | 248 +++++++- mixs6/Human-skinMigsPl.md | 263 +++++++- mixs6/Human-skinMigsVi.md | 288 ++++++++- mixs6/Human-skinMimag.md | 308 +++++++++- mixs6/Human-skinMimarksC.md | 193 +++++- mixs6/Human-skinMimarksS.md | 213 ++++++- mixs6/Human-skinMisag.md | 313 +++++++++- mixs6/Human-skinMiuvig.md | 378 +++++++++++- mixs6/Human-vaginal.md | 58 +- mixs6/Human-vaginalMe.md | 228 ++++++- mixs6/Human-vaginalMigsBa.md | 293 ++++++++- mixs6/Human-vaginalMigsEu.md | 293 ++++++++- mixs6/Human-vaginalMigsOrg.md | 248 +++++++- mixs6/Human-vaginalMigsPl.md | 263 +++++++- mixs6/Human-vaginalMigsVi.md | 288 ++++++++- mixs6/Human-vaginalMimag.md | 308 +++++++++- mixs6/Human-vaginalMimarksC.md | 193 +++++- mixs6/Human-vaginalMimarksS.md | 213 ++++++- mixs6/Human-vaginalMisag.md | 313 +++++++++- mixs6/Human-vaginalMiuvig.md | 378 +++++++++++- mixs6/HydrocarbonResources-cores.md | 122 ++-- mixs6/HydrocarbonResources-coresMe.md | 292 +++++++-- mixs6/HydrocarbonResources-coresMigsBa.md | 357 +++++++++-- mixs6/HydrocarbonResources-coresMigsEu.md | 357 +++++++++-- mixs6/HydrocarbonResources-coresMigsOrg.md | 312 ++++++++-- mixs6/HydrocarbonResources-coresMigsPl.md | 327 ++++++++-- mixs6/HydrocarbonResources-coresMigsVi.md | 352 +++++++++-- mixs6/HydrocarbonResources-coresMimag.md | 372 ++++++++++-- mixs6/HydrocarbonResources-coresMimarksC.md | 257 ++++++-- mixs6/HydrocarbonResources-coresMimarksS.md | 277 +++++++-- mixs6/HydrocarbonResources-coresMisag.md | 377 ++++++++++-- mixs6/HydrocarbonResources-coresMiuvig.md | 442 ++++++++++++-- mixs6/HydrocarbonResources-fluidsSwabs.md | 128 ++-- mixs6/HydrocarbonResources-fluidsSwabsMe.md | 298 ++++++++-- .../HydrocarbonResources-fluidsSwabsMigsBa.md | 363 ++++++++++-- .../HydrocarbonResources-fluidsSwabsMigsEu.md | 363 ++++++++++-- ...HydrocarbonResources-fluidsSwabsMigsOrg.md | 318 ++++++++-- .../HydrocarbonResources-fluidsSwabsMigsPl.md | 333 +++++++++-- .../HydrocarbonResources-fluidsSwabsMigsVi.md | 358 +++++++++-- .../HydrocarbonResources-fluidsSwabsMimag.md | 378 ++++++++++-- ...ydrocarbonResources-fluidsSwabsMimarksC.md | 263 ++++++-- ...ydrocarbonResources-fluidsSwabsMimarksS.md | 283 +++++++-- .../HydrocarbonResources-fluidsSwabsMisag.md | 383 ++++++++++-- .../HydrocarbonResources-fluidsSwabsMiuvig.md | 448 ++++++++++++-- mixs6/Me.md | 86 ++- mixs6/MicrobialMatBiofilm.md | 134 +++-- mixs6/MicrobialMatBiofilmMe.md | 304 ++++++++-- mixs6/MicrobialMatBiofilmMigsBa.md | 369 ++++++++++-- mixs6/MicrobialMatBiofilmMigsEu.md | 369 ++++++++++-- mixs6/MicrobialMatBiofilmMigsOrg.md | 324 ++++++++-- mixs6/MicrobialMatBiofilmMigsPl.md | 339 +++++++++-- mixs6/MicrobialMatBiofilmMigsVi.md | 364 ++++++++++-- mixs6/MicrobialMatBiofilmMimag.md | 384 ++++++++++-- mixs6/MicrobialMatBiofilmMimarksC.md | 269 +++++++-- mixs6/MicrobialMatBiofilmMimarksS.md | 289 +++++++-- mixs6/MicrobialMatBiofilmMisag.md | 389 ++++++++++-- mixs6/MicrobialMatBiofilmMiuvig.md | 454 ++++++++++++-- mixs6/MigsBa.md | 112 +++- mixs6/MigsEu.md | 112 +++- mixs6/MigsOrg.md | 94 ++- mixs6/MigsPl.md | 100 +++- mixs6/MigsVi.md | 110 +++- mixs6/Mimag.md | 118 +++- mixs6/MimarksC.md | 72 ++- mixs6/MimarksS.md | 80 ++- mixs6/Misag.md | 120 +++- ...ellaneousNaturalOrArtificialEnvironment.md | 100 +++- ...laneousNaturalOrArtificialEnvironmentMe.md | 270 ++++++++- ...ousNaturalOrArtificialEnvironmentMigsBa.md | 335 ++++++++++- ...ousNaturalOrArtificialEnvironmentMigsEu.md | 335 ++++++++++- ...usNaturalOrArtificialEnvironmentMigsOrg.md | 290 ++++++++- ...ousNaturalOrArtificialEnvironmentMigsPl.md | 305 +++++++++- ...ousNaturalOrArtificialEnvironmentMigsVi.md | 330 ++++++++++- ...eousNaturalOrArtificialEnvironmentMimag.md | 350 ++++++++++- ...sNaturalOrArtificialEnvironmentMimarksC.md | 235 +++++++- ...sNaturalOrArtificialEnvironmentMimarksS.md | 255 +++++++- ...eousNaturalOrArtificialEnvironmentMisag.md | 355 ++++++++++- ...ousNaturalOrArtificialEnvironmentMiuvig.md | 420 ++++++++++++- mixs6/Miuvig.md | 146 ++++- mixs6/Plant-associated.md | 60 +- mixs6/Plant-associatedMe.md | 230 ++++++- mixs6/Plant-associatedMigsBa.md | 295 ++++++++- mixs6/Plant-associatedMigsEu.md | 295 ++++++++- mixs6/Plant-associatedMigsOrg.md | 250 +++++++- mixs6/Plant-associatedMigsPl.md | 265 ++++++++- mixs6/Plant-associatedMigsVi.md | 290 ++++++++- mixs6/Plant-associatedMimag.md | 310 +++++++++- mixs6/Plant-associatedMimarksC.md | 195 +++++- mixs6/Plant-associatedMimarksS.md | 215 ++++++- mixs6/Plant-associatedMisag.md | 315 +++++++++- mixs6/Plant-associatedMiuvig.md | 380 +++++++++++- mixs6/Sediment.md | 138 +++-- mixs6/SedimentMe.md | 308 ++++++++-- mixs6/SedimentMigsBa.md | 373 ++++++++++-- mixs6/SedimentMigsEu.md | 373 ++++++++++-- mixs6/SedimentMigsOrg.md | 328 ++++++++-- mixs6/SedimentMigsPl.md | 343 +++++++++-- mixs6/SedimentMigsVi.md | 368 ++++++++++-- mixs6/SedimentMimag.md | 388 ++++++++++-- mixs6/SedimentMimarksC.md | 273 +++++++-- mixs6/SedimentMimarksS.md | 293 +++++++-- mixs6/SedimentMisag.md | 393 ++++++++++-- mixs6/SedimentMiuvig.md | 458 ++++++++++++-- mixs6/Soil.md | 68 ++- mixs6/SoilMe.md | 238 +++++++- mixs6/SoilMigsBa.md | 303 +++++++++- mixs6/SoilMigsEu.md | 303 +++++++++- mixs6/SoilMigsOrg.md | 258 +++++++- mixs6/SoilMigsPl.md | 273 ++++++++- mixs6/SoilMigsVi.md | 298 +++++++++- mixs6/SoilMimag.md | 318 +++++++++- mixs6/SoilMimarksC.md | 203 ++++++- mixs6/SoilMimarksS.md | 223 ++++++- mixs6/SoilMisag.md | 323 +++++++++- mixs6/SoilMiuvig.md | 388 +++++++++++- mixs6/WastewaterSludge.md | 68 ++- mixs6/WastewaterSludgeMe.md | 238 +++++++- mixs6/WastewaterSludgeMigsBa.md | 303 +++++++++- mixs6/WastewaterSludgeMigsEu.md | 303 +++++++++- mixs6/WastewaterSludgeMigsOrg.md | 258 +++++++- mixs6/WastewaterSludgeMigsPl.md | 273 ++++++++- mixs6/WastewaterSludgeMigsVi.md | 298 +++++++++- mixs6/WastewaterSludgeMimag.md | 318 +++++++++- mixs6/WastewaterSludgeMimarksC.md | 203 ++++++- mixs6/WastewaterSludgeMimarksS.md | 223 ++++++- mixs6/WastewaterSludgeMisag.md | 323 +++++++++- mixs6/WastewaterSludgeMiuvig.md | 388 +++++++++++- mixs6/Water.md | 170 +++--- mixs6/WaterMe.md | 340 ++++++++--- mixs6/WaterMigsBa.md | 405 ++++++++++--- mixs6/WaterMigsEu.md | 405 ++++++++++--- mixs6/WaterMigsOrg.md | 360 ++++++++--- mixs6/WaterMigsPl.md | 375 +++++++++--- mixs6/WaterMigsVi.md | 400 ++++++++++--- mixs6/WaterMimag.md | 420 ++++++++++--- mixs6/WaterMimarksC.md | 305 +++++++--- mixs6/WaterMimarksS.md | 325 +++++++--- mixs6/WaterMisag.md | 425 ++++++++++--- mixs6/WaterMiuvig.md | 490 ++++++++++++--- mixs6/abs_air_humidity.md | 2 +- mixs6/adapters.md | 32 +- mixs6/air_temp.md | 2 +- mixs6/al_sat.md | 2 +- mixs6/alkalinity.md | 2 +- mixs6/alkyl_diethers.md | 2 +- mixs6/alt.md | 228 ++++++- mixs6/aminopept_act.md | 2 +- mixs6/ammonium.md | 2 +- mixs6/amount_light.md | 2 +- mixs6/annot.md | 31 +- mixs6/annual_precpt.md | 2 +- mixs6/annual_temp.md | 2 +- mixs6/api.md | 2 +- mixs6/assembly_name.md | 31 +- mixs6/assembly_qual.md | 31 +- mixs6/assembly_software.md | 32 +- mixs6/avg_dew_point.md | 2 +- mixs6/avg_occup.md | 2 +- mixs6/avg_temp.md | 2 +- mixs6/bac_prod.md | 2 +- mixs6/bac_resp.md | 2 +- mixs6/bacteria_carb_prod.md | 2 +- mixs6/barometric_press.md | 2 +- mixs6/benzene.md | 2 +- mixs6/bin_param.md | 24 +- mixs6/bin_software.md | 24 +- mixs6/biochem_oxygen_dem.md | 2 +- mixs6/biotic_relationship.md | 27 +- mixs6/bishomohopanol.md | 2 +- mixs6/bromide.md | 2 +- mixs6/built_struc_age.md | 2 +- mixs6/calcium.md | 2 +- mixs6/carb_dioxide.md | 2 +- mixs6/carb_monoxide.md | 2 +- mixs6/carb_nitro_ratio.md | 2 +- mixs6/ceil_area.md | 2 +- mixs6/ceil_thermal_mass.md | 2 +- mixs6/chem_oxygen_dem.md | 2 +- mixs6/chimera_check.md | 24 +- mixs6/chloride.md | 2 +- mixs6/chlorophyll.md | 2 +- mixs6/collection_date.md | 237 +++++++- mixs6/compl_appr.md | 25 +- mixs6/compl_score.md | 30 +- mixs6/compl_software.md | 30 +- mixs6/conduc.md | 2 +- mixs6/contam_score.md | 24 +- mixs6/contam_screen_input.md | 24 +- mixs6/contam_screen_param.md | 24 +- mixs6/decontam_software.md | 24 +- mixs6/density.md | 2 +- mixs6/depth.md | 227 ++++++- mixs6/detec_type.md | 23 +- mixs6/dew_point.md | 2 +- mixs6/diss_carb_dioxide.md | 2 +- mixs6/diss_hydrogen.md | 2 +- mixs6/diss_inorg_carb.md | 2 +- mixs6/diss_inorg_nitro.md | 2 +- mixs6/diss_inorg_phosp.md | 2 +- mixs6/diss_iron.md | 2 +- mixs6/diss_org_carb.md | 2 +- mixs6/diss_org_nitro.md | 2 +- mixs6/diss_oxygen.md | 2 +- mixs6/diss_oxygen_fluid.md | 2 +- mixs6/door_size.md | 2 +- mixs6/down_par.md | 2 +- mixs6/efficiency_percent.md | 2 +- mixs6/elev.md | 228 ++++++- mixs6/encoded_traits.md | 25 +- mixs6/env_broad_scale.md | 237 +++++++- mixs6/env_local_scale.md | 237 +++++++- mixs6/env_medium.md | 237 +++++++- mixs6/env_package.md | 34 +- mixs6/estimated_size.md | 28 +- mixs6/ethylbenzene.md | 2 +- mixs6/exp_duct.md | 2 +- mixs6/experimental_factor.md | 33 +- mixs6/extrachrom_elements.md | 26 +- mixs6/extreme_salinity.md | 2 +- mixs6/feat_pred.md | 31 +- mixs6/floor_age.md | 2 +- mixs6/floor_area.md | 2 +- mixs6/floor_thermal_mass.md | 2 +- mixs6/fluor.md | 2 +- mixs6/geo_loc_name.md | 238 +++++++- mixs6/glucosidase_act.md | 2 +- mixs6/hcr_fw_salinity.md | 2 +- mixs6/health_disease_stat.md | 25 +- mixs6/height_carper_fiber.md | 2 +- mixs6/host_age.md | 2 +- mixs6/host_blood_press_diast.md | 2 +- mixs6/host_blood_press_syst.md | 2 +- mixs6/host_body_mass_index.md | 2 +- mixs6/host_body_temp.md | 2 +- mixs6/host_dry_mass.md | 2 +- mixs6/host_height.md | 2 +- mixs6/host_length.md | 2 +- mixs6/host_pred_appr.md | 23 +- mixs6/host_pred_est_acc.md | 23 +- mixs6/host_pulse.md | 2 +- mixs6/host_spec_range.md | 28 +- mixs6/host_tot_mass.md | 2 +- mixs6/host_wet_mass.md | 2 +- mixs6/humidity.md | 2 +- mixs6/index.md | 559 +++++++++++++++++- mixs6/indust_eff_percent.md | 2 +- mixs6/inside_lux.md | 2 +- mixs6/investigation_type.md | 34 +- mixs6/isol_growth_condt.md | 28 +- mixs6/iwf.md | 2 +- mixs6/lat_lon.md | 238 +++++++- mixs6/lib_layout.md | 32 +- mixs6/lib_reads_seqd.md | 32 +- mixs6/lib_screen.md | 32 +- mixs6/lib_size.md | 32 +- mixs6/lib_vector.md | 32 +- mixs6/light_intensity.md | 2 +- mixs6/mag_cov_software.md | 24 +- mixs6/magnesium.md | 2 +- mixs6/mean_frict_vel.md | 2 +- mixs6/mean_peak_frict_vel.md | 2 +- mixs6/methane.md | 2 +- mixs6/microbial_biomass.md | 2 +- mixs6/mid.md | 27 +- mixs6/nitrate.md | 2 +- mixs6/nitrite.md | 2 +- mixs6/nitro.md | 2 +- mixs6/nucl_acid_amp.md | 33 +- mixs6/nucl_acid_ext.md | 33 +- mixs6/num_replicons.md | 25 +- mixs6/number_contig.md | 31 +- mixs6/occup_density_samp.md | 2 +- mixs6/org_carb.md | 2 +- mixs6/org_matter.md | 2 +- mixs6/org_nitro.md | 2 +- mixs6/owc_tvdss.md | 2 +- mixs6/oxygen.md | 2 +- mixs6/part_org_carb.md | 2 +- mixs6/part_org_nitro.md | 2 +- mixs6/pathogenicity.md | 27 +- mixs6/pcr_cond.md | 24 +- mixs6/pcr_primers.md | 24 +- mixs6/petroleum_hydrocarb.md | 2 +- mixs6/ph.md | 2 +- mixs6/phosphate.md | 2 +- mixs6/photon_flux.md | 2 +- mixs6/ploidy.md | 23 +- mixs6/potassium.md | 2 +- mixs6/pour_point.md | 2 +- mixs6/pred_genome_struc.md | 23 +- mixs6/pred_genome_type.md | 23 +- mixs6/pressure.md | 2 +- mixs6/primary_prod.md | 2 +- mixs6/prod_rate.md | 2 +- mixs6/project_name.md | 33 +- mixs6/propagation.md | 26 +- mixs6/reassembly_bin.md | 24 +- mixs6/redox_potential.md | 2 +- mixs6/ref_biomaterial.md | 31 +- mixs6/ref_db.md | 31 +- mixs6/rel_air_humidity.md | 2 +- mixs6/rel_humidity_out.md | 2 +- mixs6/rel_to_oxygen.md | 28 +- mixs6/room_air_exch_rate.md | 2 +- mixs6/root_med_ph.md | 2 +- mixs6/salinity.md | 2 +- mixs6/samp_collect_device.md | 33 +- mixs6/samp_mat_process.md | 33 +- mixs6/samp_salinity.md | 2 +- mixs6/samp_size.md | 35 +- mixs6/samp_store_temp.md | 2 +- mixs6/samp_time_out.md | 2 +- mixs6/samp_vol_we_dna_ext.md | 2 +- mixs6/sample_name.md | 34 +- mixs6/season_precpt.md | 2 +- mixs6/season_temp.md | 2 +- mixs6/seq_meth.md | 33 +- mixs6/seq_quality_check.md | 24 +- mixs6/silicate.md | 2 +- mixs6/sim_search_meth.md | 31 +- mixs6/single_cell_lysis_appr.md | 24 +- mixs6/single_cell_lysis_prot.md | 24 +- mixs6/size_frac.md | 27 +- mixs6/size_frac_low.md | 2 +- mixs6/size_frac_up.md | 2 +- mixs6/slope_aspect.md | 2 +- mixs6/slope_gradient.md | 2 +- mixs6/sludge_retent_time.md | 2 +- mixs6/sodium.md | 2 +- mixs6/solar_irradiance.md | 2 +- mixs6/soluble_react_phosp.md | 2 +- mixs6/sop.md | 33 +- mixs6/sort_tech.md | 24 +- mixs6/source_mat_id.md | 33 +- mixs6/source_uvig.md | 23 +- mixs6/specific_host.md | 27 +- mixs6/specific_humidity.md | 2 +- mixs6/submitted_to_insdc.md | 33 +- mixs6/subspecf_gen_lin.md | 28 +- mixs6/sulfate.md | 2 +- mixs6/sulfate_fw.md | 2 +- mixs6/sulfide.md | 2 +- mixs6/surf_humidity.md | 2 +- mixs6/surf_moisture.md | 2 +- mixs6/surf_moisture_ph.md | 2 +- mixs6/surf_temp.md | 2 +- mixs6/suspend_part_matter.md | 2 +- mixs6/tan.md | 2 +- mixs6/target_gene.md | 24 +- mixs6/target_subfragment.md | 24 +- mixs6/tax_class.md | 31 +- mixs6/tax_ident.md | 30 +- mixs6/temp.md | 2 +- mixs6/temp_out.md | 2 +- mixs6/texture.md | 2 +- mixs6/toluene.md | 2 +- mixs6/tot_carb.md | 2 +- mixs6/tot_depth_water_col.md | 2 +- mixs6/tot_diss_nitro.md | 2 +- mixs6/tot_inorg_nitro.md | 2 +- mixs6/tot_iron.md | 2 +- mixs6/tot_nitro.md | 2 +- mixs6/tot_nitro_content.md | 2 +- mixs6/tot_org_carb.md | 2 +- mixs6/tot_part_carb.md | 2 +- mixs6/tot_phosp.md | 2 +- mixs6/tot_phosphate.md | 2 +- mixs6/tot_sulfur.md | 2 +- mixs6/trna_ext_software.md | 25 +- mixs6/trnas.md | 25 +- mixs6/trophic_level.md | 25 +- mixs6/turbidity.md | 2 +- mixs6/tvdss_of_hcr_pressure.md | 2 +- mixs6/tvdss_of_hcr_temp.md | 2 +- mixs6/typ_occup_density.md | 2 +- mixs6/url.md | 34 +- mixs6/ventilation_rate.md | 2 +- mixs6/vfa.md | 2 +- mixs6/vfa_fw.md | 2 +- mixs6/vir_ident_software.md | 23 +- mixs6/virus_enrich_appr.md | 24 +- mixs6/votu_class_appr.md | 23 +- mixs6/votu_db.md | 23 +- mixs6/votu_seq_comp_appr.md | 23 +- mixs6/wall_area.md | 2 +- mixs6/wall_height.md | 2 +- mixs6/wall_thermal_mass.md | 2 +- mixs6/water_content.md | 2 +- mixs6/water_current.md | 2 +- mixs6/water_cut.md | 2 +- mixs6/water_feat_size.md | 2 +- mixs6/water_production_rate.md | 2 +- mixs6/wga_amp_appr.md | 24 +- mixs6/wga_amp_kit.md | 24 +- mixs6/wind_speed.md | 2 +- mixs6/x_16s_recover.md | 24 +- mixs6/x_16s_recover_software.md | 24 +- mixs6/xylene.md | 2 +- 475 files changed, 57426 insertions(+), 7700 deletions(-) diff --git a/mixs6/Air.md b/mixs6/Air.md index 1bbc0f52..6c73d101 100644 --- a/mixs6/Air.md +++ b/mixs6/Air.md @@ -7,7 +7,7 @@ air URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[AirMiuvig],[AirMisag],[AirMimarksS],[AirMimarksC],[AirMimag],[AirMigsVi],[AirMigsPl],[AirMigsOrg],[AirMigsEu],[AirMigsBa],[AirMe],[Air|barometric_press:string%20%3F;carb_dioxide:string%20%3F;carb_monoxide:string%20%3F;chem_administration:string%20%3F;humidity:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;organism_count:organism_count_enum%20%3F;oxygen:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;perturbation:string%20%3F;pollutants:string%20%3F;resp_part_matter:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;solar_irradiance:string%20%3F;temp:string%20%3F;ventilation_rate:string%20%3F;ventilation_type:string%20%3F;volatile_org_comp:string%20%3F;wind_direction:string%20%3F;wind_speed:string%20%3F]^-[AirMiuvig],[Air]^-[AirMisag],[Air]^-[AirMimarksS],[Air]^-[AirMimarksC],[Air]^-[AirMimag],[Air]^-[AirMigsVi],[Air]^-[AirMigsPl],[Air]^-[AirMigsOrg],[Air]^-[AirMigsEu],[Air]^-[AirMigsBa],[Air]^-[AirMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMiuvig],[AirMisag],[AirMimarksS],[AirMimarksC],[AirMimag],[AirMigsVi],[AirMigsPl],[AirMigsOrg],[AirMigsEu],[AirMigsBa],[AirMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -69,7 +105,7 @@ URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -85,7 +121,7 @@ URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -97,23 +133,23 @@ URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -129,5 +165,5 @@ URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md index dcaddab5..f43fbec5 100644 --- a/mixs6/AirMe.md +++ b/mixs6/AirMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with me URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[AirMe|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Me],[Air]^-[AirMe],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[AirMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Me],[Air]^-[AirMe],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,175 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsBa.md b/mixs6/AirMigsBa.md index 85ad2916..98553550 100644 --- a/mixs6/AirMigsBa.md +++ b/mixs6/AirMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with migs_ba URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[AirMigsBa|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsBa],[Air]^-[AirMigsBa],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[AirMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsBa],[Air]^-[AirMigsBa],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,240 @@ URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsEu.md b/mixs6/AirMigsEu.md index 4c797eee..3d02b098 100644 --- a/mixs6/AirMigsEu.md +++ b/mixs6/AirMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with migs_eu URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[AirMigsEu|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsEu],[Air]^-[AirMigsEu],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[AirMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsEu],[Air]^-[AirMigsEu],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,240 @@ URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md index 8f239c30..54cbac53 100644 --- a/mixs6/AirMigsOrg.md +++ b/mixs6/AirMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with migs_org URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[AirMigsOrg|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsOrg],[Air]^-[AirMigsOrg],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[AirMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsOrg],[Air]^-[AirMigsOrg],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,195 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsPl.md b/mixs6/AirMigsPl.md index 54f8f531..61101aab 100644 --- a/mixs6/AirMigsPl.md +++ b/mixs6/AirMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with migs_pl URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[AirMigsPl|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsPl],[Air]^-[AirMigsPl],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[AirMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsPl],[Air]^-[AirMigsPl],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,210 @@ URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMigsVi.md b/mixs6/AirMigsVi.md index 5c84c69a..d2e69c97 100644 --- a/mixs6/AirMigsVi.md +++ b/mixs6/AirMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with migs_vi URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[AirMigsVi|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MigsVi],[Air]^-[AirMigsVi],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[AirMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsVi],[Air]^-[AirMigsVi],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,235 @@ URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md index 9888fc5e..57e62106 100644 --- a/mixs6/AirMimag.md +++ b/mixs6/AirMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with mimag URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[AirMimag|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Mimag],[Air]^-[AirMimag],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[AirMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Mimag],[Air]^-[AirMimag],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,255 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMimarksC.md b/mixs6/AirMimarksC.md index 0c094042..29d27af6 100644 --- a/mixs6/AirMimarksC.md +++ b/mixs6/AirMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with mimarks_c URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[AirMimarksC|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MimarksC],[Air]^-[AirMimarksC],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[AirMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MimarksC],[Air]^-[AirMimarksC],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,140 @@ URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMimarksS.md b/mixs6/AirMimarksS.md index e3b35698..99fe9ddb 100644 --- a/mixs6/AirMimarksS.md +++ b/mixs6/AirMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with mimarks_s URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[AirMimarksS|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[MimarksS],[Air]^-[AirMimarksS],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[AirMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MimarksS],[Air]^-[AirMimarksS],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,160 @@ URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md index e15023af..a3582fa1 100644 --- a/mixs6/AirMisag.md +++ b/mixs6/AirMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with misag URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[AirMisag|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Misag],[Air]^-[AirMisag],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[AirMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Misag],[Air]^-[AirMisag],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,260 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md index 2cea0619..b855979d 100644 --- a/mixs6/AirMiuvig.md +++ b/mixs6/AirMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for air with miuvig URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[AirMiuvig|barometric_press(i):string%20%3F;carb_dioxide(i):string%20%3F;carb_monoxide(i):string%20%3F;chem_administration(i):string%20%3F;humidity(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxygen(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;solar_irradiance(i):string%20%3F;temp(i):string%20%3F;ventilation_rate(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;wind_speed(i):string%20%3F]uses%20-.->[Miuvig],[Air]^-[AirMiuvig],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[AirMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Miuvig],[Air]^-[AirMiuvig],[Air]) ## Parents @@ -22,29 +22,65 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) ### Inherited from air: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [barometric_press](barometric_press.md) OPT * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 millibar None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [carb_monoxide](carb_monoxide.md) OPT * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 parts per million None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [humidity](humidity.md) OPT * Description: Amount of water vapour in the air, at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -60,7 +96,7 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) * Example: aerobic None * [oxygen](oxygen.md) OPT * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 600 parts per million None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -76,7 +112,7 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) * Example: PM2.5;10 microgram per cubic meter None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -88,23 +124,23 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [solar_irradiance](solar_irradiance.md) OPT * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.36 kilowatts per square meter per day None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [ventilation_rate](ventilation_rate.md) OPT * Description: Ventilation rate of the system in the sampled premises - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 750 cubic meter per minute None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -120,5 +156,325 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) * Example: Northwest None * [wind_speed](wind_speed.md) OPT * Description: Speed of wind measured at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironment.md b/mixs6/BuiltEnvironment.md index 3d637627..c836e5b9 100644 --- a/mixs6/BuiltEnvironment.md +++ b/mixs6/BuiltEnvironment.md @@ -7,7 +7,7 @@ built environment URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[BuiltEnvironmentMiuvig],[BuiltEnvironmentMisag],[BuiltEnvironmentMimarksS],[BuiltEnvironmentMimarksC],[BuiltEnvironmentMimag],[BuiltEnvironmentMigsVi],[BuiltEnvironmentMigsPl],[BuiltEnvironmentMigsOrg],[BuiltEnvironmentMigsEu],[BuiltEnvironmentMigsBa],[BuiltEnvironmentMe],[BuiltEnvironment|surf_material:surf_material_enum%20%3F;surf_air_cont:surf_air_cont_enum%20%3F;rel_air_humidity:string%20%3F;abs_air_humidity:string%20%3F;surf_humidity:string%20%3F;air_temp:string%20%3F;surf_temp:string%20%3F;surf_moisture_ph:string%20%3F;build_occup_type:build_occup_type_enum%20%3F;surf_moisture:string%20%3F;dew_point:string%20%3F;carb_dioxide:string%20%3F;ventilation_type:string%20%3F;organism_count:organism_count_enum%20%3F;indoor_space:indoor_space_enum%20%3F;indoor_surf:indoor_surf_enum%20%3F;filter_type:filter_type_enum%20%3F;heat_cool_type:heat_cool_type_enum%20%3F;substructure_type:substructure_type_enum%20%3F;building_setting:building_setting_enum%20%3F;light_type:light_type_enum%20%3F;samp_sort_meth:string%20%3F;space_typ_state:string%20%3F;typ_occup_density:string%20%3F;occup_samp:string%20%3F;occup_density_samp:string%20%3F;address:string%20%3F;adj_room:string%20%3F;aero_struc:string%20%3F;amount_light:string%20%3F;arch_struc:arch_struc_enum%20%3F;avg_occup:string%20%3F;avg_dew_point:string%20%3F;avg_temp:string%20%3F;bathroom_count:string%20%3F;bedroom_count:string%20%3F;built_struc_age:string%20%3F;built_struc_set:string%20%3F;built_struc_type:string%20%3F;ceil_area:string%20%3F;ceil_cond:ceil_cond_enum%20%3F;ceil_finish_mat:ceil_finish_mat_enum%20%3F;ceil_water_mold:string%20%3F;ceil_struc:string%20%3F;ceil_texture:ceil_texture_enum%20%3F;ceil_thermal_mass:string%20%3F;ceil_type:ceil_type_enum%20%3F;cool_syst_id:string%20%3F;date_last_rain:string%20%3F;build_docs:build_docs_enum%20%3F;door_size:string%20%3F;door_cond:door_cond_enum%20%3F;door_direct:door_direct_enum%20%3F;door_loc:door_loc_enum%20%3F;door_mat:door_mat_enum%20%3F;door_move:door_move_enum%20%3F;door_water_mold:string%20%3F;door_type:door_type_enum%20%3F;door_comp_type:door_comp_type_enum%20%3F;door_type_metal:door_type_metal_enum%20%3F;door_type_wood:door_type_wood_enum%20%3F;drawings:drawings_enum%20%3F;elevator:string%20%3F;escalator:string%20%3F;exp_duct:string%20%3F;exp_pipe:string%20%3F;ext_door:string%20%3F;fireplace_type:string%20%3F;floor_age:string%20%3F;floor_area:string%20%3F;floor_cond:floor_cond_enum%20%3F;floor_count:string%20%3F;floor_finish_mat:floor_finish_mat_enum%20%3F;floor_water_mold:floor_water_mold_enum%20%3F;floor_struc:floor_struc_enum%20%3F;floor_thermal_mass:string%20%3F;freq_clean:string%20%3F;freq_cook:string%20%3F;furniture:furniture_enum%20%3F;gender_restroom:string%20%3F;hall_count:string%20%3F;handidness:handidness_enum%20%3F;heat_deliv_loc:heat_deliv_loc_enum%20%3F;heat_system_deliv_meth:string%20%3F;heat_system_id:string%20%3F;height_carper_fiber:string%20%3F;inside_lux:string%20%3F;int_wall_cond:int_wall_cond_enum%20%3F;last_clean:string%20%3F;max_occup:string%20%3F;mech_struc:mech_struc_enum%20%3F;number_plants:string%20%3F;number_pets:string%20%3F;number_resident:string%20%3F;occup_document:occup_document_enum%20%3F;ext_wall_orient:ext_wall_orient_enum%20%3F;ext_window_orient:ext_window_orient_enum%20%3F;rel_humidity_out:string%20%3F;pres_animal:pres_animal_enum%20%3F;quad_pos:quad_pos_enum%20%3F;rel_samp_loc:rel_samp_loc_enum%20%3F;room_air_exch_rate:string%20%3F;room_architec_element:string%20%3F;room_condt:room_condt_enum%20%3F;room_count:string%20%3F;room_dim:string%20%3F;room_door_dist:string%20%3F;room_loc:room_loc_enum%20%3F;room_moist_damage_hist:string%20%3F;room_net_area:string%20%3F;room_occup:string%20%3F;room_samp_pos:room_samp_pos_enum%20%3F;room_type:room_type_enum%20%3F;room_vol:string%20%3F;room_window_count:string%20%3F;room_connected:room_connected_enum%20%3F;room_hallway:string%20%3F;room_door_share:string%20%3F;room_wall_share:string%20%3F;samp_weather:samp_weather_enum%20%3F;samp_floor:samp_floor_enum%20%3F;samp_room_id:string%20%3F;samp_time_out:string%20%3F;season:string%20%3F;season_use:season_use_enum%20%3F;shading_device_cond:shading_device_cond_enum%20%3F;shading_device_loc:string%20%3F;shading_device_mat:string%20%3F;shading_device_water_mold:string%20%3F;shading_device_type:shading_device_type_enum%20%3F;specific_humidity:string%20%3F;specific:specific_enum%20%3F;temp_out:string%20%3F;train_line:train_line_enum%20%3F;train_stat_loc:train_stat_loc_enum%20%3F;train_stop_loc:train_stop_loc_enum%20%3F;vis_media:vis_media_enum%20%3F;wall_area:string%20%3F;wall_const_type:wall_const_type_enum%20%3F;wall_finish_mat:wall_finish_mat_enum%20%3F;wall_height:string%20%3F;wall_loc:wall_loc_enum%20%3F;wall_water_mold:string%20%3F;wall_surf_treatment:wall_surf_treatment_enum%20%3F;wall_texture:wall_texture_enum%20%3F;wall_thermal_mass:string%20%3F;water_feat_size:string%20%3F;water_feat_type:water_feat_type_enum%20%3F;weekday:weekday_enum%20%3F;window_size:string%20%3F;window_cond:window_cond_enum%20%3F;window_cover:window_cover_enum%20%3F;window_horiz_pos:window_horiz_pos_enum%20%3F;window_loc:window_loc_enum%20%3F;window_mat:window_mat_enum%20%3F;window_open_freq:string%20%3F;window_water_mold:string%20%3F;window_status:string%20%3F;window_type:window_type_enum%20%3F;window_vert_pos:window_vert_pos_enum%20%3F]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMiuvig],[BuiltEnvironmentMisag],[BuiltEnvironmentMimarksS],[BuiltEnvironmentMimarksC],[BuiltEnvironmentMimag],[BuiltEnvironmentMigsVi],[BuiltEnvironmentMigsPl],[BuiltEnvironmentMigsOrg],[BuiltEnvironmentMigsEu],[BuiltEnvironmentMigsBa],[BuiltEnvironmentMe],[QuantityValue]OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -49,11 +49,15 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -61,15 +65,15 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -93,7 +97,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -105,11 +109,11 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -129,7 +133,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -139,6 +143,10 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -147,9 +155,13 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -177,7 +189,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -199,17 +211,33 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -237,11 +265,11 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -261,7 +289,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -283,6 +311,10 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -309,7 +341,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -321,7 +353,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -331,6 +363,10 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -357,7 +393,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -381,11 +417,11 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -393,7 +429,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -477,7 +513,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -521,7 +557,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -533,7 +569,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -541,19 +577,19 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -569,7 +605,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -581,7 +617,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -593,7 +629,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -609,7 +645,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -617,7 +653,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled diff --git a/mixs6/BuiltEnvironmentMe.md b/mixs6/BuiltEnvironmentMe.md index 70e78e19..4b33e069 100644 --- a/mixs6/BuiltEnvironmentMe.md +++ b/mixs6/BuiltEnvironmentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with me URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmentMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[BuiltEnvironmentMe|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%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+![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[BuiltEnvironmentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):tra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## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,173 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsBa.md b/mixs6/BuiltEnvironmentMigsBa.md index f9a56c4d..f68d3071 100644 --- a/mixs6/BuiltEnvironmentMigsBa.md +++ b/mixs6/BuiltEnvironmentMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with migs_ba URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[BuiltEnvironmentMigsBa|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[BuiltEnvironmentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,238 @@ URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsEu.md b/mixs6/BuiltEnvironmentMigsEu.md index 24c89376..9871f7a7 100644 --- a/mixs6/BuiltEnvironmentMigsEu.md +++ b/mixs6/BuiltEnvironmentMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with migs_eu URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[BuiltEnvironmentMigsEu|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[BuiltEnvironmentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,238 @@ URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsOrg.md b/mixs6/BuiltEnvironmentMigsOrg.md index e27f8237..7827e881 100644 --- a/mixs6/BuiltEnvironmentMigsOrg.md +++ b/mixs6/BuiltEnvironmentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with migs_org URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[BuiltEnvironmentMigsOrg|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[BuiltEnvironmentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,193 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsPl.md b/mixs6/BuiltEnvironmentMigsPl.md index 6edb111f..72596b81 100644 --- a/mixs6/BuiltEnvironmentMigsPl.md +++ b/mixs6/BuiltEnvironmentMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with migs_pl URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[BuiltEnvironmentMigsPl|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[BuiltEnvironmentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,208 @@ URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsVi.md b/mixs6/BuiltEnvironmentMigsVi.md index b47e32ec..106076ee 100644 --- a/mixs6/BuiltEnvironmentMigsVi.md +++ b/mixs6/BuiltEnvironmentMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with migs_vi URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[BuiltEnvironmentMigsVi|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[BuiltEnvironmentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,233 @@ URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/BuiltEnvironmentMimag.md b/mixs6/BuiltEnvironmentMimag.md index 9bf0f85e..602bb639 100644 --- a/mixs6/BuiltEnvironmentMimag.md +++ b/mixs6/BuiltEnvironmentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with mimag URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnvironmentMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[BuiltEnvironmentMimag|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Mimag],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[BuiltEnvironmentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Mimag],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,253 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimarksC.md b/mixs6/BuiltEnvironmentMimarksC.md index baa22c03..cd61e641 100644 --- a/mixs6/BuiltEnvironmentMimarksC.md +++ b/mixs6/BuiltEnvironmentMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with mimarks_c URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[BuiltEnvironmentMimarksC|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[BuiltEnvironmentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,138 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvi * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimarksS.md b/mixs6/BuiltEnvironmentMimarksS.md index c4841229..f4b6a99a 100644 --- a/mixs6/BuiltEnvironmentMimarksS.md +++ b/mixs6/BuiltEnvironmentMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with mimarks_s URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[BuiltEnvironmentMimarksS|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[BuiltEnvironmentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,158 @@ URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvi * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMisag.md b/mixs6/BuiltEnvironmentMisag.md index 19fd53b7..ea0bec0d 100644 --- a/mixs6/BuiltEnvironmentMisag.md +++ b/mixs6/BuiltEnvironmentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with misag URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnvironmentMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[BuiltEnvironmentMisag|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Misag],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[BuiltEnvironmentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Misag],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,258 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMiuvig.md b/mixs6/BuiltEnvironmentMiuvig.md index 83e88792..a1905895 100644 --- a/mixs6/BuiltEnvironmentMiuvig.md +++ b/mixs6/BuiltEnvironmentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for built environment with miuvig URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnvironmentMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[BuiltEnvironmentMiuvig|surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;rel_air_humidity(i):string%20%3F;abs_air_humidity(i):string%20%3F;surf_humidity(i):string%20%3F;air_temp(i):string%20%3F;surf_temp(i):string%20%3F;surf_moisture_ph(i):string%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;surf_moisture(i):string%20%3F;dew_point(i):string%20%3F;carb_dioxide(i):string%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):string%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):string%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;amount_light(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):string%20%3F;avg_dew_point(i):string%20%3F;avg_temp(i):string%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_age(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_area(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_thermal_mass(i):string%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_size(i):string%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_duct(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_age(i):string%20%3F;floor_area(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;floor_thermal_mass(i):string%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;height_carper_fiber(i):string%20%3F;inside_lux(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;rel_humidity_out(i):string%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_air_exch_rate(i):string%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):string%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific_humidity(i):string%20%3F;specific(i):specific_enum%20%3F;temp_out(i):string%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_area(i):string%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_height(i):string%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;wall_thermal_mass(i):string%20%3F;water_feat_size(i):string%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Miuvig],[BuiltEnvironment]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[BuiltEnvironmentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Miuvig],[BuiltEnvironment]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * [abs_air_humidity](abs_air_humidity.md) OPT * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 9 gram per gram None * [address](address.md) OPT * Description: The street name and building number where the sampling occurred. @@ -40,11 +40,15 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: plane None * [air_temp](air_temp.md) OPT * Description: Temperature of the air at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amount_light](amount_light.md) OPT * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [arch_struc](arch_struc.md) OPT * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction @@ -52,15 +56,15 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: shed None * [avg_dew_point](avg_dew_point.md) OPT * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25.5 degree Celsius None * [avg_occup](avg_occup.md) OPT * Description: Daily average occupancy of room - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 2 None * [avg_temp](avg_temp.md) OPT * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None * [bathroom_count](bathroom_count.md) OPT * Description: The number of bathrooms in the building @@ -84,7 +88,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: rural None * [built_struc_age](built_struc_age.md) OPT * Description: The age of the built structure since construction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 None * [built_struc_set](built_struc_set.md) OPT * Description: The characterization of the location of the built structure as high or low human density @@ -96,11 +100,11 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [carb_dioxide](carb_dioxide.md) OPT * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 410 parts per million None * [ceil_area](ceil_area.md) OPT * Description: The area of the ceiling space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 square meter None * [ceil_cond](ceil_cond.md) OPT * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -120,7 +124,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [ceil_thermal_mass](ceil_thermal_mass.md) OPT * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [ceil_type](ceil_type.md) OPT * Description: The type of ceiling according to the ceiling's appearance or construction @@ -130,6 +134,10 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the ceiling * range: [String](types/String.md) * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier * range: [String](types/String.md) @@ -138,9 +146,13 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The date of the last time it rained * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dew_point](dew_point.md) OPT * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 degree Celsius None * [door_comp_type](door_comp_type.md) OPT * Description: The composite type of the door @@ -168,7 +180,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: swinging None * [door_size](door_size.md) OPT * Description: The size of the door - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 square meter None * [door_type](door_type.md) OPT * Description: The type of door material @@ -190,17 +202,33 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents * range: * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [elevator](elevator.md) OPT * Description: The number of elevators within the built structure * range: [String](types/String.md) * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [escalator](escalator.md) OPT * Description: The number of escalators within the built structure * range: [String](types/String.md) * Example: 4 None * [exp_duct](exp_duct.md) OPT * Description: The amount of exposed ductwork in the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [exp_pipe](exp_pipe.md) OPT * Description: The number of exposed pipes in the room @@ -228,11 +256,11 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood burning None * [floor_age](floor_age.md) OPT * Description: The time period since installment of the carpet or flooring - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_area](floor_area.md) OPT * Description: The area of the floor space within the room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_cond](floor_cond.md) OPT * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -252,7 +280,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: concrete None * [floor_thermal_mass](floor_thermal_mass.md) OPT * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [floor_water_mold](floor_water_mold.md) OPT * Description: Signs of the presence of mold or mildew in a room @@ -274,6 +302,10 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The gender type of the restroom * range: [String](types/String.md) * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hall_count](hall_count.md) OPT * Description: The total count of hallways and cooridors in the built structure * range: [String](types/String.md) @@ -300,7 +332,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [height_carper_fiber](height_carper_fiber.md) OPT * Description: The average carpet fiber height in the indoor environment - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [indoor_space](indoor_space.md) OPT * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used @@ -312,7 +344,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wall None * [inside_lux](inside_lux.md) OPT * Description: The recorded value at sampling time (power density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [int_wall_cond](int_wall_cond.md) OPT * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas @@ -322,6 +354,10 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: The last time the floor was cleaned (swept, mopped, vacuumed) * range: [String](types/String.md) * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_type](light_type.md) OPT * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light * range: @@ -348,7 +384,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [occup_density_samp](occup_density_samp.md) OPT * Description: Average number of occupants at time of sampling per square footage - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [occup_document](occup_document.md) OPT * Description: The type of documentation of occupancy @@ -372,11 +408,11 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: West side None * [rel_air_humidity](rel_air_humidity.md) OPT * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 80% None * [rel_humidity_out](rel_humidity_out.md) OPT * Description: The recorded outside relative humidity value at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12 per kilogram of air None * [rel_samp_loc](rel_samp_loc.md) OPT * Description: The sampling location within the train car @@ -384,7 +420,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: center of car None * [room_air_exch_rate](room_air_exch_rate.md) OPT * Description: The rate at which outside air replaces indoor air in a given space - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [room_architec_element](room_architec_element.md) OPT * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure @@ -468,7 +504,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: None * [samp_time_out](samp_time_out.md) OPT * Description: The recent and long term history of outside sampling - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: None * [samp_weather](samp_weather.md) OPT * Description: The weather on the sampling day @@ -512,7 +548,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: construction None * [specific_humidity](specific_humidity.md) OPT * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 per kilogram of air None * [substructure_type](substructure_type.md) OPT * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level @@ -524,7 +560,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: radon None * [surf_humidity](surf_humidity.md) OPT * Description: Surfaces: water activity as a function of air and material moisture - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10% None * [surf_material](surf_material.md) OPT * Description: Surface materials at the point of sampling @@ -532,19 +568,19 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [surf_moisture](surf_moisture.md) OPT * Description: Water held on a surface - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.01 gram per square meter None * [surf_moisture_ph](surf_moisture_ph.md) OPT * Description: ph measurement of surface - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7 None * [surf_temp](surf_temp.md) OPT * Description: Temperature of the surface at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [temp_out](temp_out.md) OPT * Description: The recorded temperature value at sampling time outside - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 degree Celsius None * [train_line](train_line.md) OPT * Description: The subway line name @@ -560,7 +596,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: end None * [typ_occup_density](typ_occup_density.md) OPT * Description: Customary or normal density of occupants - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 25 None * [ventilation_type](ventilation_type.md) OPT * Description: Ventilation system used in the sampled premises @@ -572,7 +608,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 3D scans None * [wall_area](wall_area.md) OPT * Description: The total area of the sampled room's walls - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_const_type](wall_const_type.md) OPT * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. @@ -584,7 +620,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: wood None * [wall_height](wall_height.md) OPT * Description: The average height of the walls in the sampled room - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_loc](wall_loc.md) OPT * Description: The relative location of the wall within the room @@ -600,7 +636,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: popcorn None * [wall_thermal_mass](wall_thermal_mass.md) OPT * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wall_water_mold](wall_water_mold.md) OPT * Description: Signs of the presence of mold or mildew on a wall @@ -608,7 +644,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Example: no presence of mold visible None * [water_feat_size](water_feat_size.md) OPT * Description: The size of the water feature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_feat_type](water_feat_type.md) OPT * Description: The type of water feature present within the building being sampled @@ -662,3 +698,323 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * Description: Signs of the presence of mold or mildew on the window. * range: [String](types/String.md) * Example: no presence of mold visible None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Core.md b/mixs6/Core.md index 3efff02d..37ab3fec 100644 --- a/mixs6/Core.md +++ b/mixs6/Core.md @@ -2,29 +2,12 @@ # Class: Core -core package +Core package. Do not use this directly, this is used to build other packages URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[CoreMiuvig],[CoreMisag],[CoreMimarksS],[CoreMimarksC],[CoreMimag],[CoreMigsVi],[CoreMigsPl],[CoreMigsOrg],[CoreMigsEu],[CoreMigsBa],[CoreMe],[Core|submitted_to_insdc:string%20%3F;investigation_type:investigation_type_enum%20%3F;sample_name:string%20%3F;project_name:string%20%3F;experimental_factor:string%20%3F;lat_lon:string%20%3F;depth:string%20%3F;alt:string%20%3F;elev:string%20%3F;geo_loc_name:string%20%3F;collection_date:string%20%3F;env_broad_scale:string%20%3F;env_local_scale:string%20%3F;env_medium:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;samp_size:string%20%3F;source_uvig:source_uvig_enum%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string%20%3F;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum%20%3F;seq_quality_check:string%20%3F;chimera_check:string%20%3F;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;contam_score:string%20%3F;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string%20%3F;pred_genome_type:pred_genome_type_enum%20%3F;pred_genome_struc:pred_genome_struc_enum%20%3F;detec_type:string%20%3F;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F]^-[CoreMiuvig],[Core]^-[CoreMisag],[Core]^-[CoreMimarksS],[Core]^-[CoreMimarksC],[Core]^-[CoreMimag],[Core]^-[CoreMigsVi],[Core]^-[CoreMigsPl],[Core]^-[CoreMigsOrg],[Core]^-[CoreMigsEu],[Core]^-[CoreMigsBa],[Core]^-[CoreMe]) - -## Children - - * [CoreMe](CoreMe.md) - Combinatorial checklist for core with me - * [CoreMigsBa](CoreMigsBa.md) - Combinatorial checklist for core with migs_ba - * [CoreMigsEu](CoreMigsEu.md) - Combinatorial checklist for core with migs_eu - * [CoreMigsOrg](CoreMigsOrg.md) - Combinatorial checklist for core with migs_org - * [CoreMigsPl](CoreMigsPl.md) - Combinatorial checklist for core with migs_pl - * [CoreMigsVi](CoreMigsVi.md) - Combinatorial checklist for core with migs_vi - * [CoreMimag](CoreMimag.md) - Combinatorial checklist for core with mimag - * [CoreMimarksC](CoreMimarksC.md) - Combinatorial checklist for core with mimarks_c - * [CoreMimarksS](CoreMimarksS.md) - Combinatorial checklist for core with mimarks_s - * [CoreMisag](CoreMisag.md) - Combinatorial checklist for core with misag - * [CoreMiuvig](CoreMiuvig.md) - Combinatorial checklist for core with miuvig - -## Referenced by class - +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue]OPT * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annot](annot.md) OPT * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter @@ -113,7 +96,7 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * Example: independent sequence (UViG) None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [encoded_traits](encoded_traits.md) OPT * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage @@ -285,7 +268,7 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * Example: filtering of seawater, storing samples in ethanol None * [samp_size](samp_size.md) OPT * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 liter None * [sample_name](sample_name.md) OPT * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. diff --git a/mixs6/Host-associated.md b/mixs6/Host-associated.md index a107b9f9..5f438a70 100644 --- a/mixs6/Host-associated.md +++ b/mixs6/Host-associated.md @@ -7,7 +7,7 @@ host-associated URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Host-associatedMiuvig],[Host-associatedMisag],[Host-associatedMimarksS],[Host-associatedMimarksC],[Host-associatedMimag],[Host-associatedMigsVi],[Host-associatedMigsPl],[Host-associatedMigsOrg],[Host-associatedMigsEu],[Host-associatedMigsBa],[Host-associatedMe],[Host-associated|ances_data:string%20%3F;biol_stat:biol_stat_enum%20%3F;genetic_mod:string%20%3F;host_common_name:string%20%3F;samp_capt_status:samp_capt_status_enum%20%3F;samp_dis_stage:string%20%3F;host_taxid:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_life_stage:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;chem_administration:string%20%3F;host_body_habitat:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_length:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_growth_cond:string%20%3F;host_substrate:string%20%3F;host_family_relationship:string%20%3F;host_infra_specific_name:string%20%3F;host_infra_specific_rank:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_dry_mass:string%20%3F;host_blood_press_diast:string%20%3F;host_blood_press_syst:string%20%3F;host_color:string%20%3F;host_shape:string%20%3F;gravidity:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Host-associatedMiuvig],[Host-associated]^-[Host-associatedMisag],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]^-[Host-associatedMimag],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]^-[Host-associatedMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMiuvig],[Host-associatedMisag],[Host-associatedMimarksS],[Host-associatedMimarksC],[Host-associatedMimag],[Host-associatedMigsVi],[Host-associatedMigsPl],[Host-associatedMigsOrg],[Host-associatedMigsEu],[Host-associatedMigsBa],[Host-associatedMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -43,25 +47,53 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -77,7 +109,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -97,7 +129,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -113,7 +145,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -129,7 +161,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -161,8 +193,12 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -189,7 +225,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -201,13 +237,13 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None diff --git a/mixs6/Host-associatedMe.md b/mixs6/Host-associatedMe.md index dbc9599a..38a32a28 100644 --- a/mixs6/Host-associatedMe.md +++ b/mixs6/Host-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with me URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Host-associatedMe|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Host-associated]^-[Host-associatedMe],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Host-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Host-associated]^-[Host-associatedMe],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,183 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsBa.md b/mixs6/Host-associatedMigsBa.md index dc57b474..d604faf4 100644 --- a/mixs6/Host-associatedMigsBa.md +++ b/mixs6/Host-associatedMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with migs_ba URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associatedMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Host-associatedMigsBa|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Host-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,248 @@ URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associa * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsEu.md b/mixs6/Host-associatedMigsEu.md index 91e06a04..eff49de4 100644 --- a/mixs6/Host-associatedMigsEu.md +++ b/mixs6/Host-associatedMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with migs_eu URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associatedMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Host-associatedMigsEu|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Host-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,248 @@ URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associa * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsOrg.md b/mixs6/Host-associatedMigsOrg.md index 063ba237..8d5603c2 100644 --- a/mixs6/Host-associatedMigsOrg.md +++ b/mixs6/Host-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with migs_org URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associatedMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Host-associatedMigsOrg|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Host-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,203 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsPl.md b/mixs6/Host-associatedMigsPl.md index aeb1ddef..4ddbbefc 100644 --- a/mixs6/Host-associatedMigsPl.md +++ b/mixs6/Host-associatedMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with migs_pl URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associatedMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Host-associatedMigsPl|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Host-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,218 @@ URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associa * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsVi.md b/mixs6/Host-associatedMigsVi.md index 0cece668..0017d829 100644 --- a/mixs6/Host-associatedMigsVi.md +++ b/mixs6/Host-associatedMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with migs_vi URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associatedMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Host-associatedMigsVi|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Host-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,243 @@ URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associa * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Host-associatedMimag.md b/mixs6/Host-associatedMimag.md index 569540b3..422afd1b 100644 --- a/mixs6/Host-associatedMimag.md +++ b/mixs6/Host-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with mimag URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associatedMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Host-associatedMimag|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Host-associated]^-[Host-associatedMimag],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Host-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Host-associated]^-[Host-associatedMimag],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,263 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimarksC.md b/mixs6/Host-associatedMimarksC.md index e06f7e49..5e96e37d 100644 --- a/mixs6/Host-associatedMimarksC.md +++ b/mixs6/Host-associatedMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with mimarks_c URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-associatedMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Host-associatedMimarksC|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Host-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,148 @@ URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimarksS.md b/mixs6/Host-associatedMimarksS.md index 32088ebe..415226b3 100644 --- a/mixs6/Host-associatedMimarksS.md +++ b/mixs6/Host-associatedMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with mimarks_s URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-associatedMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Host-associatedMimarksS|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Host-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,168 @@ URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMisag.md b/mixs6/Host-associatedMisag.md index abcac9a8..bdb4dd4b 100644 --- a/mixs6/Host-associatedMisag.md +++ b/mixs6/Host-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with misag URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associatedMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Host-associatedMisag|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Host-associated]^-[Host-associatedMisag],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Host-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Host-associated]^-[Host-associatedMisag],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,268 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMiuvig.md b/mixs6/Host-associatedMiuvig.md index df915e36..9260f3cd 100644 --- a/mixs6/Host-associatedMiuvig.md +++ b/mixs6/Host-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for host-associated with miuvig URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associatedMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Host-associatedMiuvig|ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_length(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_dry_mass(i):string%20%3F;host_blood_press_diast(i):string%20%3F;host_blood_press_syst(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Host-associated]^-[Host-associatedMiuvig],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Host-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Host-associated]^-[Host-associatedMiuvig],[Host-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -34,25 +38,53 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [genetic_mod](genetic_mod.md) OPT * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravidity](gravidity.md) OPT * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used * range: [String](types/String.md) * Example: yes;due date:2018-05-11 None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_blood_press_diast](host_blood_press_diast.md) OPT * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_blood_press_syst](host_blood_press_syst.md) OPT * Description: Resting systolic blood pressure, measured as mm mercury - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [host_body_habitat](host_body_habitat.md) OPT * Description: Original body habitat where the sample was obtained from @@ -68,7 +100,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_color](host_color.md) OPT * Description: The color of host @@ -88,7 +120,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_family_relationship](host_family_relationship.md) OPT * Description: Relationships to other hosts in the same study; can include multiple relationships @@ -104,7 +136,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -120,7 +152,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: corn feed;P2H None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -152,8 +184,12 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) @@ -180,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -192,13 +228,333 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associated.md b/mixs6/Human-associated.md index a2d7a21d..0b21f326 100644 --- a/mixs6/Human-associated.md +++ b/mixs6/Human-associated.md @@ -7,7 +7,7 @@ human-associated URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-associatedMiuvig],[Human-associatedMisag],[Human-associatedMimarksS],[Human-associatedMimarksC],[Human-associatedMimag],[Human-associatedMigsVi],[Human-associatedMigsPl],[Human-associatedMigsOrg],[Human-associatedMigsEu],[Human-associatedMigsBa],[Human-associatedMe],[Human-associated|host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;smoker:string%20%3F;host_hiv_stat:string%20%3F;drug_usage:drug_usage_enum%20%3F;host_body_mass_index:string%20%3F;diet_last_six_month:string%20%3F;weight_loss_3_month:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;pet_farm_animal:string%20%3F;travel_out_six_month:string%20%3F;twin_sibling:string%20%3F;medic_hist_perform:string%20%3F;study_complt_stat:study_complt_stat_enum%20%3F;pulmonary_disord:string%20%3F;nose_throat_disord:string%20%3F;blood_blood_disord:string%20%3F;host_pulse:string%20%3F;gestation_state:string%20%3F;maternal_health_stat:string%20%3F;foetal_health_stat:string%20%3F;amniotic_fluid_color:string%20%3F;urogenit_tract_disor:string%20%3F;urine_collect_meth:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-associatedMiuvig],[Human-associated]^-[Human-associatedMisag],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]^-[Human-associatedMimag],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]^-[Human-associatedMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMiuvig],[Human-associatedMisag],[Human-associatedMimarksS],[Human-associatedMimarksC],[Human-associatedMimag],[Human-associatedMigsVi],[Human-associatedMigsPl],[Human-associatedMigsOrg],[Human-associatedMigsEu],[Human-associatedMigsBa],[Human-associatedMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -43,6 +47,14 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -51,21 +63,41 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -77,7 +109,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -97,7 +129,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -117,7 +149,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -129,7 +161,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -139,6 +171,10 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -177,7 +213,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -189,11 +225,11 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -205,7 +241,7 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels diff --git a/mixs6/Human-associatedMe.md b/mixs6/Human-associatedMe.md index f44940f5..e7515f51 100644 --- a/mixs6/Human-associatedMe.md +++ b/mixs6/Human-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with me URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associatedMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-associatedMe|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-associated]^-[Human-associatedMe],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-associated]^-[Human-associatedMe],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,173 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsBa.md b/mixs6/Human-associatedMigsBa.md index 520a2585..f4e1f626 100644 --- a/mixs6/Human-associatedMigsBa.md +++ b/mixs6/Human-associatedMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with migs_ba URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-associatedMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-associatedMigsBa|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,238 @@ URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-assoc * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsEu.md b/mixs6/Human-associatedMigsEu.md index 0c982d86..69ac9b79 100644 --- a/mixs6/Human-associatedMigsEu.md +++ b/mixs6/Human-associatedMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with migs_eu URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-associatedMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-associatedMigsEu|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,238 @@ URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-assoc * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsOrg.md b/mixs6/Human-associatedMigsOrg.md index 78babe13..bcd015d4 100644 --- a/mixs6/Human-associatedMigsOrg.md +++ b/mixs6/Human-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with migs_org URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-associatedMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-associatedMigsOrg|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,193 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsPl.md b/mixs6/Human-associatedMigsPl.md index a887224d..a59c23a5 100644 --- a/mixs6/Human-associatedMigsPl.md +++ b/mixs6/Human-associatedMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with migs_pl URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-associatedMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-associatedMigsPl|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,208 @@ URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-assoc * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsVi.md b/mixs6/Human-associatedMigsVi.md index 03fbe9ea..5b3945a0 100644 --- a/mixs6/Human-associatedMigsVi.md +++ b/mixs6/Human-associatedMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with migs_vi URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-associatedMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-associatedMigsVi|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,233 @@ URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-assoc * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-associatedMimag.md b/mixs6/Human-associatedMimag.md index 0757320c..2876429e 100644 --- a/mixs6/Human-associatedMimag.md +++ b/mixs6/Human-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with mimag URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associatedMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-associatedMimag|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-associated]^-[Human-associatedMimag],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-associated]^-[Human-associatedMimag],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,253 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimarksC.md b/mixs6/Human-associatedMimarksC.md index f7d67ec3..5b10e12f 100644 --- a/mixs6/Human-associatedMimarksC.md +++ b/mixs6/Human-associatedMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with mimarks_c URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-associatedMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-associatedMimarksC|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,138 @@ URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-ass * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimarksS.md b/mixs6/Human-associatedMimarksS.md index 6e169013..78f5d6d8 100644 --- a/mixs6/Human-associatedMimarksS.md +++ b/mixs6/Human-associatedMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with mimarks_s URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-associatedMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-associatedMimarksS|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,158 @@ URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-ass * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMisag.md b/mixs6/Human-associatedMisag.md index ed066b20..073a1419 100644 --- a/mixs6/Human-associatedMisag.md +++ b/mixs6/Human-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with misag URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associatedMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-associatedMisag|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-associated]^-[Human-associatedMisag],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-associated]^-[Human-associatedMisag],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,258 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMiuvig.md b/mixs6/Human-associatedMiuvig.md index 76b11e4f..a695973c 100644 --- a/mixs6/Human-associatedMiuvig.md +++ b/mixs6/Human-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-associated with miuvig URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-associatedMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-associatedMiuvig|host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;host_body_mass_index(i):string%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;host_pulse(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-associated]^-[Human-associatedMiuvig],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-associated]^-[Human-associatedMiuvig],[Human-associated]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT * Description: Specification of the color of the amniotic fluid sample * range: [String](types/String.md) @@ -34,6 +38,14 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT * Description: Specification of major diet changes in the last six months, if yes the change should be specified * range: [String](types/String.md) @@ -42,21 +54,41 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used * range: * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [foetal_health_stat](foetal_health_stat.md) OPT * Description: Specification of foetal health status, should also include abortion * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gestation_state](gestation_state.md) OPT * Description: Specification of the gestation state * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_hiv_stat](host_hiv_stat.md) OPT * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] @@ -108,7 +140,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -120,7 +152,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -130,6 +162,10 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [maternal_health_stat](maternal_health_stat.md) OPT * Description: Specification of the maternal health status * range: [String](types/String.md) @@ -168,7 +204,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -180,11 +216,11 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [smoker](smoker.md) OPT * Description: Specification of smoking status @@ -196,7 +232,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Example: no;non-compliance None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [travel_out_six_month](travel_out_six_month.md) OPT * Description: Specification of the countries travelled in the last six months; can include multiple travels @@ -218,3 +254,323 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss * range: [String](types/String.md) * Example: yes;5 kilogram None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gut.md b/mixs6/Human-gut.md index 5770d8c8..bc2dd462 100644 --- a/mixs6/Human-gut.md +++ b/mixs6/Human-gut.md @@ -7,7 +7,7 @@ human-gut URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-gutMiuvig],[Human-gutMisag],[Human-gutMimarksS],[Human-gutMimarksC],[Human-gutMimag],[Human-gutMigsVi],[Human-gutMigsPl],[Human-gutMigsOrg],[Human-gutMigsEu],[Human-gutMigsBa],[Human-gutMe],[Human-gut|gastrointest_disord:string%20%3F;liver_disord:string%20%3F;special_diet:special_diet_enum%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-gutMiuvig],[Human-gut]^-[Human-gutMisag],[Human-gut]^-[Human-gutMimarksS],[Human-gut]^-[Human-gutMimarksC],[Human-gut]^-[Human-gutMimag],[Human-gut]^-[Human-gutMigsVi],[Human-gut]^-[Human-gutMigsPl],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]^-[Human-gutMigsEu],[Human-gut]^-[Human-gutMigsBa],[Human-gut]^-[Human-gutMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMiuvig],[Human-gutMisag],[Human-gutMimarksS],[Human-gutMimarksC],[Human-gutMimag],[Human-gutMigsVi],[Human-gutMigsPl],[Human-gutMigsOrg],[Human-gutMigsEu],[Human-gutMigsBa],[Human-gutMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -57,7 +89,7 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -77,7 +109,7 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -93,7 +125,7 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -105,7 +137,7 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -115,6 +147,10 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -141,7 +177,7 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -153,11 +189,11 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -165,5 +201,5 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None diff --git a/mixs6/Human-gutMe.md b/mixs6/Human-gutMe.md index 5fa750a8..d7e5ca7a 100644 --- a/mixs6/Human-gutMe.md +++ b/mixs6/Human-gutMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with me URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-gutMe|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-gut]^-[Human-gutMe],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-gutMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-gut]^-[Human-gutMe],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,175 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsBa.md b/mixs6/Human-gutMigsBa.md index 985d991d..6cb96bd3 100644 --- a/mixs6/Human-gutMigsBa.md +++ b/mixs6/Human-gutMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with migs_ba URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-gutMigsBa|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-gut]^-[Human-gutMigsBa],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-gutMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-gut]^-[Human-gutMigsBa],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,240 @@ URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsEu.md b/mixs6/Human-gutMigsEu.md index 96db2503..b9ef44b5 100644 --- a/mixs6/Human-gutMigsEu.md +++ b/mixs6/Human-gutMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with migs_eu URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-gutMigsEu|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-gut]^-[Human-gutMigsEu],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-gutMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-gut]^-[Human-gutMigsEu],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,240 @@ URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsOrg.md b/mixs6/Human-gutMigsOrg.md index 1fff7b95..794c99b7 100644 --- a/mixs6/Human-gutMigsOrg.md +++ b/mixs6/Human-gutMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with migs_org URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-gutMigsOrg|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-gutMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,195 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsPl.md b/mixs6/Human-gutMigsPl.md index 0b03d981..3d56e081 100644 --- a/mixs6/Human-gutMigsPl.md +++ b/mixs6/Human-gutMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with migs_pl URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-gutMigsPl|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-gut]^-[Human-gutMigsPl],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-gutMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-gut]^-[Human-gutMigsPl],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,210 @@ URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsVi.md b/mixs6/Human-gutMigsVi.md index 7b6fab31..cc6888a7 100644 --- a/mixs6/Human-gutMigsVi.md +++ b/mixs6/Human-gutMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with migs_vi URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-gutMigsVi|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-gut]^-[Human-gutMigsVi],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-gutMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-gut]^-[Human-gutMigsVi],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,235 @@ URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-gutMimag.md b/mixs6/Human-gutMimag.md index 9fc8df7b..b8c7ab64 100644 --- a/mixs6/Human-gutMimag.md +++ b/mixs6/Human-gutMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with mimag URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-gutMimag|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-gut]^-[Human-gutMimag],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-gutMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-gut]^-[Human-gutMimag],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,255 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimarksC.md b/mixs6/Human-gutMimarksC.md index e74fba54..cdbb39ad 100644 --- a/mixs6/Human-gutMimarksC.md +++ b/mixs6/Human-gutMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with mimarks_c URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-gutMimarksC|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-gut]^-[Human-gutMimarksC],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-gutMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-gut]^-[Human-gutMimarksC],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,140 @@ URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimarksS.md b/mixs6/Human-gutMimarksS.md index a760ab33..3082b52d 100644 --- a/mixs6/Human-gutMimarksS.md +++ b/mixs6/Human-gutMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with mimarks_s URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-gutMimarksS|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-gut]^-[Human-gutMimarksS],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-gutMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-gut]^-[Human-gutMimarksS],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,160 @@ URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarks * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMisag.md b/mixs6/Human-gutMisag.md index f86d9401..b7abd73d 100644 --- a/mixs6/Human-gutMisag.md +++ b/mixs6/Human-gutMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with misag URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-gutMisag|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-gut]^-[Human-gutMisag],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-gutMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-gut]^-[Human-gutMisag],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,260 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMiuvig.md b/mixs6/Human-gutMiuvig.md index b89a1b87..b79c93ec 100644 --- a/mixs6/Human-gutMiuvig.md +++ b/mixs6/Human-gutMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-gut with miuvig URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-gutMiuvig|gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-gut]^-[Human-gutMiuvig],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-gutMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-gut]^-[Human-gutMiuvig],[Human-gut]) ## Parents @@ -22,21 +22,53 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) ### Inherited from human-gut: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gastrointest_disord](gastrointest_disord.md) OPT * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -48,7 +80,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -68,7 +100,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -84,7 +116,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -96,7 +128,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -106,6 +138,10 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [liver_disord](liver_disord.md) OPT * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,11 +180,11 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [special_diet](special_diet.md) OPT * Description: Specification of special diet; can include multiple special diets @@ -156,5 +192,325 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * Example: other:vegan None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oral.md b/mixs6/Human-oral.md index 80d0deb6..267dbefb 100644 --- a/mixs6/Human-oral.md +++ b/mixs6/Human-oral.md @@ -7,7 +7,7 @@ human-oral URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-oralMiuvig],[Human-oralMisag],[Human-oralMimarksS],[Human-oralMimarksC],[Human-oralMimag],[Human-oralMigsVi],[Human-oralMigsPl],[Human-oralMigsOrg],[Human-oralMigsEu],[Human-oralMigsBa],[Human-oralMe],[Human-oral|nose_mouth_teeth_throat_disord:string%20%3F;time_last_toothbrush:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-oralMiuvig],[Human-oral]^-[Human-oralMisag],[Human-oral]^-[Human-oralMimarksS],[Human-oral]^-[Human-oralMimarksC],[Human-oral]^-[Human-oralMimag],[Human-oral]^-[Human-oralMigsVi],[Human-oral]^-[Human-oralMigsPl],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]^-[Human-oralMigsEu],[Human-oral]^-[Human-oralMigsBa],[Human-oral]^-[Human-oralMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMiuvig],[Human-oralMisag],[Human-oralMimarksS],[Human-oralMimarksC],[Human-oralMimag],[Human-oralMigsVi],[Human-oralMigsPl],[Human-oralMigsOrg],[Human-oralMigsEu],[Human-oralMigsBa],[Human-oralMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -53,7 +85,7 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -73,7 +105,7 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -89,7 +121,7 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -101,7 +133,7 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -111,6 +143,10 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -137,7 +173,7 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -149,15 +185,15 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing diff --git a/mixs6/Human-oralMe.md b/mixs6/Human-oralMe.md index 6f821d81..ba99823d 100644 --- a/mixs6/Human-oralMe.md +++ b/mixs6/Human-oralMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with me URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-oralMe|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-oral]^-[Human-oralMe],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-oralMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-oral]^-[Human-oralMe],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,187 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsBa.md b/mixs6/Human-oralMigsBa.md index 61bf01c9..3c4e251e 100644 --- a/mixs6/Human-oralMigsBa.md +++ b/mixs6/Human-oralMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with migs_ba URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-oralMigsBa|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-oral]^-[Human-oralMigsBa],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-oralMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-oral]^-[Human-oralMigsBa],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,252 @@ URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsEu.md b/mixs6/Human-oralMigsEu.md index edffa206..f40bb0c9 100644 --- a/mixs6/Human-oralMigsEu.md +++ b/mixs6/Human-oralMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with migs_eu URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-oralMigsEu|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-oral]^-[Human-oralMigsEu],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-oralMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-oral]^-[Human-oralMigsEu],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,252 @@ URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsOrg.md b/mixs6/Human-oralMigsOrg.md index 7f07e232..36c3a9c3 100644 --- a/mixs6/Human-oralMigsOrg.md +++ b/mixs6/Human-oralMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with migs_org URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-oralMigsOrg|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-oralMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,207 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsPl.md b/mixs6/Human-oralMigsPl.md index a7f22b21..d72c77be 100644 --- a/mixs6/Human-oralMigsPl.md +++ b/mixs6/Human-oralMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with migs_pl URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-oralMigsPl|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-oral]^-[Human-oralMigsPl],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-oralMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-oral]^-[Human-oralMigsPl],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,222 @@ URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsVi.md b/mixs6/Human-oralMigsVi.md index 8c18d896..211f81ac 100644 --- a/mixs6/Human-oralMigsVi.md +++ b/mixs6/Human-oralMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with migs_vi URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-oralMigsVi|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-oral]^-[Human-oralMigsVi],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-oralMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-oral]^-[Human-oralMigsVi],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,247 @@ URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-oralMimag.md b/mixs6/Human-oralMimag.md index ba3ca9ab..e5236953 100644 --- a/mixs6/Human-oralMimag.md +++ b/mixs6/Human-oralMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with mimag URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-oralMimag|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-oral]^-[Human-oralMimag],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-oralMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-oral]^-[Human-oralMimag],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,267 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimarksC.md b/mixs6/Human-oralMimarksC.md index e6157f95..7b9b2f58 100644 --- a/mixs6/Human-oralMimarksC.md +++ b/mixs6/Human-oralMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with mimarks_c URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-oralMimarksC|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-oral]^-[Human-oralMimarksC],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-oralMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-oral]^-[Human-oralMimarksC],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,152 @@ URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimar * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimarksS.md b/mixs6/Human-oralMimarksS.md index 911d4fc6..7eb12e84 100644 --- a/mixs6/Human-oralMimarksS.md +++ b/mixs6/Human-oralMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with mimarks_s URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-oralMimarksS|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-oral]^-[Human-oralMimarksS],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-oralMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-oral]^-[Human-oralMimarksS],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,172 @@ URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimar * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMisag.md b/mixs6/Human-oralMisag.md index 7f71fd62..9aa69691 100644 --- a/mixs6/Human-oralMisag.md +++ b/mixs6/Human-oralMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with misag URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-oralMisag|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-oral]^-[Human-oralMisag],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-oralMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-oral]^-[Human-oralMisag],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,272 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMiuvig.md b/mixs6/Human-oralMiuvig.md index d2eabedc..0b4ce634 100644 --- a/mixs6/Human-oralMiuvig.md +++ b/mixs6/Human-oralMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-oral with miuvig URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-oralMiuvig|nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-oral]^-[Human-oralMiuvig],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-oralMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-oral]^-[Human-oralMiuvig],[Human-oral]) ## Parents @@ -22,17 +22,49 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) ### Inherited from human-oral: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -44,7 +76,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -64,7 +96,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -80,7 +112,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -102,6 +134,10 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -128,7 +164,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -140,17 +176,337 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_last_toothbrush](time_last_toothbrush.md) OPT * Description: Specification of the time since last toothbrushing * range: [String](types/String.md) * Example: P2H45M None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skin.md b/mixs6/Human-skin.md index 43f170f0..33246725 100644 --- a/mixs6/Human-skin.md +++ b/mixs6/Human-skin.md @@ -7,7 +7,7 @@ human-skin URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-skinMiuvig],[Human-skinMisag],[Human-skinMimarksS],[Human-skinMimarksC],[Human-skinMimag],[Human-skinMigsVi],[Human-skinMigsPl],[Human-skinMigsOrg],[Human-skinMigsEu],[Human-skinMigsBa],[Human-skinMe],[Human-skin|dermatology_disord:string%20%3F;time_since_last_wash:string%20%3F;dominant_hand:dominant_hand_enum%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;misc_param:string%20%3F]^-[Human-skinMiuvig],[Human-skin]^-[Human-skinMisag],[Human-skin]^-[Human-skinMimarksS],[Human-skin]^-[Human-skinMimarksC],[Human-skin]^-[Human-skinMimag],[Human-skin]^-[Human-skinMigsVi],[Human-skin]^-[Human-skinMigsPl],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]^-[Human-skinMigsEu],[Human-skin]^-[Human-skinMigsBa],[Human-skin]^-[Human-skinMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMiuvig],[Human-skinMisag],[Human-skinMimarksS],[Human-skinMimarksC],[Human-skinMimag],[Human-skinMigsVi],[Human-skinMigsPl],[Human-skinMigsOrg],[Human-skinMigsEu],[Human-skinMigsBa],[Human-skinMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -43,13 +55,33 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -61,7 +93,7 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -81,7 +113,7 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -97,7 +129,7 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -109,7 +141,7 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -119,6 +151,10 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -141,7 +177,7 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -153,15 +189,15 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash diff --git a/mixs6/Human-skinMe.md b/mixs6/Human-skinMe.md index c33dd8b3..dfdfd495 100644 --- a/mixs6/Human-skinMe.md +++ b/mixs6/Human-skinMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with me URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-skinMe|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-skin]^-[Human-skinMe],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-skinMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-skin]^-[Human-skinMe],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,187 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsBa.md b/mixs6/Human-skinMigsBa.md index f96bc46c..ecf26c74 100644 --- a/mixs6/Human-skinMigsBa.md +++ b/mixs6/Human-skinMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with migs_ba URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-skinMigsBa|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-skin]^-[Human-skinMigsBa],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-skinMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-skin]^-[Human-skinMigsBa],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,252 @@ URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsEu.md b/mixs6/Human-skinMigsEu.md index dc67a32c..775aaeb8 100644 --- a/mixs6/Human-skinMigsEu.md +++ b/mixs6/Human-skinMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with migs_eu URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-skinMigsEu|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-skin]^-[Human-skinMigsEu],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-skinMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-skin]^-[Human-skinMigsEu],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,252 @@ URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsOrg.md b/mixs6/Human-skinMigsOrg.md index 9df122d4..f039e57e 100644 --- a/mixs6/Human-skinMigsOrg.md +++ b/mixs6/Human-skinMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with migs_org URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-skinMigsOrg|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-skinMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,207 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsPl.md b/mixs6/Human-skinMigsPl.md index 7eb286e0..fdb939cc 100644 --- a/mixs6/Human-skinMigsPl.md +++ b/mixs6/Human-skinMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with migs_pl URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-skinMigsPl|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-skin]^-[Human-skinMigsPl],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-skinMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-skin]^-[Human-skinMigsPl],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,222 @@ URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsVi.md b/mixs6/Human-skinMigsVi.md index 6ad8768c..f7cf4a4c 100644 --- a/mixs6/Human-skinMigsVi.md +++ b/mixs6/Human-skinMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with migs_vi URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-skinMigsVi|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-skin]^-[Human-skinMigsVi],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-skinMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-skin]^-[Human-skinMigsVi],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,247 @@ URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-skinMimag.md b/mixs6/Human-skinMimag.md index 2b7c3fb8..8e5432c4 100644 --- a/mixs6/Human-skinMimag.md +++ b/mixs6/Human-skinMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with mimag URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-skinMimag|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-skin]^-[Human-skinMimag],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-skinMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-skin]^-[Human-skinMimag],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,267 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimarksC.md b/mixs6/Human-skinMimarksC.md index 99a68d5e..1cde0bff 100644 --- a/mixs6/Human-skinMimarksC.md +++ b/mixs6/Human-skinMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with mimarks_c URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-skinMimarksC|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-skin]^-[Human-skinMimarksC],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-skinMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-skin]^-[Human-skinMimarksC],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,152 @@ URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimar * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimarksS.md b/mixs6/Human-skinMimarksS.md index fe708229..7efef9fe 100644 --- a/mixs6/Human-skinMimarksS.md +++ b/mixs6/Human-skinMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with mimarks_s URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-skinMimarksS|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-skin]^-[Human-skinMimarksS],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-skinMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-skin]^-[Human-skinMimarksS],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,172 @@ URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimar * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMisag.md b/mixs6/Human-skinMisag.md index 0099bc06..248f0747 100644 --- a/mixs6/Human-skinMisag.md +++ b/mixs6/Human-skinMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with misag URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-skinMisag|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-skin]^-[Human-skinMisag],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-skinMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-skin]^-[Human-skinMisag],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,272 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMiuvig.md b/mixs6/Human-skinMiuvig.md index dde7af07..aea1554a 100644 --- a/mixs6/Human-skinMiuvig.md +++ b/mixs6/Human-skinMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-skin with miuvig URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-skinMiuvig|dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-skin]^-[Human-skinMiuvig],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-skinMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-skin]^-[Human-skinMiuvig],[Human-skin]) ## Parents @@ -22,10 +22,22 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) ### Inherited from human-skin: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [dermatology_disord](dermatology_disord.md) OPT * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * range: [String](types/String.md) @@ -34,13 +46,33 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Description: Dominant hand of the subject * range: * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -52,7 +84,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -72,7 +104,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -88,7 +120,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -100,7 +132,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [ihmc_ethnicity](ihmc_ethnicity.md) OPT * Description: Ethnicity of the subject @@ -110,6 +142,10 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -132,7 +168,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -144,17 +180,337 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [time_since_last_wash](time_since_last_wash.md) OPT * Description: Specification of the time since last wash * range: [String](types/String.md) * Example: P1D None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginal.md b/mixs6/Human-vaginal.md index 58e4bc26..77f37d11 100644 --- a/mixs6/Human-vaginal.md +++ b/mixs6/Human-vaginal.md @@ -7,7 +7,7 @@ human-vaginal URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Human-vaginalMiuvig],[Human-vaginalMisag],[Human-vaginalMimarksS],[Human-vaginalMimarksC],[Human-vaginalMimag],[Human-vaginalMigsVi],[Human-vaginalMigsPl],[Human-vaginalMigsOrg],[Human-vaginalMigsEu],[Human-vaginalMigsBa],[Human-vaginalMe],[Human-vaginal|menarche:string%20%3F;sexual_act:string%20%3F;pregnancy:string%20%3F;douche:string%20%3F;birth_control:string%20%3F;menopause:string%20%3F;hrt:string%20%3F;hysterectomy:string%20%3F;gynecologic_disord:string%20%3F;urogenit_disord:string%20%3F;host_subject_id:string%20%3F;host_age:string%20%3F;host_sex:host_sex_enum%20%3F;host_disease_stat:string%20%3F;ihmc_medication_code:string%20%3F;chem_administration:string%20%3F;host_body_site:string%20%3F;host_body_product:string%20%3F;host_tot_mass:string%20%3F;host_height:string%20%3F;host_diet:string%20%3F;host_last_meal:string%20%3F;host_family_relationship:string%20%3F;host_genotype:string%20%3F;host_phenotype:string%20%3F;host_body_temp:string%20%3F;host_body_mass_index:string%20%3F;ihmc_ethnicity:string%20%3F;host_occupation:string%20%3F;medic_hist_perform:string%20%3F;host_pulse:string%20%3F;perturbation:string%20%3F;samp_salinity:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;temp:string%20%3F;organism_count:organism_count_enum%20%3F;samp_vol_we_dna_ext:string%20%3F;samp_store_temp:string%20%3F;samp_store_loc:string%20%3F;samp_store_dur:string%20%3F;misc_param:string%20%3F]^-[Human-vaginalMiuvig],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]^-[Human-vaginalMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMiuvig],[Human-vaginalMisag],[Human-vaginalMimarksS],[Human-vaginalMimarksC],[Human-vaginalMimag],[Human-vaginalMigsVi],[Human-vaginalMigsPl],[Human-vaginalMigsOrg],[Human-vaginalMigsEu],[Human-vaginalMigsBa],[Human-vaginalMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -39,21 +43,49 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -65,7 +97,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -85,7 +117,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -101,7 +133,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -113,7 +145,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -131,6 +163,10 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -165,7 +201,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -177,11 +213,11 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -189,7 +225,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). diff --git a/mixs6/Human-vaginalMe.md b/mixs6/Human-vaginalMe.md index eaf2ac89..fd9e0b5e 100644 --- a/mixs6/Human-vaginalMe.md +++ b/mixs6/Human-vaginalMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with me URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[Human-vaginalMe|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-vaginal]^-[Human-vaginalMe],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-vaginalMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-vaginal]^-[Human-vaginalMe],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,179 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsBa.md b/mixs6/Human-vaginalMigsBa.md index d6c948ca..96a70a1b 100644 --- a/mixs6/Human-vaginalMigsBa.md +++ b/mixs6/Human-vaginalMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with migs_ba URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[Human-vaginalMigsBa|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-vaginalMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,244 @@ URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalM * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsEu.md b/mixs6/Human-vaginalMigsEu.md index a488e056..d3b1241e 100644 --- a/mixs6/Human-vaginalMigsEu.md +++ b/mixs6/Human-vaginalMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with migs_eu URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[Human-vaginalMigsEu|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-vaginalMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,244 @@ URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalM * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsOrg.md b/mixs6/Human-vaginalMigsOrg.md index fa48b833..a959ed25 100644 --- a/mixs6/Human-vaginalMigsOrg.md +++ b/mixs6/Human-vaginalMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with migs_org URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginalMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[Human-vaginalMigsOrg|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-vaginalMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,199 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsPl.md b/mixs6/Human-vaginalMigsPl.md index 31100692..9a00bba3 100644 --- a/mixs6/Human-vaginalMigsPl.md +++ b/mixs6/Human-vaginalMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with migs_pl URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[Human-vaginalMigsPl|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-vaginalMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,214 @@ URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalM * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsVi.md b/mixs6/Human-vaginalMigsVi.md index 52ab6228..86c5abcc 100644 --- a/mixs6/Human-vaginalMigsVi.md +++ b/mixs6/Human-vaginalMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with migs_vi URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[Human-vaginalMigsVi|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-vaginalMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,239 @@ URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalM * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-vaginalMimag.md b/mixs6/Human-vaginalMimag.md index b162860b..aae33fc9 100644 --- a/mixs6/Human-vaginalMimag.md +++ b/mixs6/Human-vaginalMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with mimag URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[Human-vaginalMimag|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-vaginalMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,259 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimarksC.md b/mixs6/Human-vaginalMimarksC.md index 5ca86e03..03e168f1 100644 --- a/mixs6/Human-vaginalMimarksC.md +++ b/mixs6/Human-vaginalMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with mimarks_c URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vaginalMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[Human-vaginalMimarksC|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-vaginalMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,144 @@ URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vagina * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimarksS.md b/mixs6/Human-vaginalMimarksS.md index 75341ab1..2750fe70 100644 --- a/mixs6/Human-vaginalMimarksS.md +++ b/mixs6/Human-vaginalMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with mimarks_s URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vaginalMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[Human-vaginalMimarksS|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-vaginalMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,164 @@ URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vagina * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMisag.md b/mixs6/Human-vaginalMisag.md index 46b09f83..75bc2671 100644 --- a/mixs6/Human-vaginalMisag.md +++ b/mixs6/Human-vaginalMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with misag URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[Human-vaginalMisag|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-vaginalMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,264 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMiuvig.md b/mixs6/Human-vaginalMiuvig.md index 78cad60b..291113b7 100644 --- a/mixs6/Human-vaginalMiuvig.md +++ b/mixs6/Human-vaginalMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for human-vaginal with miuvig URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[Human-vaginalMiuvig|menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_age(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_tot_mass(i):string%20%3F;host_height(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_body_temp(i):string%20%3F;host_body_mass_index(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;host_pulse(i):string%20%3F;perturbation(i):string%20%3F;samp_salinity(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;temp(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;samp_vol_we_dna_ext(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-vaginal]^-[Human-vaginalMiuvig],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-vaginalMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-vaginal]^-[Human-vaginalMiuvig],[Human-vaginal]) ## Parents @@ -22,6 +22,10 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [birth_control](birth_control.md) OPT * Description: Specification of birth control medication used * range: [String](types/String.md) @@ -30,21 +34,49 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi * range: [String](types/String.md) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche * range: [String](types/String.md) * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gynecologic_disord](gynecologic_disord.md) OPT * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). * range: [String](types/String.md) * Example: None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_body_mass_index](host_body_mass_index.md) OPT * Description: Body mass index, calculated as weight/(height)squared - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 22 kilogram per square meter None * [host_body_product](host_body_product.md) OPT * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon @@ -56,7 +88,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: gill [UBERON:0002535] None * [host_body_temp](host_body_temp.md) OPT * Description: Core body temperature of the host when sample was collected - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 15 degree Celsius None * [host_diet](host_diet.md) OPT * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types @@ -76,7 +108,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_last_meal](host_last_meal.md) OPT * Description: Content of last meal and time since feeding; can include multiple values @@ -92,7 +124,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: elongated [PATO:0001154] None * [host_pulse](host_pulse.md) OPT * Description: Resting pulse, measured as beats per minute - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 beats per minute None * [host_sex](host_sex.md) OPT * Description: Physical sex of the host @@ -104,7 +136,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: MPI123 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date @@ -122,6 +154,10 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [medic_hist_perform](medic_hist_perform.md) OPT * Description: Whether full medical history was collected * range: [String](types/String.md) @@ -156,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -168,11 +204,11 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sexual_act](sexual_act.md) OPT * Description: Current sexual partner and frequency of sex @@ -180,9 +216,329 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [urogenit_disord](urogenit_disord.md) OPT * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). * range: [String](types/String.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-cores.md b/mixs6/HydrocarbonResources-cores.md index a110479f..081e6f24 100644 --- a/mixs6/HydrocarbonResources-cores.md +++ b/mixs6/HydrocarbonResources-cores.md @@ -7,7 +7,7 @@ hydrocarbon resources-cores URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/HydrocarbonResources-cores) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-coresMisag],[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-coresMimag],[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-coresMe],[HydrocarbonResources-cores|hcr:hcr_enum%20%3F;hc_produced:hc_produced_enum%20%3F;basin:string%20%3F;field:string%20%3F;reservoir:string%20%3F;hcr_temp:string%20%3F;tvdss_of_hcr_temp:string%20%3F;hcr_pressure:string%20%3F;tvdss_of_hcr_pressure:string%20%3F;permeability:string%20%3F;porosity:string%20%3F;lithology:lithology_enum%20%3F;depos_env:depos_env_enum%20%3F;hcr_geol_age:hcr_geol_age_enum%20%3F;owc_tvdss:string%20%3F;hcr_fw_salinity:string%20%3F;sulfate_fw:string%20%3F;vfa_fw:string%20%3F;sr_kerog_type:sr_kerog_type_enum%20%3F;sr_lithology:sr_lithology_enum%20%3F;sr_dep_env:sr_dep_env_enum%20%3F;sr_geol_age:sr_geol_age_enum%20%3F;samp_well_name:string%20%3F;win:string%20%3F;samp_type:samp_type_enum%20%3F;samp_subtype:samp_subtype_enum%20%3F;temp:string%20%3F;pressure:string%20%3F;samp_tvdss:string%20%3F;samp_md:samp_md_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;samp_transport_cond:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_vol_we_dna_ext:string%20%3F;organism_count:organism_count_enum%20%3F;organism_count_qpcr_info:string%20%3F;ph:string%20%3F;samp_salinity:string%20%3F;alkalinity:string%20%3F;alkalinity_method:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;tot_sulfur:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;ammonium:string%20%3F;tot_nitro:string%20%3F;diss_iron:string%20%3F;sodium:string%20%3F;chloride:string%20%3F;potassium:string%20%3F;magnesium:string%20%3F;calcium:string%20%3F;tot_iron:string%20%3F;diss_org_carb:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_phosp:string%20%3F;tot_phosp:string%20%3F;suspend_solids:string%20%3F;density:string%20%3F;diss_carb_dioxide:string%20%3F;diss_oxygen_fluid:string%20%3F;vfa:string%20%3F;benzene:string%20%3F;toluene:string%20%3F;ethylbenzene:string%20%3F;xylene:string%20%3F;api:string%20%3F;tan:string%20%3F;viscosity:string%20%3F;pour_point:string%20%3F;saturates_pc:string%20%3F;aromatics_pc:string%20%3F;resins_pc:string%20%3F;asphaltenes_pc:string%20%3F;misc_param:string%20%3F;additional_info:string%20%3F]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-coresMisag],[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-coresMimag],[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-coresMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -65,56 +69,84 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -125,7 +157,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -139,13 +171,17 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -153,11 +189,11 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -169,7 +205,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -181,7 +217,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -189,15 +225,15 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -213,7 +249,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -225,7 +261,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -245,7 +281,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -257,7 +293,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -277,15 +313,15 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -293,47 +329,47 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -345,5 +381,5 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None diff --git a/mixs6/HydrocarbonResources-coresMe.md b/mixs6/HydrocarbonResources-coresMe.md index ae868b8a..1bee79d9 100644 --- a/mixs6/HydrocarbonResources-coresMe.md +++ b/mixs6/HydrocarbonResources-coresMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with me URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[HydrocarbonResources-coresMe|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[HydrocarbonResources-coresMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,175 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsBa.md b/mixs6/HydrocarbonResources-coresMigsBa.md index b6c618af..be15c999 100644 --- a/mixs6/HydrocarbonResources-coresMigsBa.md +++ b/mixs6/HydrocarbonResources-coresMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with migs_ba URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[HydrocarbonResources-coresMigsBa|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[HydrocarbonResources-coresMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,240 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsEu.md b/mixs6/HydrocarbonResources-coresMigsEu.md index 0f016aff..810d29c7 100644 --- a/mixs6/HydrocarbonResources-coresMigsEu.md +++ b/mixs6/HydrocarbonResources-coresMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with migs_eu URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[HydrocarbonResources-coresMigsEu|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[HydrocarbonResources-coresMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,240 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsOrg.md b/mixs6/HydrocarbonResources-coresMigsOrg.md index 2fe36db2..cadcc628 100644 --- a/mixs6/HydrocarbonResources-coresMigsOrg.md +++ b/mixs6/HydrocarbonResources-coresMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with migs_org URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[HydrocarbonResources-coresMigsOrg|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[HydrocarbonResources-coresMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,195 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsPl.md b/mixs6/HydrocarbonResources-coresMigsPl.md index 383dee09..17d74dfc 100644 --- a/mixs6/HydrocarbonResources-coresMigsPl.md +++ b/mixs6/HydrocarbonResources-coresMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with migs_pl URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[HydrocarbonResources-coresMigsPl|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[HydrocarbonResources-coresMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,210 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsVi.md b/mixs6/HydrocarbonResources-coresMigsVi.md index cb25267f..350509ff 100644 --- a/mixs6/HydrocarbonResources-coresMigsVi.md +++ b/mixs6/HydrocarbonResources-coresMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with migs_vi URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[HydrocarbonResources-coresMigsVi|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[HydrocarbonResources-coresMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,235 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-coresMimag.md b/mixs6/HydrocarbonResources-coresMimag.md index f23986e1..3d8a7582 100644 --- a/mixs6/HydrocarbonResources-coresMimag.md +++ b/mixs6/HydrocarbonResources-coresMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with mimag URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[HydrocarbonResources-coresMimag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[HydrocarbonResources-coresMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,255 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimarksC.md b/mixs6/HydrocarbonResources-coresMimarksC.md index f99e8687..a0555025 100644 --- a/mixs6/HydrocarbonResources-coresMimarksC.md +++ b/mixs6/HydrocarbonResources-coresMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with mimarks_c URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[HydrocarbonResources-coresMimarksC|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[HydrocarbonResources-coresMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,140 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimarksS.md b/mixs6/HydrocarbonResources-coresMimarksS.md index 521bcae5..bfecefce 100644 --- a/mixs6/HydrocarbonResources-coresMimarksS.md +++ b/mixs6/HydrocarbonResources-coresMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with mimarks_s URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[HydrocarbonResources-coresMimarksS|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[HydrocarbonResources-coresMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,160 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMisag.md b/mixs6/HydrocarbonResources-coresMisag.md index 16413e68..74062409 100644 --- a/mixs6/HydrocarbonResources-coresMisag.md +++ b/mixs6/HydrocarbonResources-coresMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with misag URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[HydrocarbonResources-coresMisag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[HydrocarbonResources-coresMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,260 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMiuvig.md b/mixs6/HydrocarbonResources-coresMiuvig.md index 836030d7..0735fde7 100644 --- a/mixs6/HydrocarbonResources-coresMiuvig.md +++ b/mixs6/HydrocarbonResources-coresMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-cores with miuvig URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[HydrocarbonResources-coresMiuvig|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;owc_tvdss(i):string%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[HydrocarbonResources-coresMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]) ## Parents @@ -28,19 +28,23 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -56,56 +60,84 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -116,7 +148,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -130,13 +162,17 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Description: Original temperature of the hydrocarbon resource * range: [String](types/String.md) * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -144,11 +180,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -160,7 +196,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [owc_tvdss](owc_tvdss.md) OPT * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [oxy_stat_samp](oxy_stat_samp.md) OPT * Description: Oxygenation status of sample @@ -172,7 +208,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [porosity](porosity.md) OPT * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample @@ -180,15 +216,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -204,7 +240,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: 1534 meter;MSL None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,7 +252,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sr_dep_env](sr_dep_env.md) OPT * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field @@ -268,15 +304,15 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: Coal None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -284,47 +320,47 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -336,5 +372,325 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabs.md b/mixs6/HydrocarbonResources-fluidsSwabs.md index 1c5414f0..389af4da 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabs.md +++ b/mixs6/HydrocarbonResources-fluidsSwabs.md @@ -7,7 +7,7 @@ hydrocarbon resources-fluids/swabs URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabs) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs|hcr:hcr_enum%20%3F;hc_produced:hc_produced_enum%20%3F;basin:string%20%3F;field:string%20%3F;reservoir:string%20%3F;hcr_temp:string%20%3F;tvdss_of_hcr_temp:string%20%3F;hcr_pressure:string%20%3F;tvdss_of_hcr_pressure:string%20%3F;lithology:lithology_enum%20%3F;depos_env:depos_env_enum%20%3F;hcr_geol_age:hcr_geol_age_enum%20%3F;hcr_fw_salinity:string%20%3F;sulfate_fw:string%20%3F;vfa_fw:string%20%3F;prod_start_date:string%20%3F;prod_rate:string%20%3F;water_production_rate:string%20%3F;water_cut:string%20%3F;iwf:string%20%3F;add_recov_method:add_recov_method_enum%20%3F;iw_bt_date_well:string%20%3F;biocide:string%20%3F;biocide_admin_method:string%20%3F;chem_treatment:string%20%3F;chem_treatment_method:string%20%3F;samp_loc_corr_rate:string%20%3F;samp_well_name:string%20%3F;win:string%20%3F;samp_type:samp_type_enum%20%3F;samp_subtype:samp_subtype_enum%20%3F;samp_collection_point:samp_collection_point_enum%20%3F;temp:string%20%3F;pressure:string%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;samp_preserv:string%20%3F;samp_transport_cond:string%20%3F;samp_store_temp:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_vol_we_dna_ext:string%20%3F;organism_count:organism_count_enum%20%3F;organism_count_qpcr_info:string%20%3F;ph:string%20%3F;samp_salinity:string%20%3F;alkalinity:string%20%3F;alkalinity_method:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;tot_sulfur:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;ammonium:string%20%3F;tot_nitro:string%20%3F;diss_iron:string%20%3F;sodium:string%20%3F;chloride:string%20%3F;potassium:string%20%3F;magnesium:string%20%3F;calcium:string%20%3F;tot_iron:string%20%3F;diss_org_carb:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_phosp:string%20%3F;tot_phosp:string%20%3F;suspend_solids:string%20%3F;density:string%20%3F;diss_carb_dioxide:string%20%3F;diss_oxygen_fluid:string%20%3F;vfa:string%20%3F;benzene:string%20%3F;toluene:string%20%3F;ethylbenzene:string%20%3F;xylene:string%20%3F;api:string%20%3F;tan:string%20%3F;viscosity:string%20%3F;pour_point:string%20%3F;saturates_pc:string%20%3F;aromatics_pc:string%20%3F;resins_pc:string%20%3F;asphaltenes_pc:string%20%3F;misc_param:string%20%3F;additional_info:string%20%3F]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabsMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -69,7 +73,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -81,7 +85,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -93,48 +97,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -145,7 +177,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -165,15 +197,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -181,11 +217,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -201,23 +237,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -245,7 +281,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -257,7 +293,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -273,7 +309,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -285,19 +321,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -305,47 +341,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -353,11 +389,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -365,5 +401,5 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMe.md b/mixs6/HydrocarbonResources-fluidsSwabsMe.md index da9af04e..f0e9bf2c 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMe.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with me URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[HydrocarbonResources-fluidsSwabsMe|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[HydrocarbonResources-fluidsSwabsMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,175 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md index 220f2ac8..bcff39ea 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,240 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/v * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md index f48329b8..decfdce9 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,240 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/v * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md index abc25b2f..4b979239 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,195 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md index f59aa331..ee801ccb 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,210 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/v * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md index 6fc7cbf2..3f1ffa7c 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,235 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/v * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md index 3a5c223a..af71dc40 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[HydrocarbonResources-fluidsSwabsMimag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[HydrocarbonResources-fluidsSwabsMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,255 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md index ea23f581..bb3878b5 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,140 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md index 719b8571..6567e263 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,160 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md index fe6519d3..45e33445 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[HydrocarbonResources-fluidsSwabsMisag|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[HydrocarbonResources-fluidsSwabsMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,260 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md index cd2dcc74..02056f3c 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig|hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;tvdss_of_hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;tvdss_of_hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;hcr_fw_salinity(i):string%20%3F;sulfate_fw(i):string%20%3F;vfa_fw(i):string%20%3F;prod_start_date(i):string%20%3F;prod_rate(i):string%20%3F;water_production_rate(i):string%20%3F;water_cut(i):string%20%3F;iwf(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;temp(i):string%20%3F;pressure(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):string%20%3F;samp_salinity(i):string%20%3F;alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;tot_sulfur(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;ammonium(i):string%20%3F;tot_nitro(i):string%20%3F;diss_iron(i):string%20%3F;sodium(i):string%20%3F;chloride(i):string%20%3F;potassium(i):string%20%3F;magnesium(i):string%20%3F;calcium(i):string%20%3F;tot_iron(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;tot_phosp(i):string%20%3F;suspend_solids(i):string%20%3F;density(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_oxygen_fluid(i):string%20%3F;vfa(i):string%20%3F;benzene(i):string%20%3F;toluene(i):string%20%3F;ethylbenzene(i):string%20%3F;xylene(i):string%20%3F;api(i):string%20%3F;tan(i):string%20%3F;viscosity(i):string%20%3F;pour_point(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]) ## Parents @@ -32,19 +32,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement * range: [String](types/String.md) * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [api](api.md) OPT * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [aromatics_pc](aromatics_pc.md) OPT * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) @@ -60,7 +64,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [benzene](benzene.md) OPT * Description: Concentration of benzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [biocide](biocide.md) OPT * Description: List of biocides (commercial name of product and supplier) and date of administration @@ -72,7 +76,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_treatment](chem_treatment.md) OPT * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included @@ -84,48 +88,76 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depos_env](depos_env.md) OPT * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field * range: * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_iron](diss_iron.md) OPT * Description: Concentration of dissolved iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [ethylbenzene](ethylbenzene.md) OPT * Description: Concentration of ethylbenzene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [field](field.md) OPT * Description: Name of the hydrocarbon field (e.g. Albacora) * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [hc_produced](hc_produced.md) OPT * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field * range: @@ -136,7 +168,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: Oil Sand None * [hcr_fw_salinity](hcr_fw_salinity.md) OPT * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [hcr_geol_age](hcr_geol_age.md) OPT * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field @@ -156,15 +188,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [lithology](lithology.md) OPT * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field * range: * Example: Volcanic None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,11 +208,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -192,23 +228,23 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: aerobic None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pour_point](pour_point.md) OPT * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [prod_rate](prod_rate.md) OPT * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production @@ -236,7 +272,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -248,7 +284,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_subtype](samp_subtype.md) OPT * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field @@ -264,7 +300,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: solid deposit None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [samp_well_name](samp_well_name.md) OPT * Description: Name of the well (e.g. BXA1123) where sample was taken @@ -276,19 +312,19 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfate_fw](sulfate_fw.md) OPT * Description: Original sulfate concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_solids](suspend_solids.md) OPT * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances @@ -296,47 +332,47 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [tan](tan.md) OPT * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [toluene](toluene.md) OPT * Description: Concentration of toluene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_iron](tot_iron.md) OPT * Description: Concentration of total iron in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [tot_sulfur](tot_sulfur.md) OPT * Description: Concentration of total sulfur in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT * Description: Concentration of Volatile Fatty Acids in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa_fw](vfa_fw.md) OPT * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [viscosity](viscosity.md) OPT * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) @@ -344,11 +380,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [water_cut](water_cut.md) OPT * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_production_rate](water_production_rate.md) OPT * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [win](win.md) OPT * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) @@ -356,5 +392,325 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * Example: None * [xylene](xylene.md) OPT * Description: Concentration of xylene in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Me.md b/mixs6/Me.md index 4d7a762e..71316e7a 100644 --- a/mixs6/Me.md +++ b/mixs6/Me.md @@ -7,13 +7,12 @@ me Checklist URI: [mixs.vocab:Me](https://w3id.org/mixs/vocab/Me) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe]uses%20-.->[Me],[WastewaterSludgeMe]uses%20-.->[Me],[SoilMe]uses%20-.->[Me],[SedimentMe]uses%20-.->[Me],[Plant-associatedMe]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironmentMe]uses%20-.->[Me],[MicrobialMatBiofilmMe]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabsMe]uses%20-.->[Me],[HydrocarbonResources-coresMe]uses%20-.->[Me],[Human-vaginalMe]uses%20-.->[Me],[Human-skinMe]uses%20-.->[Me],[Human-oralMe]uses%20-.->[Me],[Human-gutMe]uses%20-.->[Me],[Human-associatedMe]uses%20-.->[Me],[Host-associatedMe]uses%20-.->[Me],[CoreMe]uses%20-.->[Me],[BuiltEnvironmentMe]uses%20-.->[Me],[AirMe]uses%20-.->[Me],[WaterMe],[WastewaterSludgeMe],[SoilMe],[SedimentMe],[Plant-associatedMe],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MicrobialMatBiofilmMe],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-coresMe],[Human-vaginalMe],[Human-skinMe],[Human-oralMe],[Human-gutMe],[Human-associatedMe],[Host-associatedMe],[CoreMe],[BuiltEnvironmentMe],[AirMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Me],[WastewaterSludgeMe]uses%20-.->[Me],[SoilMe]uses%20-.->[Me],[SedimentMe]uses%20-.->[Me],[Plant-associatedMe]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironmentMe]uses%20-.->[Me],[MicrobialMatBiofilmMe]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabsMe]uses%20-.->[Me],[HydrocarbonResources-coresMe]uses%20-.->[Me],[Human-vaginalMe]uses%20-.->[Me],[Human-skinMe]uses%20-.->[Me],[Human-oralMe]uses%20-.->[Me],[Human-gutMe]uses%20-.->[Me],[Human-associatedMe]uses%20-.->[Me],[Host-associatedMe]uses%20-.->[Me],[BuiltEnvironmentMe]uses%20-.->[Me],[AirMe]uses%20-.->[Me],[WaterMe],[WastewaterSludgeMe],[SoilMe],[SedimentMe],[Plant-associatedMe],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MicrobialMatBiofilmMe],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-coresMe],[Human-vaginalMe],[Human-skinMe],[Human-oralMe],[Human-gutMe],[Human-associatedMe],[Host-associatedMe],[BuiltEnvironmentMe],[AirMe]) ## Mixin for * [AirMe](AirMe.md) (mixin) - Combinatorial checklist for air with me * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) (mixin) - Combinatorial checklist for built environment with me - * [CoreMe](CoreMe.md) (mixin) - Combinatorial checklist for core with me * [Host-associatedMe](Host-associatedMe.md) (mixin) - Combinatorial checklist for host-associated with me * [Human-associatedMe](Human-associatedMe.md) (mixin) - Combinatorial checklist for human-associated with me * [Human-gutMe](Human-gutMe.md) (mixin) - Combinatorial checklist for human-gut with me @@ -35,3 +34,86 @@ URI: [mixs.vocab:Me](https://w3id.org/mixs/vocab/Me) ## Attributes + +### Own + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + * [me➞collection_date](me_collection_date.md) REQ + * range: [String](types/String.md) + * [me➞env_broad_scale](me_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [me➞env_local_scale](me_env_local_scale.md) REQ + * range: [String](types/String.md) + * [me➞env_medium](me_env_medium.md) REQ + * range: [String](types/String.md) + * [me➞env_package](me_env_package.md) OPT + * range: + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + * [me➞geo_loc_name](me_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + * [me➞lat_lon](me_lat_lon.md) REQ + * range: [String](types/String.md) + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilm.md b/mixs6/MicrobialMatBiofilm.md index 46bceaed..31e94fdf 100644 --- a/mixs6/MicrobialMatBiofilm.md +++ b/mixs6/MicrobialMatBiofilm.md @@ -7,7 +7,7 @@ microbial mat/biofilm URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBiofilm) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilmMisag],[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilmMimag],[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilmMe],[MicrobialMatBiofilm|alkalinity:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;bacteria_carb_prod:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;glucosidase_act:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;part_org_carb:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;tot_carb:string%20%3F;tot_nitro_content:string%20%3F;tot_org_carb:string%20%3F;turbidity:string%20%3F;water_content:string%20%3F]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilmMisag],[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilmMimag],[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilmMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -57,19 +61,19 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -77,59 +81,91 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -141,27 +177,27 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -173,7 +209,7 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -181,11 +217,11 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -193,7 +229,7 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -201,19 +237,19 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -225,49 +261,49 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None diff --git a/mixs6/MicrobialMatBiofilmMe.md b/mixs6/MicrobialMatBiofilmMe.md index 2a70f29c..8d247317 100644 --- a/mixs6/MicrobialMatBiofilmMe.md +++ b/mixs6/MicrobialMatBiofilmMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with me URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MicrobialMatBiofilmMe|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Me],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe],[MicrobialMatBiofilm],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Me],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe],[MicrobialMatBiofilm],[Me]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,219 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsBa.md b/mixs6/MicrobialMatBiofilmMigsBa.md index 71e56501..58276d97 100644 --- a/mixs6/MicrobialMatBiofilmMigsBa.md +++ b/mixs6/MicrobialMatBiofilmMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with migs_ba URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[MicrobialMatBiofilmMigsBa|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[MicrobialMatBiofilmMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,284 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/Microbia * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsEu.md b/mixs6/MicrobialMatBiofilmMigsEu.md index ac85c75d..605a7bf8 100644 --- a/mixs6/MicrobialMatBiofilmMigsEu.md +++ b/mixs6/MicrobialMatBiofilmMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with migs_eu URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[MicrobialMatBiofilmMigsEu|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[MicrobialMatBiofilmMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,284 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/Microbia * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsOrg.md b/mixs6/MicrobialMatBiofilmMigsOrg.md index 23e637d0..592bf61a 100644 --- a/mixs6/MicrobialMatBiofilmMigsOrg.md +++ b/mixs6/MicrobialMatBiofilmMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with migs_org URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[MicrobialMatBiofilmMigsOrg|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[MicrobialMatBiofilmMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,239 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsPl.md b/mixs6/MicrobialMatBiofilmMigsPl.md index 71e8c22e..01caf50c 100644 --- a/mixs6/MicrobialMatBiofilmMigsPl.md +++ b/mixs6/MicrobialMatBiofilmMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with migs_pl URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[MicrobialMatBiofilmMigsPl|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[MicrobialMatBiofilmMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,254 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/Microbia * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsVi.md b/mixs6/MicrobialMatBiofilmMigsVi.md index b3cffdd9..96a174b1 100644 --- a/mixs6/MicrobialMatBiofilmMigsVi.md +++ b/mixs6/MicrobialMatBiofilmMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with migs_vi URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[MicrobialMatBiofilmMigsVi|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[MicrobialMatBiofilmMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,279 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/Microbia * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MicrobialMatBiofilmMimag.md b/mixs6/MicrobialMatBiofilmMimag.md index e3c05a38..b1667bb7 100644 --- a/mixs6/MicrobialMatBiofilmMimag.md +++ b/mixs6/MicrobialMatBiofilmMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with mimag URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[MicrobialMatBiofilmMimag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Mimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[MicrobialMatBiofilmMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Mimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,299 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimarksC.md b/mixs6/MicrobialMatBiofilmMimarksC.md index 96c7872b..32203a20 100644 --- a/mixs6/MicrobialMatBiofilmMimarksC.md +++ b/mixs6/MicrobialMatBiofilmMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with mimarks_c URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[MicrobialMatBiofilmMimarksC|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[MicrobialMatBiofilmMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,184 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/Microb * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimarksS.md b/mixs6/MicrobialMatBiofilmMimarksS.md index e6d8f0ab..10b03a91 100644 --- a/mixs6/MicrobialMatBiofilmMimarksS.md +++ b/mixs6/MicrobialMatBiofilmMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with mimarks_s URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[MicrobialMatBiofilmMimarksS|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[MicrobialMatBiofilmMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,204 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/Microb * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMisag.md b/mixs6/MicrobialMatBiofilmMisag.md index aa336139..f331a4cc 100644 --- a/mixs6/MicrobialMatBiofilmMisag.md +++ b/mixs6/MicrobialMatBiofilmMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with misag URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[MicrobialMatBiofilmMisag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Misag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[MicrobialMatBiofilmMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Misag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,304 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMiuvig.md b/mixs6/MicrobialMatBiofilmMiuvig.md index f2909401..c90aad19 100644 --- a/mixs6/MicrobialMatBiofilmMiuvig.md +++ b/mixs6/MicrobialMatBiofilmMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for microbial mat_biofilm with miuvig URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[MicrobialMatBiofilmMiuvig|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tot_carb(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Miuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[MicrobialMatBiofilmMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Miuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,59 +72,91 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -132,27 +168,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -164,7 +200,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -172,11 +208,11 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -184,7 +220,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -192,19 +228,19 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -216,49 +252,369 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsBa.md b/mixs6/MigsBa.md index 9c4c2ddc..7f65e1ed 100644 --- a/mixs6/MigsBa.md +++ b/mixs6/MigsBa.md @@ -7,13 +7,12 @@ migs_ba Checklist URI: [mixs.vocab:MigsBa](https://w3id.org/mixs/vocab/MigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa]uses%20-.->[MigsBa],[WastewaterSludgeMigsBa]uses%20-.->[MigsBa],[SoilMigsBa]uses%20-.->[MigsBa],[SedimentMigsBa]uses%20-.->[MigsBa],[Plant-associatedMigsBa]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa]uses%20-.->[MigsBa],[MicrobialMatBiofilmMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-coresMigsBa]uses%20-.->[MigsBa],[Human-vaginalMigsBa]uses%20-.->[MigsBa],[Human-skinMigsBa]uses%20-.->[MigsBa],[Human-oralMigsBa]uses%20-.->[MigsBa],[Human-gutMigsBa]uses%20-.->[MigsBa],[Human-associatedMigsBa]uses%20-.->[MigsBa],[Host-associatedMigsBa]uses%20-.->[MigsBa],[CoreMigsBa]uses%20-.->[MigsBa],[BuiltEnvironmentMigsBa]uses%20-.->[MigsBa],[AirMigsBa]uses%20-.->[MigsBa],[WaterMigsBa],[WastewaterSludgeMigsBa],[SoilMigsBa],[SedimentMigsBa],[Plant-associatedMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MicrobialMatBiofilmMigsBa],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-coresMigsBa],[Human-vaginalMigsBa],[Human-skinMigsBa],[Human-oralMigsBa],[Human-gutMigsBa],[Human-associatedMigsBa],[Host-associatedMigsBa],[CoreMigsBa],[BuiltEnvironmentMigsBa],[AirMigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsBa],[WastewaterSludgeMigsBa]uses%20-.->[MigsBa],[SoilMigsBa]uses%20-.->[MigsBa],[SedimentMigsBa]uses%20-.->[MigsBa],[Plant-associatedMigsBa]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa]uses%20-.->[MigsBa],[MicrobialMatBiofilmMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-coresMigsBa]uses%20-.->[MigsBa],[Human-vaginalMigsBa]uses%20-.->[MigsBa],[Human-skinMigsBa]uses%20-.->[MigsBa],[Human-oralMigsBa]uses%20-.->[MigsBa],[Human-gutMigsBa]uses%20-.->[MigsBa],[Human-associatedMigsBa]uses%20-.->[MigsBa],[Host-associatedMigsBa]uses%20-.->[MigsBa],[BuiltEnvironmentMigsBa]uses%20-.->[MigsBa],[AirMigsBa]uses%20-.->[MigsBa],[WaterMigsBa],[WastewaterSludgeMigsBa],[SoilMigsBa],[SedimentMigsBa],[Plant-associatedMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MicrobialMatBiofilmMigsBa],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-coresMigsBa],[Human-vaginalMigsBa],[Human-skinMigsBa],[Human-oralMigsBa],[Human-gutMigsBa],[Human-associatedMigsBa],[Host-associatedMigsBa],[BuiltEnvironmentMigsBa],[AirMigsBa]) ## Mixin for * [AirMigsBa](AirMigsBa.md) (mixin) - Combinatorial checklist for air with migs_ba * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) (mixin) - Combinatorial checklist for built environment with migs_ba - * [CoreMigsBa](CoreMigsBa.md) (mixin) - Combinatorial checklist for core with migs_ba * [Host-associatedMigsBa](Host-associatedMigsBa.md) (mixin) - Combinatorial checklist for host-associated with migs_ba * [Human-associatedMigsBa](Human-associatedMigsBa.md) (mixin) - Combinatorial checklist for human-associated with migs_ba * [Human-gutMigsBa](Human-gutMigsBa.md) (mixin) - Combinatorial checklist for human-gut with migs_ba @@ -35,3 +34,112 @@ URI: [mixs.vocab:MigsBa](https://w3id.org/mixs/vocab/MigsBa) ## Attributes + +### Own + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + * [migs_ba➞collection_date](migs_ba_collection_date.md) REQ + * range: [String](types/String.md) + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) REQ + * range: [String](types/String.md) + * [migs_ba➞env_medium](migs_ba_env_medium.md) REQ + * range: [String](types/String.md) + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [migs_ba➞lat_lon](migs_ba_lat_lon.md) REQ + * range: [String](types/String.md) + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsEu.md b/mixs6/MigsEu.md index b95bea82..6c1aad1b 100644 --- a/mixs6/MigsEu.md +++ b/mixs6/MigsEu.md @@ -7,13 +7,12 @@ migs_eu Checklist URI: [mixs.vocab:MigsEu](https://w3id.org/mixs/vocab/MigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu]uses%20-.->[MigsEu],[WastewaterSludgeMigsEu]uses%20-.->[MigsEu],[SoilMigsEu]uses%20-.->[MigsEu],[SedimentMigsEu]uses%20-.->[MigsEu],[Plant-associatedMigsEu]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu]uses%20-.->[MigsEu],[MicrobialMatBiofilmMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-coresMigsEu]uses%20-.->[MigsEu],[Human-vaginalMigsEu]uses%20-.->[MigsEu],[Human-skinMigsEu]uses%20-.->[MigsEu],[Human-oralMigsEu]uses%20-.->[MigsEu],[Human-gutMigsEu]uses%20-.->[MigsEu],[Human-associatedMigsEu]uses%20-.->[MigsEu],[Host-associatedMigsEu]uses%20-.->[MigsEu],[CoreMigsEu]uses%20-.->[MigsEu],[BuiltEnvironmentMigsEu]uses%20-.->[MigsEu],[AirMigsEu]uses%20-.->[MigsEu],[WaterMigsEu],[WastewaterSludgeMigsEu],[SoilMigsEu],[SedimentMigsEu],[Plant-associatedMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MicrobialMatBiofilmMigsEu],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-coresMigsEu],[Human-vaginalMigsEu],[Human-skinMigsEu],[Human-oralMigsEu],[Human-gutMigsEu],[Human-associatedMigsEu],[Host-associatedMigsEu],[CoreMigsEu],[BuiltEnvironmentMigsEu],[AirMigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsEu],[WastewaterSludgeMigsEu]uses%20-.->[MigsEu],[SoilMigsEu]uses%20-.->[MigsEu],[SedimentMigsEu]uses%20-.->[MigsEu],[Plant-associatedMigsEu]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu]uses%20-.->[MigsEu],[MicrobialMatBiofilmMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-coresMigsEu]uses%20-.->[MigsEu],[Human-vaginalMigsEu]uses%20-.->[MigsEu],[Human-skinMigsEu]uses%20-.->[MigsEu],[Human-oralMigsEu]uses%20-.->[MigsEu],[Human-gutMigsEu]uses%20-.->[MigsEu],[Human-associatedMigsEu]uses%20-.->[MigsEu],[Host-associatedMigsEu]uses%20-.->[MigsEu],[BuiltEnvironmentMigsEu]uses%20-.->[MigsEu],[AirMigsEu]uses%20-.->[MigsEu],[WaterMigsEu],[WastewaterSludgeMigsEu],[SoilMigsEu],[SedimentMigsEu],[Plant-associatedMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MicrobialMatBiofilmMigsEu],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-coresMigsEu],[Human-vaginalMigsEu],[Human-skinMigsEu],[Human-oralMigsEu],[Human-gutMigsEu],[Human-associatedMigsEu],[Host-associatedMigsEu],[BuiltEnvironmentMigsEu],[AirMigsEu]) ## Mixin for * [AirMigsEu](AirMigsEu.md) (mixin) - Combinatorial checklist for air with migs_eu * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) (mixin) - Combinatorial checklist for built environment with migs_eu - * [CoreMigsEu](CoreMigsEu.md) (mixin) - Combinatorial checklist for core with migs_eu * [Host-associatedMigsEu](Host-associatedMigsEu.md) (mixin) - Combinatorial checklist for host-associated with migs_eu * [Human-associatedMigsEu](Human-associatedMigsEu.md) (mixin) - Combinatorial checklist for human-associated with migs_eu * [Human-gutMigsEu](Human-gutMigsEu.md) (mixin) - Combinatorial checklist for human-gut with migs_eu @@ -35,3 +34,112 @@ URI: [mixs.vocab:MigsEu](https://w3id.org/mixs/vocab/MigsEu) ## Attributes + +### Own + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + * [migs_eu➞collection_date](migs_eu_collection_date.md) REQ + * range: [String](types/String.md) + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) REQ + * range: [String](types/String.md) + * [migs_eu➞env_medium](migs_eu_env_medium.md) REQ + * range: [String](types/String.md) + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [migs_eu➞lat_lon](migs_eu_lat_lon.md) REQ + * range: [String](types/String.md) + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsOrg.md b/mixs6/MigsOrg.md index 63d64f6d..74eee03c 100644 --- a/mixs6/MigsOrg.md +++ b/mixs6/MigsOrg.md @@ -7,13 +7,12 @@ migs_org Checklist URI: [mixs.vocab:MigsOrg](https://w3id.org/mixs/vocab/MigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg]uses%20-.->[MigsOrg],[WastewaterSludgeMigsOrg]uses%20-.->[MigsOrg],[SoilMigsOrg]uses%20-.->[MigsOrg],[SedimentMigsOrg]uses%20-.->[MigsOrg],[Plant-associatedMigsOrg]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg]uses%20-.->[MigsOrg],[MicrobialMatBiofilmMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-coresMigsOrg]uses%20-.->[MigsOrg],[Human-vaginalMigsOrg]uses%20-.->[MigsOrg],[Human-skinMigsOrg]uses%20-.->[MigsOrg],[Human-oralMigsOrg]uses%20-.->[MigsOrg],[Human-gutMigsOrg]uses%20-.->[MigsOrg],[Human-associatedMigsOrg]uses%20-.->[MigsOrg],[Host-associatedMigsOrg]uses%20-.->[MigsOrg],[CoreMigsOrg]uses%20-.->[MigsOrg],[BuiltEnvironmentMigsOrg]uses%20-.->[MigsOrg],[AirMigsOrg]uses%20-.->[MigsOrg],[WaterMigsOrg],[WastewaterSludgeMigsOrg],[SoilMigsOrg],[SedimentMigsOrg],[Plant-associatedMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MicrobialMatBiofilmMigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-coresMigsOrg],[Human-vaginalMigsOrg],[Human-skinMigsOrg],[Human-oralMigsOrg],[Human-gutMigsOrg],[Human-associatedMigsOrg],[Host-associatedMigsOrg],[CoreMigsOrg],[BuiltEnvironmentMigsOrg],[AirMigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsOrg],[WastewaterSludgeMigsOrg]uses%20-.->[MigsOrg],[SoilMigsOrg]uses%20-.->[MigsOrg],[SedimentMigsOrg]uses%20-.->[MigsOrg],[Plant-associatedMigsOrg]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg]uses%20-.->[MigsOrg],[MicrobialMatBiofilmMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-coresMigsOrg]uses%20-.->[MigsOrg],[Human-vaginalMigsOrg]uses%20-.->[MigsOrg],[Human-skinMigsOrg]uses%20-.->[MigsOrg],[Human-oralMigsOrg]uses%20-.->[MigsOrg],[Human-gutMigsOrg]uses%20-.->[MigsOrg],[Human-associatedMigsOrg]uses%20-.->[MigsOrg],[Host-associatedMigsOrg]uses%20-.->[MigsOrg],[BuiltEnvironmentMigsOrg]uses%20-.->[MigsOrg],[AirMigsOrg]uses%20-.->[MigsOrg],[WaterMigsOrg],[WastewaterSludgeMigsOrg],[SoilMigsOrg],[SedimentMigsOrg],[Plant-associatedMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MicrobialMatBiofilmMigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-coresMigsOrg],[Human-vaginalMigsOrg],[Human-skinMigsOrg],[Human-oralMigsOrg],[Human-gutMigsOrg],[Human-associatedMigsOrg],[Host-associatedMigsOrg],[BuiltEnvironmentMigsOrg],[AirMigsOrg]) ## Mixin for * [AirMigsOrg](AirMigsOrg.md) (mixin) - Combinatorial checklist for air with migs_org * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) (mixin) - Combinatorial checklist for built environment with migs_org - * [CoreMigsOrg](CoreMigsOrg.md) (mixin) - Combinatorial checklist for core with migs_org * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) (mixin) - Combinatorial checklist for host-associated with migs_org * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) (mixin) - Combinatorial checklist for human-associated with migs_org * [Human-gutMigsOrg](Human-gutMigsOrg.md) (mixin) - Combinatorial checklist for human-gut with migs_org @@ -35,3 +34,94 @@ URI: [mixs.vocab:MigsOrg](https://w3id.org/mixs/vocab/MigsOrg) ## Attributes + +### Own + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + * [migs_org➞collection_date](migs_org_collection_date.md) REQ + * range: [String](types/String.md) + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [migs_org➞env_local_scale](migs_org_env_local_scale.md) REQ + * range: [String](types/String.md) + * [migs_org➞env_medium](migs_org_env_medium.md) REQ + * range: [String](types/String.md) + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [migs_org➞lat_lon](migs_org_lat_lon.md) REQ + * range: [String](types/String.md) + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsPl.md b/mixs6/MigsPl.md index 3e8fe35e..93b47854 100644 --- a/mixs6/MigsPl.md +++ b/mixs6/MigsPl.md @@ -7,13 +7,12 @@ migs_pl Checklist URI: [mixs.vocab:MigsPl](https://w3id.org/mixs/vocab/MigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl]uses%20-.->[MigsPl],[WastewaterSludgeMigsPl]uses%20-.->[MigsPl],[SoilMigsPl]uses%20-.->[MigsPl],[SedimentMigsPl]uses%20-.->[MigsPl],[Plant-associatedMigsPl]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl]uses%20-.->[MigsPl],[MicrobialMatBiofilmMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-coresMigsPl]uses%20-.->[MigsPl],[Human-vaginalMigsPl]uses%20-.->[MigsPl],[Human-skinMigsPl]uses%20-.->[MigsPl],[Human-oralMigsPl]uses%20-.->[MigsPl],[Human-gutMigsPl]uses%20-.->[MigsPl],[Human-associatedMigsPl]uses%20-.->[MigsPl],[Host-associatedMigsPl]uses%20-.->[MigsPl],[CoreMigsPl]uses%20-.->[MigsPl],[BuiltEnvironmentMigsPl]uses%20-.->[MigsPl],[AirMigsPl]uses%20-.->[MigsPl],[WaterMigsPl],[WastewaterSludgeMigsPl],[SoilMigsPl],[SedimentMigsPl],[Plant-associatedMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MicrobialMatBiofilmMigsPl],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-coresMigsPl],[Human-vaginalMigsPl],[Human-skinMigsPl],[Human-oralMigsPl],[Human-gutMigsPl],[Human-associatedMigsPl],[Host-associatedMigsPl],[CoreMigsPl],[BuiltEnvironmentMigsPl],[AirMigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsPl],[WastewaterSludgeMigsPl]uses%20-.->[MigsPl],[SoilMigsPl]uses%20-.->[MigsPl],[SedimentMigsPl]uses%20-.->[MigsPl],[Plant-associatedMigsPl]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl]uses%20-.->[MigsPl],[MicrobialMatBiofilmMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-coresMigsPl]uses%20-.->[MigsPl],[Human-vaginalMigsPl]uses%20-.->[MigsPl],[Human-skinMigsPl]uses%20-.->[MigsPl],[Human-oralMigsPl]uses%20-.->[MigsPl],[Human-gutMigsPl]uses%20-.->[MigsPl],[Human-associatedMigsPl]uses%20-.->[MigsPl],[Host-associatedMigsPl]uses%20-.->[MigsPl],[BuiltEnvironmentMigsPl]uses%20-.->[MigsPl],[AirMigsPl]uses%20-.->[MigsPl],[WaterMigsPl],[WastewaterSludgeMigsPl],[SoilMigsPl],[SedimentMigsPl],[Plant-associatedMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MicrobialMatBiofilmMigsPl],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-coresMigsPl],[Human-vaginalMigsPl],[Human-skinMigsPl],[Human-oralMigsPl],[Human-gutMigsPl],[Human-associatedMigsPl],[Host-associatedMigsPl],[BuiltEnvironmentMigsPl],[AirMigsPl]) ## Mixin for * [AirMigsPl](AirMigsPl.md) (mixin) - Combinatorial checklist for air with migs_pl * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) (mixin) - Combinatorial checklist for built environment with migs_pl - * [CoreMigsPl](CoreMigsPl.md) (mixin) - Combinatorial checklist for core with migs_pl * [Host-associatedMigsPl](Host-associatedMigsPl.md) (mixin) - Combinatorial checklist for host-associated with migs_pl * [Human-associatedMigsPl](Human-associatedMigsPl.md) (mixin) - Combinatorial checklist for human-associated with migs_pl * [Human-gutMigsPl](Human-gutMigsPl.md) (mixin) - Combinatorial checklist for human-gut with migs_pl @@ -35,3 +34,100 @@ URI: [mixs.vocab:MigsPl](https://w3id.org/mixs/vocab/MigsPl) ## Attributes + +### Own + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + * [migs_pl➞collection_date](migs_pl_collection_date.md) REQ + * range: [String](types/String.md) + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) REQ + * range: [String](types/String.md) + * [migs_pl➞env_medium](migs_pl_env_medium.md) REQ + * range: [String](types/String.md) + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [migs_pl➞lat_lon](migs_pl_lat_lon.md) REQ + * range: [String](types/String.md) + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MigsVi.md b/mixs6/MigsVi.md index a95a674d..c45db5cb 100644 --- a/mixs6/MigsVi.md +++ b/mixs6/MigsVi.md @@ -7,13 +7,12 @@ migs_vi Checklist URI: [mixs.vocab:MigsVi](https://w3id.org/mixs/vocab/MigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi]uses%20-.->[MigsVi],[WastewaterSludgeMigsVi]uses%20-.->[MigsVi],[SoilMigsVi]uses%20-.->[MigsVi],[SedimentMigsVi]uses%20-.->[MigsVi],[Plant-associatedMigsVi]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi]uses%20-.->[MigsVi],[MicrobialMatBiofilmMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-coresMigsVi]uses%20-.->[MigsVi],[Human-vaginalMigsVi]uses%20-.->[MigsVi],[Human-skinMigsVi]uses%20-.->[MigsVi],[Human-oralMigsVi]uses%20-.->[MigsVi],[Human-gutMigsVi]uses%20-.->[MigsVi],[Human-associatedMigsVi]uses%20-.->[MigsVi],[Host-associatedMigsVi]uses%20-.->[MigsVi],[CoreMigsVi]uses%20-.->[MigsVi],[BuiltEnvironmentMigsVi]uses%20-.->[MigsVi],[AirMigsVi]uses%20-.->[MigsVi],[WaterMigsVi],[WastewaterSludgeMigsVi],[SoilMigsVi],[SedimentMigsVi],[Plant-associatedMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MicrobialMatBiofilmMigsVi],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-coresMigsVi],[Human-vaginalMigsVi],[Human-skinMigsVi],[Human-oralMigsVi],[Human-gutMigsVi],[Human-associatedMigsVi],[Host-associatedMigsVi],[CoreMigsVi],[BuiltEnvironmentMigsVi],[AirMigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsVi],[WastewaterSludgeMigsVi]uses%20-.->[MigsVi],[SoilMigsVi]uses%20-.->[MigsVi],[SedimentMigsVi]uses%20-.->[MigsVi],[Plant-associatedMigsVi]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi]uses%20-.->[MigsVi],[MicrobialMatBiofilmMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-coresMigsVi]uses%20-.->[MigsVi],[Human-vaginalMigsVi]uses%20-.->[MigsVi],[Human-skinMigsVi]uses%20-.->[MigsVi],[Human-oralMigsVi]uses%20-.->[MigsVi],[Human-gutMigsVi]uses%20-.->[MigsVi],[Human-associatedMigsVi]uses%20-.->[MigsVi],[Host-associatedMigsVi]uses%20-.->[MigsVi],[BuiltEnvironmentMigsVi]uses%20-.->[MigsVi],[AirMigsVi]uses%20-.->[MigsVi],[WaterMigsVi],[WastewaterSludgeMigsVi],[SoilMigsVi],[SedimentMigsVi],[Plant-associatedMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MicrobialMatBiofilmMigsVi],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-coresMigsVi],[Human-vaginalMigsVi],[Human-skinMigsVi],[Human-oralMigsVi],[Human-gutMigsVi],[Human-associatedMigsVi],[Host-associatedMigsVi],[BuiltEnvironmentMigsVi],[AirMigsVi]) ## Mixin for * [AirMigsVi](AirMigsVi.md) (mixin) - Combinatorial checklist for air with migs_vi * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) (mixin) - Combinatorial checklist for built environment with migs_vi - * [CoreMigsVi](CoreMigsVi.md) (mixin) - Combinatorial checklist for core with migs_vi * [Host-associatedMigsVi](Host-associatedMigsVi.md) (mixin) - Combinatorial checklist for host-associated with migs_vi * [Human-associatedMigsVi](Human-associatedMigsVi.md) (mixin) - Combinatorial checklist for human-associated with migs_vi * [Human-gutMigsVi](Human-gutMigsVi.md) (mixin) - Combinatorial checklist for human-gut with migs_vi @@ -35,3 +34,110 @@ URI: [mixs.vocab:MigsVi](https://w3id.org/mixs/vocab/MigsVi) ## Attributes + +### Own + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + * [migs_vi➞collection_date](migs_vi_collection_date.md) REQ + * range: [String](types/String.md) + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) REQ + * range: [String](types/String.md) + * [migs_vi➞env_medium](migs_vi_env_medium.md) REQ + * range: [String](types/String.md) + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [migs_vi➞lat_lon](migs_vi_lat_lon.md) REQ + * range: [String](types/String.md) + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Mimag.md b/mixs6/Mimag.md index 52e0c140..7f0d0072 100644 --- a/mixs6/Mimag.md +++ b/mixs6/Mimag.md @@ -7,13 +7,12 @@ mimag Checklist URI: [mixs.vocab:Mimag](https://w3id.org/mixs/vocab/Mimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag]uses%20-.->[Mimag],[WastewaterSludgeMimag]uses%20-.->[Mimag],[SoilMimag]uses%20-.->[Mimag],[SedimentMimag]uses%20-.->[Mimag],[Plant-associatedMimag]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag]uses%20-.->[Mimag],[MicrobialMatBiofilmMimag]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabsMimag]uses%20-.->[Mimag],[HydrocarbonResources-coresMimag]uses%20-.->[Mimag],[Human-vaginalMimag]uses%20-.->[Mimag],[Human-skinMimag]uses%20-.->[Mimag],[Human-oralMimag]uses%20-.->[Mimag],[Human-gutMimag]uses%20-.->[Mimag],[Human-associatedMimag]uses%20-.->[Mimag],[Host-associatedMimag]uses%20-.->[Mimag],[CoreMimag]uses%20-.->[Mimag],[BuiltEnvironmentMimag]uses%20-.->[Mimag],[AirMimag]uses%20-.->[Mimag],[WaterMimag],[WastewaterSludgeMimag],[SoilMimag],[SedimentMimag],[Plant-associatedMimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MicrobialMatBiofilmMimag],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-coresMimag],[Human-vaginalMimag],[Human-skinMimag],[Human-oralMimag],[Human-gutMimag],[Human-associatedMimag],[Host-associatedMimag],[CoreMimag],[BuiltEnvironmentMimag],[AirMimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Mimag],[WastewaterSludgeMimag]uses%20-.->[Mimag],[SoilMimag]uses%20-.->[Mimag],[SedimentMimag]uses%20-.->[Mimag],[Plant-associatedMimag]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag]uses%20-.->[Mimag],[MicrobialMatBiofilmMimag]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabsMimag]uses%20-.->[Mimag],[HydrocarbonResources-coresMimag]uses%20-.->[Mimag],[Human-vaginalMimag]uses%20-.->[Mimag],[Human-skinMimag]uses%20-.->[Mimag],[Human-oralMimag]uses%20-.->[Mimag],[Human-gutMimag]uses%20-.->[Mimag],[Human-associatedMimag]uses%20-.->[Mimag],[Host-associatedMimag]uses%20-.->[Mimag],[BuiltEnvironmentMimag]uses%20-.->[Mimag],[AirMimag]uses%20-.->[Mimag],[WaterMimag],[WastewaterSludgeMimag],[SoilMimag],[SedimentMimag],[Plant-associatedMimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MicrobialMatBiofilmMimag],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-coresMimag],[Human-vaginalMimag],[Human-skinMimag],[Human-oralMimag],[Human-gutMimag],[Human-associatedMimag],[Host-associatedMimag],[BuiltEnvironmentMimag],[AirMimag]) ## Mixin for * [AirMimag](AirMimag.md) (mixin) - Combinatorial checklist for air with mimag * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) (mixin) - Combinatorial checklist for built environment with mimag - * [CoreMimag](CoreMimag.md) (mixin) - Combinatorial checklist for core with mimag * [Host-associatedMimag](Host-associatedMimag.md) (mixin) - Combinatorial checklist for host-associated with mimag * [Human-associatedMimag](Human-associatedMimag.md) (mixin) - Combinatorial checklist for human-associated with mimag * [Human-gutMimag](Human-gutMimag.md) (mixin) - Combinatorial checklist for human-gut with mimag @@ -35,3 +34,118 @@ URI: [mixs.vocab:Mimag](https://w3id.org/mixs/vocab/Mimag) ## Attributes + +### Own + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + * [mimag➞collection_date](mimag_collection_date.md) REQ + * range: [String](types/String.md) + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + * [mimag➞env_broad_scale](mimag_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [mimag➞env_local_scale](mimag_env_local_scale.md) REQ + * range: [String](types/String.md) + * [mimag➞env_medium](mimag_env_medium.md) REQ + * range: [String](types/String.md) + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + * [mimag➞geo_loc_name](mimag_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + * [mimag➞lat_lon](mimag_lat_lon.md) REQ + * range: [String](types/String.md) + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MimarksC.md b/mixs6/MimarksC.md index 39ab66e3..4a96e8a1 100644 --- a/mixs6/MimarksC.md +++ b/mixs6/MimarksC.md @@ -7,13 +7,12 @@ mimarks_c Checklist URI: [mixs.vocab:MimarksC](https://w3id.org/mixs/vocab/MimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC]uses%20-.->[MimarksC],[WastewaterSludgeMimarksC]uses%20-.->[MimarksC],[SoilMimarksC]uses%20-.->[MimarksC],[SedimentMimarksC]uses%20-.->[MimarksC],[Plant-associatedMimarksC]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC]uses%20-.->[MimarksC],[MicrobialMatBiofilmMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-coresMimarksC]uses%20-.->[MimarksC],[Human-vaginalMimarksC]uses%20-.->[MimarksC],[Human-skinMimarksC]uses%20-.->[MimarksC],[Human-oralMimarksC]uses%20-.->[MimarksC],[Human-gutMimarksC]uses%20-.->[MimarksC],[Human-associatedMimarksC]uses%20-.->[MimarksC],[Host-associatedMimarksC]uses%20-.->[MimarksC],[CoreMimarksC]uses%20-.->[MimarksC],[BuiltEnvironmentMimarksC]uses%20-.->[MimarksC],[AirMimarksC]uses%20-.->[MimarksC],[WaterMimarksC],[WastewaterSludgeMimarksC],[SoilMimarksC],[SedimentMimarksC],[Plant-associatedMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MicrobialMatBiofilmMimarksC],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-coresMimarksC],[Human-vaginalMimarksC],[Human-skinMimarksC],[Human-oralMimarksC],[Human-gutMimarksC],[Human-associatedMimarksC],[Host-associatedMimarksC],[CoreMimarksC],[BuiltEnvironmentMimarksC],[AirMimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MimarksC],[WastewaterSludgeMimarksC]uses%20-.->[MimarksC],[SoilMimarksC]uses%20-.->[MimarksC],[SedimentMimarksC]uses%20-.->[MimarksC],[Plant-associatedMimarksC]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC]uses%20-.->[MimarksC],[MicrobialMatBiofilmMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-coresMimarksC]uses%20-.->[MimarksC],[Human-vaginalMimarksC]uses%20-.->[MimarksC],[Human-skinMimarksC]uses%20-.->[MimarksC],[Human-oralMimarksC]uses%20-.->[MimarksC],[Human-gutMimarksC]uses%20-.->[MimarksC],[Human-associatedMimarksC]uses%20-.->[MimarksC],[Host-associatedMimarksC]uses%20-.->[MimarksC],[BuiltEnvironmentMimarksC]uses%20-.->[MimarksC],[AirMimarksC]uses%20-.->[MimarksC],[WaterMimarksC],[WastewaterSludgeMimarksC],[SoilMimarksC],[SedimentMimarksC],[Plant-associatedMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MicrobialMatBiofilmMimarksC],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-coresMimarksC],[Human-vaginalMimarksC],[Human-skinMimarksC],[Human-oralMimarksC],[Human-gutMimarksC],[Human-associatedMimarksC],[Host-associatedMimarksC],[BuiltEnvironmentMimarksC],[AirMimarksC]) ## Mixin for * [AirMimarksC](AirMimarksC.md) (mixin) - Combinatorial checklist for air with mimarks_c * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) (mixin) - Combinatorial checklist for built environment with mimarks_c - * [CoreMimarksC](CoreMimarksC.md) (mixin) - Combinatorial checklist for core with mimarks_c * [Host-associatedMimarksC](Host-associatedMimarksC.md) (mixin) - Combinatorial checklist for host-associated with mimarks_c * [Human-associatedMimarksC](Human-associatedMimarksC.md) (mixin) - Combinatorial checklist for human-associated with mimarks_c * [Human-gutMimarksC](Human-gutMimarksC.md) (mixin) - Combinatorial checklist for human-gut with mimarks_c @@ -35,3 +34,72 @@ URI: [mixs.vocab:MimarksC](https://w3id.org/mixs/vocab/MimarksC) ## Attributes + +### Own + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞collection_date](mimarks_c_collection_date.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞env_medium](mimarks_c_env_medium.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MimarksS.md b/mixs6/MimarksS.md index eb4ebef4..a03c0cbd 100644 --- a/mixs6/MimarksS.md +++ b/mixs6/MimarksS.md @@ -7,13 +7,12 @@ mimarks_s Checklist URI: [mixs.vocab:MimarksS](https://w3id.org/mixs/vocab/MimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS]uses%20-.->[MimarksS],[WastewaterSludgeMimarksS]uses%20-.->[MimarksS],[SoilMimarksS]uses%20-.->[MimarksS],[SedimentMimarksS]uses%20-.->[MimarksS],[Plant-associatedMimarksS]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS]uses%20-.->[MimarksS],[MicrobialMatBiofilmMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-coresMimarksS]uses%20-.->[MimarksS],[Human-vaginalMimarksS]uses%20-.->[MimarksS],[Human-skinMimarksS]uses%20-.->[MimarksS],[Human-oralMimarksS]uses%20-.->[MimarksS],[Human-gutMimarksS]uses%20-.->[MimarksS],[Human-associatedMimarksS]uses%20-.->[MimarksS],[Host-associatedMimarksS]uses%20-.->[MimarksS],[CoreMimarksS]uses%20-.->[MimarksS],[BuiltEnvironmentMimarksS]uses%20-.->[MimarksS],[AirMimarksS]uses%20-.->[MimarksS],[WaterMimarksS],[WastewaterSludgeMimarksS],[SoilMimarksS],[SedimentMimarksS],[Plant-associatedMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MicrobialMatBiofilmMimarksS],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-coresMimarksS],[Human-vaginalMimarksS],[Human-skinMimarksS],[Human-oralMimarksS],[Human-gutMimarksS],[Human-associatedMimarksS],[Host-associatedMimarksS],[CoreMimarksS],[BuiltEnvironmentMimarksS],[AirMimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MimarksS],[WastewaterSludgeMimarksS]uses%20-.->[MimarksS],[SoilMimarksS]uses%20-.->[MimarksS],[SedimentMimarksS]uses%20-.->[MimarksS],[Plant-associatedMimarksS]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS]uses%20-.->[MimarksS],[MicrobialMatBiofilmMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-coresMimarksS]uses%20-.->[MimarksS],[Human-vaginalMimarksS]uses%20-.->[MimarksS],[Human-skinMimarksS]uses%20-.->[MimarksS],[Human-oralMimarksS]uses%20-.->[MimarksS],[Human-gutMimarksS]uses%20-.->[MimarksS],[Human-associatedMimarksS]uses%20-.->[MimarksS],[Host-associatedMimarksS]uses%20-.->[MimarksS],[BuiltEnvironmentMimarksS]uses%20-.->[MimarksS],[AirMimarksS]uses%20-.->[MimarksS],[WaterMimarksS],[WastewaterSludgeMimarksS],[SoilMimarksS],[SedimentMimarksS],[Plant-associatedMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MicrobialMatBiofilmMimarksS],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-coresMimarksS],[Human-vaginalMimarksS],[Human-skinMimarksS],[Human-oralMimarksS],[Human-gutMimarksS],[Human-associatedMimarksS],[Host-associatedMimarksS],[BuiltEnvironmentMimarksS],[AirMimarksS]) ## Mixin for * [AirMimarksS](AirMimarksS.md) (mixin) - Combinatorial checklist for air with mimarks_s * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) (mixin) - Combinatorial checklist for built environment with mimarks_s - * [CoreMimarksS](CoreMimarksS.md) (mixin) - Combinatorial checklist for core with mimarks_s * [Host-associatedMimarksS](Host-associatedMimarksS.md) (mixin) - Combinatorial checklist for host-associated with mimarks_s * [Human-associatedMimarksS](Human-associatedMimarksS.md) (mixin) - Combinatorial checklist for human-associated with mimarks_s * [Human-gutMimarksS](Human-gutMimarksS.md) (mixin) - Combinatorial checklist for human-gut with mimarks_s @@ -35,3 +34,80 @@ URI: [mixs.vocab:MimarksS](https://w3id.org/mixs/vocab/MimarksS) ## Attributes + +### Own + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞collection_date](mimarks_s_collection_date.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞env_medium](mimarks_s_env_medium.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Misag.md b/mixs6/Misag.md index 149f3453..697d9fb3 100644 --- a/mixs6/Misag.md +++ b/mixs6/Misag.md @@ -7,13 +7,12 @@ misag Checklist URI: [mixs.vocab:Misag](https://w3id.org/mixs/vocab/Misag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag]uses%20-.->[Misag],[WastewaterSludgeMisag]uses%20-.->[Misag],[SoilMisag]uses%20-.->[Misag],[SedimentMisag]uses%20-.->[Misag],[Plant-associatedMisag]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironmentMisag]uses%20-.->[Misag],[MicrobialMatBiofilmMisag]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabsMisag]uses%20-.->[Misag],[HydrocarbonResources-coresMisag]uses%20-.->[Misag],[Human-vaginalMisag]uses%20-.->[Misag],[Human-skinMisag]uses%20-.->[Misag],[Human-oralMisag]uses%20-.->[Misag],[Human-gutMisag]uses%20-.->[Misag],[Human-associatedMisag]uses%20-.->[Misag],[Host-associatedMisag]uses%20-.->[Misag],[CoreMisag]uses%20-.->[Misag],[BuiltEnvironmentMisag]uses%20-.->[Misag],[AirMisag]uses%20-.->[Misag],[WaterMisag],[WastewaterSludgeMisag],[SoilMisag],[SedimentMisag],[Plant-associatedMisag],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MicrobialMatBiofilmMisag],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-coresMisag],[Human-vaginalMisag],[Human-skinMisag],[Human-oralMisag],[Human-gutMisag],[Human-associatedMisag],[Host-associatedMisag],[CoreMisag],[BuiltEnvironmentMisag],[AirMisag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Misag],[WastewaterSludgeMisag]uses%20-.->[Misag],[SoilMisag]uses%20-.->[Misag],[SedimentMisag]uses%20-.->[Misag],[Plant-associatedMisag]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironmentMisag]uses%20-.->[Misag],[MicrobialMatBiofilmMisag]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabsMisag]uses%20-.->[Misag],[HydrocarbonResources-coresMisag]uses%20-.->[Misag],[Human-vaginalMisag]uses%20-.->[Misag],[Human-skinMisag]uses%20-.->[Misag],[Human-oralMisag]uses%20-.->[Misag],[Human-gutMisag]uses%20-.->[Misag],[Human-associatedMisag]uses%20-.->[Misag],[Host-associatedMisag]uses%20-.->[Misag],[BuiltEnvironmentMisag]uses%20-.->[Misag],[AirMisag]uses%20-.->[Misag],[WaterMisag],[WastewaterSludgeMisag],[SoilMisag],[SedimentMisag],[Plant-associatedMisag],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MicrobialMatBiofilmMisag],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-coresMisag],[Human-vaginalMisag],[Human-skinMisag],[Human-oralMisag],[Human-gutMisag],[Human-associatedMisag],[Host-associatedMisag],[BuiltEnvironmentMisag],[AirMisag]) ## Mixin for * [AirMisag](AirMisag.md) (mixin) - Combinatorial checklist for air with misag * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) (mixin) - Combinatorial checklist for built environment with misag - * [CoreMisag](CoreMisag.md) (mixin) - Combinatorial checklist for core with misag * [Host-associatedMisag](Host-associatedMisag.md) (mixin) - Combinatorial checklist for host-associated with misag * [Human-associatedMisag](Human-associatedMisag.md) (mixin) - Combinatorial checklist for human-associated with misag * [Human-gutMisag](Human-gutMisag.md) (mixin) - Combinatorial checklist for human-gut with misag @@ -35,3 +34,120 @@ URI: [mixs.vocab:Misag](https://w3id.org/mixs/vocab/Misag) ## Attributes + +### Own + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + * [misag➞collection_date](misag_collection_date.md) REQ + * range: [String](types/String.md) + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + * [misag➞env_broad_scale](misag_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [misag➞env_local_scale](misag_env_local_scale.md) REQ + * range: [String](types/String.md) + * [misag➞env_medium](misag_env_medium.md) REQ + * range: [String](types/String.md) + * [misag➞env_package](misag_env_package.md) OPT + * range: + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + * [misag➞geo_loc_name](misag_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + * [misag➞lat_lon](misag_lat_lon.md) REQ + * range: [String](types/String.md) + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md index a0a6c132..c3229252 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md @@ -7,7 +7,7 @@ miscellaneous natural or artificial environment URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment|alkalinity:string%20%3F;ammonium:string%20%3F;biomass:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;misc_param:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;perturbation:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;water_current:string%20%3F]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -45,11 +49,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -57,67 +61,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -133,11 +169,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -145,15 +181,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -165,33 +201,33 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md index 9094066e..bc5cd283 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMe|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment],[Me]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,203 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md index cdf4666e..a8b55543 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsBa|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment],[MigsBa]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,268 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md index 52c5b664..07182c20 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsEu|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment],[MigsEu]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,268 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md index 5432641c..3daecfa1 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MigsOrg]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,223 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md index 02f9623e..915cce32 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsPl|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment],[MigsPl]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,238 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md index b0e93ae1..e5833c4b 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMigsVi|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment],[MigsVi]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,263 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md index ebae0da5..afe96989 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimag|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment],[Mimag]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,283 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md index eddc635d..279c3fe9 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimarksC|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksC]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,168 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3 * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md index b0da0478..76fa6617 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMimarksS|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksS]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,188 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3 * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md index 9951c9cc..995098e2 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MiscellaneousNaturalOrArtificialEnvironmentMisag|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment],[Misag]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,288 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md index 926735a3..90cacc5a 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for miscellaneous natural or artificial environment with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig|alkalinity(i):string%20%3F;ammonium(i):string%20%3F;biomass(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -36,11 +40,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * Example: total;20 gram None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -48,67 +52,99 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -124,11 +160,11 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -136,15 +172,15 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * Example: 2.98 milligram per liter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -156,33 +192,353 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Miuvig.md b/mixs6/Miuvig.md index 091eb141..37d1902f 100644 --- a/mixs6/Miuvig.md +++ b/mixs6/Miuvig.md @@ -7,13 +7,12 @@ miuvig Checklist URI: [mixs.vocab:Miuvig](https://w3id.org/mixs/vocab/Miuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig]uses%20-.->[Miuvig],[WastewaterSludgeMiuvig]uses%20-.->[Miuvig],[SoilMiuvig]uses%20-.->[Miuvig],[SedimentMiuvig]uses%20-.->[Miuvig],[Plant-associatedMiuvig]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig]uses%20-.->[Miuvig],[MicrobialMatBiofilmMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-coresMiuvig]uses%20-.->[Miuvig],[Human-vaginalMiuvig]uses%20-.->[Miuvig],[Human-skinMiuvig]uses%20-.->[Miuvig],[Human-oralMiuvig]uses%20-.->[Miuvig],[Human-gutMiuvig]uses%20-.->[Miuvig],[Human-associatedMiuvig]uses%20-.->[Miuvig],[Host-associatedMiuvig]uses%20-.->[Miuvig],[CoreMiuvig]uses%20-.->[Miuvig],[BuiltEnvironmentMiuvig]uses%20-.->[Miuvig],[AirMiuvig]uses%20-.->[Miuvig],[WaterMiuvig],[WastewaterSludgeMiuvig],[SoilMiuvig],[SedimentMiuvig],[Plant-associatedMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MicrobialMatBiofilmMiuvig],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-coresMiuvig],[Human-vaginalMiuvig],[Human-skinMiuvig],[Human-oralMiuvig],[Human-gutMiuvig],[Human-associatedMiuvig],[Host-associatedMiuvig],[CoreMiuvig],[BuiltEnvironmentMiuvig],[AirMiuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Miuvig],[WastewaterSludgeMiuvig]uses%20-.->[Miuvig],[SoilMiuvig]uses%20-.->[Miuvig],[SedimentMiuvig]uses%20-.->[Miuvig],[Plant-associatedMiuvig]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig]uses%20-.->[Miuvig],[MicrobialMatBiofilmMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-coresMiuvig]uses%20-.->[Miuvig],[Human-vaginalMiuvig]uses%20-.->[Miuvig],[Human-skinMiuvig]uses%20-.->[Miuvig],[Human-oralMiuvig]uses%20-.->[Miuvig],[Human-gutMiuvig]uses%20-.->[Miuvig],[Human-associatedMiuvig]uses%20-.->[Miuvig],[Host-associatedMiuvig]uses%20-.->[Miuvig],[BuiltEnvironmentMiuvig]uses%20-.->[Miuvig],[AirMiuvig]uses%20-.->[Miuvig],[WaterMiuvig],[WastewaterSludgeMiuvig],[SoilMiuvig],[SedimentMiuvig],[Plant-associatedMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MicrobialMatBiofilmMiuvig],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-coresMiuvig],[Human-vaginalMiuvig],[Human-skinMiuvig],[Human-oralMiuvig],[Human-gutMiuvig],[Human-associatedMiuvig],[Host-associatedMiuvig],[BuiltEnvironmentMiuvig],[AirMiuvig]) ## Mixin for * [AirMiuvig](AirMiuvig.md) (mixin) - Combinatorial checklist for air with miuvig * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) (mixin) - Combinatorial checklist for built environment with miuvig - * [CoreMiuvig](CoreMiuvig.md) (mixin) - Combinatorial checklist for core with miuvig * [Host-associatedMiuvig](Host-associatedMiuvig.md) (mixin) - Combinatorial checklist for host-associated with miuvig * [Human-associatedMiuvig](Human-associatedMiuvig.md) (mixin) - Combinatorial checklist for human-associated with miuvig * [Human-gutMiuvig](Human-gutMiuvig.md) (mixin) - Combinatorial checklist for human-gut with miuvig @@ -35,3 +34,146 @@ URI: [mixs.vocab:Miuvig](https://w3id.org/mixs/vocab/Miuvig) ## Attributes + +### Own + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + * [miuvig➞collection_date](miuvig_collection_date.md) REQ + * range: [String](types/String.md) + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [miuvig➞env_local_scale](miuvig_env_local_scale.md) REQ + * range: [String](types/String.md) + * [miuvig➞env_medium](miuvig_env_medium.md) REQ + * range: [String](types/String.md) + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + * [miuvig➞lat_lon](miuvig_lat_lon.md) REQ + * range: [String](types/String.md) + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associated.md b/mixs6/Plant-associated.md index 0b1d8e8d..8a310352 100644 --- a/mixs6/Plant-associated.md +++ b/mixs6/Plant-associated.md @@ -7,7 +7,7 @@ plant-associated URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMiuvig],[Plant-associatedMisag],[Plant-associatedMimarksS],[Plant-associatedMimarksC],[Plant-associatedMimag],[Plant-associatedMigsVi],[Plant-associatedMigsPl],[Plant-associatedMigsOrg],[Plant-associatedMigsEu],[Plant-associatedMigsBa],[Plant-associatedMe],[Plant-associated|air_temp_regm:string%20%3F;ances_data:string%20%3F;antibiotic_regm:string%20%3F;biol_stat:biol_stat_enum%20%3F;biotic_regm:string%20%3F;chem_administration:string%20%3F;chem_mutagen:string%20%3F;climate_environment:string%20%3F;cult_root_med:string%20%3F;fertilizer_regm:string%20%3F;fungicide_regm:string%20%3F;gaseous_environment:string%20%3F;genetic_mod:string%20%3F;gravity:string%20%3F;growth_facil:string%20%3F;growth_habit:growth_habit_enum%20%3F;growth_hormone_regm:string%20%3F;herbicide_regm:string%20%3F;host_age:string%20%3F;host_common_name:string%20%3F;host_disease_stat:string%20%3F;host_dry_mass:string%20%3F;host_genotype:string%20%3F;host_height:string%20%3F;host_infra_specific_name:string%20%3F;host_infra_specific_rank:string%20%3F;host_length:string%20%3F;host_life_stage:string%20%3F;host_phenotype:string%20%3F;host_taxid:string%20%3F;host_tot_mass:string%20%3F;host_wet_mass:string%20%3F;humidity_regm:string%20%3F;light_regm:string%20%3F;mechanical_damage:string%20%3F;mineral_nutr_regm:string%20%3F;misc_param:string%20%3F;non_mineral_nutr_regm:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph_regm:string%20%3F;perturbation:string%20%3F;pesticide_regm:string%20%3F;plant_growth_med:plant_growth_med_enum%20%3F;plant_product:string%20%3F;plant_sex:plant_sex_enum%20%3F;plant_struc:string%20%3F;radiation_regm:string%20%3F;rainfall_regm:string%20%3F;root_cond:string%20%3F;root_med_carbon:string%20%3F;root_med_macronutr:string%20%3F;root_med_micronutr:string%20%3F;root_med_suppl:string%20%3F;root_med_ph:string%20%3F;root_med_regl:string%20%3F;root_med_solid:string%20%3F;salt_regm:string%20%3F;samp_capt_status:samp_capt_status_enum%20%3F;samp_dis_stage:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;season_environment:string%20%3F;standing_water_regm:string%20%3F;temp:string%20%3F;tiss_cult_growth_med:string%20%3F;water_temp_regm:string%20%3F;watering_regm:string%20%3F]^-[Plant-associatedMiuvig],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated]^-[Plant-associatedMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMiuvig],[Plant-associatedMisag],[Plant-associatedMimarksS],[Plant-associatedMimarksC],[Plant-associatedMimag],[Plant-associatedMigsVi],[Plant-associatedMigsPl],[Plant-associatedMigsOrg],[Plant-associatedMigsEu],[Plant-associatedMigsBa],[Plant-associatedMe],[QuantityValue]OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -63,10 +67,34 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -83,6 +111,10 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -105,7 +137,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -117,7 +149,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -125,7 +157,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -137,7 +169,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -153,16 +185,20 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -245,7 +281,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -273,7 +309,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -285,11 +321,11 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -301,7 +337,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used diff --git a/mixs6/Plant-associatedMe.md b/mixs6/Plant-associatedMe.md index cdc9c1d7..0865f77c 100644 --- a/mixs6/Plant-associatedMe.md +++ b/mixs6/Plant-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with me URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associatedMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMe|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Me],[Plant-associated]^-[Plant-associatedMe],[Plant-associated],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Me],[Plant-associated]^-[Plant-associatedMe],[Plant-associated],[Me]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,173 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsBa.md b/mixs6/Plant-associatedMigsBa.md index 8a9f7e34..be306b51 100644 --- a/mixs6/Plant-associatedMigsBa.md +++ b/mixs6/Plant-associatedMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with migs_ba URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-associatedMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsBa|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsBa],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsBa],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated],[MigsBa]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,238 @@ URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsEu.md b/mixs6/Plant-associatedMigsEu.md index b1ca1161..c2b3e73e 100644 --- a/mixs6/Plant-associatedMigsEu.md +++ b/mixs6/Plant-associatedMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with migs_eu URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-associatedMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsEu|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsEu],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsEu],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated],[MigsEu]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,238 @@ URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsOrg.md b/mixs6/Plant-associatedMigsOrg.md index ba9f7455..1cb1c6e9 100644 --- a/mixs6/Plant-associatedMigsOrg.md +++ b/mixs6/Plant-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with migs_org URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-associatedMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsOrg|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsOrg],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsOrg],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated],[MigsOrg]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,193 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsPl.md b/mixs6/Plant-associatedMigsPl.md index 7ae6fe4e..7bc1bea7 100644 --- a/mixs6/Plant-associatedMigsPl.md +++ b/mixs6/Plant-associatedMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with migs_pl URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-associatedMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsPl|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsPl],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsPl],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated],[MigsPl]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,208 @@ URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsVi.md b/mixs6/Plant-associatedMigsVi.md index 27fa98f5..70e3efa3 100644 --- a/mixs6/Plant-associatedMigsVi.md +++ b/mixs6/Plant-associatedMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with migs_vi URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-associatedMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMigsVi|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsVi],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsVi],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated],[MigsVi]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,233 @@ URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Plant-associatedMimag.md b/mixs6/Plant-associatedMimag.md index 04c7d1a2..a973cc6a 100644 --- a/mixs6/Plant-associatedMimag.md +++ b/mixs6/Plant-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with mimag URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associatedMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimag|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Mimag],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Mimag],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated],[Mimag]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,253 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimarksC.md b/mixs6/Plant-associatedMimarksC.md index 08773cda..8daf889c 100644 --- a/mixs6/Plant-associatedMimarksC.md +++ b/mixs6/Plant-associatedMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with mimarks_c URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-associatedMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimarksC|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksC],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksC],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated],[MimarksC]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,138 @@ URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-ass * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimarksS.md b/mixs6/Plant-associatedMimarksS.md index 2126c285..8974d1fd 100644 --- a/mixs6/Plant-associatedMimarksS.md +++ b/mixs6/Plant-associatedMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with mimarks_s URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-associatedMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMimarksS|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksS],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksS],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated],[MimarksS]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,158 @@ URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-ass * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMisag.md b/mixs6/Plant-associatedMisag.md index 9b357997..9dacb368 100644 --- a/mixs6/Plant-associatedMisag.md +++ b/mixs6/Plant-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with misag URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associatedMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMisag|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Misag],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Misag],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated],[Misag]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,258 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMiuvig.md b/mixs6/Plant-associatedMiuvig.md index bb63fe6e..445a1e2e 100644 --- a/mixs6/Plant-associatedMiuvig.md +++ b/mixs6/Plant-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for plant-associated with miuvig URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-associatedMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Plant-associatedMiuvig|air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_age(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_dry_mass(i):string%20%3F;host_genotype(i):string%20%3F;host_height(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_length(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;host_tot_mass(i):string%20%3F;host_wet_mass(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):string%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;temp(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Miuvig],[Plant-associated]^-[Plant-associatedMiuvig],[Plant-associated],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Miuvig],[Plant-associated]^-[Plant-associatedMiuvig],[Plant-associated],[Miuvig]) ## Parents @@ -26,6 +26,10 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [ances_data](ances_data.md) OPT * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) * range: [String](types/String.md) @@ -54,10 +58,34 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * range: [String](types/String.md) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fertilizer_regm](fertilizer_regm.md) OPT * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens * range: [String](types/String.md) @@ -74,6 +102,10 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * range: [String](types/String.md) * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [gravity](gravity.md) OPT * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments * range: [String](types/String.md) @@ -96,7 +128,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [host_age](host_age.md) OPT * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 days None * [host_common_name](host_common_name.md) OPT * Description: Common name of the host, e.g. Human @@ -108,7 +140,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: rabies [DOID:11260] None * [host_dry_mass](host_dry_mass.md) OPT * Description: Measurement of dry mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 gram None * [host_genotype](host_genotype.md) OPT * Description: Observed genotype @@ -116,7 +148,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: C57BL/6 None * [host_height](host_height.md) OPT * Description: The height of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 meter None * [host_infra_specific_name](host_infra_specific_name.md) OPT * Description: Taxonomic information about the host below subspecies level @@ -128,7 +160,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: subspecies None * [host_length](host_length.md) OPT * Description: The length of subject - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter None * [host_life_stage](host_life_stage.md) OPT * Description: Description of life stage of host @@ -144,16 +176,20 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: 7955 None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [host_wet_mass](host_wet_mass.md) OPT * Description: Measurement of wet mass - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 gram None * [humidity_regm](humidity_regm.md) OPT * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_regm](light_regm.md) OPT * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. * range: [String](types/String.md) @@ -236,7 +272,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: H3BO3;6.2¬†milligram per liter None * [root_med_ph](root_med_ph.md) OPT * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.5 None * [root_med_regl](root_med_regl.md) OPT * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. @@ -264,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -276,11 +312,11 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_environment](season_environment.md) OPT * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment @@ -292,7 +328,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT * Description: Description of plant tissue culture growth media used @@ -306,3 +342,323 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Sediment.md b/mixs6/Sediment.md index b7865c01..28646d9e 100644 --- a/mixs6/Sediment.md +++ b/mixs6/Sediment.md @@ -7,7 +7,7 @@ sediment URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig],[SedimentMisag],[SedimentMimarksS],[SedimentMimarksC],[SedimentMimag],[SedimentMigsVi],[SedimentMigsPl],[SedimentMigsOrg],[SedimentMigsEu],[SedimentMigsBa],[SedimentMe],[Sediment|alkalinity:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;bacteria_carb_prod:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;glucosidase_act:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;methane:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;particle_class:string%20%3F;part_org_carb:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;porosity:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;sediment_type:sediment_type_enum%20%3F;silicate:string%20%3F;sodium:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;temp:string%20%3F;tidal_stage:tidal_stage_enum%20%3F;tot_carb:string%20%3F;tot_depth_water_col:string%20%3F;tot_nitro_content:string%20%3F;tot_org_carb:string%20%3F;turbidity:string%20%3F;water_content:string%20%3F]^-[SedimentMiuvig],[Sediment]^-[SedimentMisag],[Sediment]^-[SedimentMimarksS],[Sediment]^-[SedimentMimarksC],[Sediment]^-[SedimentMimag],[Sediment]^-[SedimentMigsVi],[Sediment]^-[SedimentMigsPl],[Sediment]^-[SedimentMigsOrg],[Sediment]^-[SedimentMigsEu],[Sediment]^-[SedimentMigsBa],[Sediment]^-[SedimentMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig],[SedimentMisag],[SedimentMimarksS],[SedimentMimarksC],[SedimentMimag],[SedimentMigsVi],[SedimentMigsPl],[SedimentMigsOrg],[SedimentMigsEu],[SedimentMigsBa],[SedimentMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -57,19 +61,19 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -77,63 +81,95 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -145,27 +181,27 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -177,7 +213,7 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -189,11 +225,11 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -201,7 +237,7 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -213,19 +249,19 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -237,11 +273,11 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -249,23 +285,23 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -273,25 +309,25 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None diff --git a/mixs6/SedimentMe.md b/mixs6/SedimentMe.md index c69a1f9d..e4d2ee98 100644 --- a/mixs6/SedimentMe.md +++ b/mixs6/SedimentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with me URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMe|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Me],[Sediment]^-[SedimentMe],[Sediment],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Me],[Sediment]^-[SedimentMe],[Sediment],[QuantityValue],[Me]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,195 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsBa.md b/mixs6/SedimentMigsBa.md index 92a51e60..e6501b5c 100644 --- a/mixs6/SedimentMigsBa.md +++ b/mixs6/SedimentMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with migs_ba URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsBa|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsBa],[Sediment]^-[SedimentMigsBa],[Sediment],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsBa],[Sediment]^-[SedimentMigsBa],[Sediment],[QuantityValue],[MigsBa]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,260 @@ URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsEu.md b/mixs6/SedimentMigsEu.md index 631f1299..3d272fc7 100644 --- a/mixs6/SedimentMigsEu.md +++ b/mixs6/SedimentMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with migs_eu URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsEu|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsEu],[Sediment]^-[SedimentMigsEu],[Sediment],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsEu],[Sediment]^-[SedimentMigsEu],[Sediment],[QuantityValue],[MigsEu]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,260 @@ URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsOrg.md b/mixs6/SedimentMigsOrg.md index c8b12ac8..98d68cd4 100644 --- a/mixs6/SedimentMigsOrg.md +++ b/mixs6/SedimentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with migs_org URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsOrg|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsOrg],[Sediment]^-[SedimentMigsOrg],[Sediment],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsOrg],[Sediment]^-[SedimentMigsOrg],[Sediment],[QuantityValue],[MigsOrg]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,215 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsPl.md b/mixs6/SedimentMigsPl.md index 3aad22f9..175a953f 100644 --- a/mixs6/SedimentMigsPl.md +++ b/mixs6/SedimentMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with migs_pl URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsPl|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsPl],[Sediment]^-[SedimentMigsPl],[Sediment],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsPl],[Sediment]^-[SedimentMigsPl],[Sediment],[QuantityValue],[MigsPl]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,230 @@ URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsVi.md b/mixs6/SedimentMigsVi.md index a15cc6ea..e0ed85ab 100644 --- a/mixs6/SedimentMigsVi.md +++ b/mixs6/SedimentMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with migs_vi URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsVi|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MigsVi],[Sediment]^-[SedimentMigsVi],[Sediment],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsVi],[Sediment]^-[SedimentMigsVi],[Sediment],[QuantityValue],[MigsVi]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,255 @@ URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SedimentMimag.md b/mixs6/SedimentMimag.md index d43727d5..574e973b 100644 --- a/mixs6/SedimentMimag.md +++ b/mixs6/SedimentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with mimag URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Mimag],[Sediment]^-[SedimentMimag],[Sediment],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Mimag],[Sediment]^-[SedimentMimag],[Sediment],[QuantityValue],[Mimag]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,275 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMimarksC.md b/mixs6/SedimentMimarksC.md index ef0d616c..5da00c06 100644 --- a/mixs6/SedimentMimarksC.md +++ b/mixs6/SedimentMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with mimarks_c URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksC|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksC],[Sediment]^-[SedimentMimarksC],[Sediment],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksC],[Sediment]^-[SedimentMimarksC],[Sediment],[QuantityValue],[MimarksC]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,160 @@ URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMimarksS.md b/mixs6/SedimentMimarksS.md index 1c64cf35..85575182 100644 --- a/mixs6/SedimentMimarksS.md +++ b/mixs6/SedimentMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with mimarks_s URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksS|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[MimarksS],[Sediment]^-[SedimentMimarksS],[Sediment],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksS],[Sediment]^-[SedimentMimarksS],[Sediment],[QuantityValue],[MimarksS]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,180 @@ URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMisag.md b/mixs6/SedimentMisag.md index 45a69ce9..ec72e9bf 100644 --- a/mixs6/SedimentMisag.md +++ b/mixs6/SedimentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with misag URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMisag|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Misag],[Sediment]^-[SedimentMisag],[Sediment],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Misag],[Sediment]^-[SedimentMisag],[Sediment],[QuantityValue],[Misag]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,280 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMiuvig.md b/mixs6/SedimentMiuvig.md index dbb8fd22..94201cfe 100644 --- a/mixs6/SedimentMiuvig.md +++ b/mixs6/SedimentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for sediment with miuvig URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig|alkalinity(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;glucosidase_act(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;methane(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;particle_class(i):string%20%3F;part_org_carb(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;silicate(i):string%20%3F;sodium(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_carb(i):string%20%3F;tot_depth_water_col(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_org_carb(i):string%20%3F;turbidity(i):string%20%3F;water_content(i):string%20%3F]uses%20-.->[Miuvig],[Sediment]^-[SedimentMiuvig],[Sediment],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Miuvig],[Sediment]^-[SedimentMiuvig],[Sediment],[QuantityValue],[Miuvig]) ## Parents @@ -24,23 +24,27 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -48,19 +52,19 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -68,63 +72,95 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [methane](methane.md) OPT * Description: Methane (gas) amount or concentration at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1800 parts per billion None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -136,27 +172,27 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -168,7 +204,7 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [particle_class](particle_class.md) OPT * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values @@ -180,11 +216,11 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -192,7 +228,7 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -204,19 +240,19 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -228,11 +264,11 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [sediment_type](sediment_type.md) OPT * Description: Information about the sediment type based on major constituents @@ -240,23 +276,23 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: biogenous None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -264,25 +300,345 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * Example: high tide None * [tot_carb](tot_carb.md) OPT * Description: Total carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Soil.md b/mixs6/Soil.md index fa176f3f..b03f851e 100644 --- a/mixs6/Soil.md +++ b/mixs6/Soil.md @@ -7,7 +7,7 @@ soil URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig],[SoilMisag],[SoilMimarksS],[SoilMimarksC],[SoilMimag],[SoilMigsVi],[SoilMigsPl],[SoilMigsOrg],[SoilMigsEu],[SoilMigsBa],[SoilMe],[Soil|cur_land_use:cur_land_use_enum%20%3F;cur_vegetation:string%20%3F;cur_vegetation_meth:string%20%3F;previous_land_use:string%20%3F;previous_land_use_meth:string%20%3F;crop_rotation:string%20%3F;agrochem_addition:string%20%3F;tillage:tillage_enum%20%3F;fire:string%20%3F;flooding:string%20%3F;extreme_event:string%20%3F;horizon:horizon_enum%20%3F;horizon_meth:string%20%3F;sieving:string%20%3F;water_content:string%20%3F;water_content_soil_meth:string%20%3F;samp_vol_we_dna_ext:string%20%3F;pool_dna_extracts:string%20%3F;store_cond:string%20%3F;link_climate_info:string%20%3F;annual_temp:string%20%3F;season_temp:string%20%3F;annual_precpt:string%20%3F;season_precpt:string%20%3F;link_class_info:string%20%3F;fao_class:fao_class_enum%20%3F;local_class:string%20%3F;local_class_meth:string%20%3F;soil_type:string%20%3F;soil_type_meth:string%20%3F;slope_gradient:string%20%3F;slope_aspect:string%20%3F;profile_position:profile_position_enum%20%3F;drainage_class:drainage_class_enum%20%3F;texture:string%20%3F;texture_meth:string%20%3F;ph:string%20%3F;ph_meth:string%20%3F;tot_org_carb:string%20%3F;tot_org_c_meth:string%20%3F;tot_nitro_content:string%20%3F;tot_nitro_content_meth:string%20%3F;microbial_biomass:string%20%3F;microbial_biomass_meth:string%20%3F;link_addit_analys:string%20%3F;extreme_salinity:string%20%3F;salinity_meth:string%20%3F;heavy_metals:string%20%3F;heavy_metals_meth:string%20%3F;al_sat:string%20%3F;al_sat_meth:string%20%3F;misc_param:string%20%3F]^-[SoilMiuvig],[Soil]^-[SoilMisag],[Soil]^-[SoilMimarksS],[Soil]^-[SoilMimarksC],[Soil]^-[SoilMimag],[Soil]^-[SoilMigsVi],[Soil]^-[SoilMigsPl],[Soil]^-[SoilMigsOrg],[Soil]^-[SoilMigsEu],[Soil]^-[SoilMigsBa],[Soil]^-[SoilMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig],[SoilMisag],[SoilMimarksS],[SoilMimarksC],[SoilMimag],[SoilMigsVi],[SoilMigsPl],[SoilMigsOrg],[SoilMigsEu],[SoilMigsBa],[SoilMe],[QuantityValue]OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -67,17 +75,37 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -91,6 +119,10 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -107,6 +139,10 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -129,7 +165,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -141,7 +177,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -169,15 +205,15 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -185,11 +221,11 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -205,7 +241,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -217,7 +253,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -229,11 +265,11 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil diff --git a/mixs6/SoilMe.md b/mixs6/SoilMe.md index d5b75606..3dae9c38 100644 --- a/mixs6/SoilMe.md +++ b/mixs6/SoilMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with me URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMe|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Soil]^-[SoilMe],[Soil],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Soil]^-[SoilMe],[Soil],[QuantityValue],[Me]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,183 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsBa.md b/mixs6/SoilMigsBa.md index ab04e1be..46f2ef02 100644 --- a/mixs6/SoilMigsBa.md +++ b/mixs6/SoilMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with migs_ba URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsBa|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Soil]^-[SoilMigsBa],[Soil],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Soil]^-[SoilMigsBa],[Soil],[QuantityValue],[MigsBa]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,248 @@ URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsEu.md b/mixs6/SoilMigsEu.md index 4552ac13..b93a9199 100644 --- a/mixs6/SoilMigsEu.md +++ b/mixs6/SoilMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with migs_eu URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsEu|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Soil]^-[SoilMigsEu],[Soil],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Soil]^-[SoilMigsEu],[Soil],[QuantityValue],[MigsEu]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,248 @@ URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsOrg.md b/mixs6/SoilMigsOrg.md index 15bddc18..313b1796 100644 --- a/mixs6/SoilMigsOrg.md +++ b/mixs6/SoilMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with migs_org URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsOrg|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Soil]^-[SoilMigsOrg],[Soil],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Soil]^-[SoilMigsOrg],[Soil],[QuantityValue],[MigsOrg]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,203 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsPl.md b/mixs6/SoilMigsPl.md index 88f3149b..75035ccf 100644 --- a/mixs6/SoilMigsPl.md +++ b/mixs6/SoilMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with migs_pl URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsPl|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Soil]^-[SoilMigsPl],[Soil],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Soil]^-[SoilMigsPl],[Soil],[QuantityValue],[MigsPl]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,218 @@ URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMigsVi.md b/mixs6/SoilMigsVi.md index c90e6092..ff60ef30 100644 --- a/mixs6/SoilMigsVi.md +++ b/mixs6/SoilMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with migs_vi URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsVi|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Soil]^-[SoilMigsVi],[Soil],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Soil]^-[SoilMigsVi],[Soil],[QuantityValue],[MigsVi]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,243 @@ URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SoilMimag.md b/mixs6/SoilMimag.md index d4ad6c7a..8f609c07 100644 --- a/mixs6/SoilMimag.md +++ b/mixs6/SoilMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with mimag URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimag|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Soil]^-[SoilMimag],[Soil],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Soil]^-[SoilMimag],[Soil],[QuantityValue],[Mimag]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,263 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMimarksC.md b/mixs6/SoilMimarksC.md index 64e66456..a9dcb3b2 100644 --- a/mixs6/SoilMimarksC.md +++ b/mixs6/SoilMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with mimarks_c URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksC|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Soil]^-[SoilMimarksC],[Soil],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Soil]^-[SoilMimarksC],[Soil],[QuantityValue],[MimarksC]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,148 @@ URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMimarksS.md b/mixs6/SoilMimarksS.md index f6e4c733..a32e8f72 100644 --- a/mixs6/SoilMimarksS.md +++ b/mixs6/SoilMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with mimarks_s URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksS|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Soil]^-[SoilMimarksS],[Soil],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Soil]^-[SoilMimarksS],[Soil],[QuantityValue],[MimarksS]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,168 @@ URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMisag.md b/mixs6/SoilMisag.md index 28d400c5..7bbdebf7 100644 --- a/mixs6/SoilMisag.md +++ b/mixs6/SoilMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with misag URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMisag|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Soil]^-[SoilMisag],[Soil],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Soil]^-[SoilMisag],[Soil],[QuantityValue],[Misag]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,268 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMiuvig.md b/mixs6/SoilMiuvig.md index a491c7bc..51d4ec13 100644 --- a/mixs6/SoilMiuvig.md +++ b/mixs6/SoilMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for soil with miuvig URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig|cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content(i):string%20%3F;water_content_soil_meth(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;annual_temp(i):string%20%3F;season_temp(i):string%20%3F;annual_precpt(i):string%20%3F;season_precpt(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;slope_gradient(i):string%20%3F;slope_aspect(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture(i):string%20%3F;texture_meth(i):string%20%3F;ph(i):string%20%3F;ph_meth(i):string%20%3F;tot_org_carb(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;extreme_salinity(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Soil]^-[SoilMiuvig],[Soil],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Soil]^-[SoilMiuvig],[Soil],[QuantityValue],[Miuvig]) ## Parents @@ -28,20 +28,28 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: roundup;5 milligram per liter;2018-06-21 None * [al_sat](al_sat.md) OPT * Description: Aluminum saturation (esp. For tropical soils) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [al_sat_meth](al_sat_meth.md) OPT * Description: Reference or method used in determining Al saturation * range: [String](types/String.md) * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [annual_temp](annual_temp.md) OPT * Description: Mean annual temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule * range: [String](types/String.md) @@ -58,17 +66,37 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Description: Reference or method used in vegetation classification * range: [String](types/String.md) * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [drainage_class](drainage_class.md) OPT * Description: Drainage classification from a standard system such as the USDA system * range: * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations * range: [String](types/String.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [fao_class](fao_class.md) OPT * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups @@ -82,6 +110,10 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Description: Historical and/or physical evidence of flooding * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [heavy_metals](heavy_metals.md) OPT * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations * range: [String](types/String.md) @@ -98,6 +130,10 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Description: Reference or method used in determining the horizon * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [link_addit_analys](link_addit_analys.md) OPT * Description: Link to additional analysis results performed on the sample * range: [String](types/String.md) @@ -120,7 +156,7 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: None * [microbial_biomass](microbial_biomass.md) OPT * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [microbial_biomass_meth](microbial_biomass_meth.md) OPT * Description: Reference or method used in determining microbial biomass @@ -132,7 +168,7 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [ph_meth](ph_meth.md) OPT * Description: Reference or method used in determining ph @@ -160,15 +196,15 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [season_precpt](season_precpt.md) OPT * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [season_temp](season_temp.md) OPT * Description: Mean seasonal temperature - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 18 degree Celsius None * [sieving](sieving.md) OPT * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved @@ -176,11 +212,11 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: None * [slope_aspect](slope_aspect.md) OPT * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [slope_gradient](slope_gradient.md) OPT * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [soil_type](soil_type.md) OPT * Description: Soil series name or other lower-level classification @@ -196,7 +232,7 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: -20 degree Celsius freezer;P2Y10D None * [texture](texture.md) OPT * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [texture_meth](texture_meth.md) OPT * Description: Reference or method used in determining soil texture @@ -208,7 +244,7 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: chisel None * [tot_nitro_content](tot_nitro_content.md) OPT * Description: Total nitrogen content of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT * Description: Reference or method used in determining the total nitrogen @@ -220,13 +256,333 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * Example: None * [tot_org_carb](tot_org_carb.md) OPT * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content](water_content.md) OPT * Description: Water content measurement - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [water_content_soil_meth](water_content_soil_meth.md) OPT * Description: Reference or method used in determining the water content of soil * range: [String](types/String.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludge.md b/mixs6/WastewaterSludge.md index 909a1a7c..c169a3de 100644 --- a/mixs6/WastewaterSludge.md +++ b/mixs6/WastewaterSludge.md @@ -7,7 +7,7 @@ wastewater/sludge URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig],[WastewaterSludgeMisag],[WastewaterSludgeMimarksS],[WastewaterSludgeMimarksC],[WastewaterSludgeMimag],[WastewaterSludgeMigsVi],[WastewaterSludgeMigsPl],[WastewaterSludgeMigsOrg],[WastewaterSludgeMigsEu],[WastewaterSludgeMigsBa],[WastewaterSludgeMe],[WastewaterSludge|alkalinity:string%20%3F;biochem_oxygen_dem:string%20%3F;chem_administration:string%20%3F;chem_oxygen_dem:string%20%3F;efficiency_percent:string%20%3F;emulsions:string%20%3F;gaseous_substances:string%20%3F;indust_eff_percent:string%20%3F;inorg_particles:string%20%3F;misc_param:string%20%3F;nitrate:string%20%3F;org_particles:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;perturbation:string%20%3F;phosphate:string%20%3F;pre_treatment:string%20%3F;primary_treatment:string%20%3F;reactor_type:string%20%3F;samp_salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;secondary_treatment:string%20%3F;sewage_type:string%20%3F;sludge_retent_time:string%20%3F;sodium:string%20%3F;soluble_inorg_mat:string%20%3F;soluble_org_mat:string%20%3F;suspend_solids:string%20%3F;temp:string%20%3F;tertiary_treatment:string%20%3F;tot_nitro:string%20%3F;tot_phosphate:string%20%3F;wastewater_type:string%20%3F]^-[WastewaterSludgeMiuvig],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge]^-[WastewaterSludgeMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig],[WastewaterSludgeMisag],[WastewaterSludgeMimarksS],[WastewaterSludgeMimarksC],[WastewaterSludgeMimag],[WastewaterSludgeMigsVi],[WastewaterSludgeMigsPl],[WastewaterSludgeMigsOrg],[WastewaterSludgeMigsEu],[WastewaterSludgeMigsBa],[WastewaterSludgeMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -45,35 +49,67 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -93,11 +129,11 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -113,7 +149,7 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -125,11 +161,11 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -141,11 +177,11 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -161,7 +197,7 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -169,11 +205,11 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. diff --git a/mixs6/WastewaterSludgeMe.md b/mixs6/WastewaterSludgeMe.md index 8bad9eaf..991d6ee4 100644 --- a/mixs6/WastewaterSludgeMe.md +++ b/mixs6/WastewaterSludgeMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with me URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludgeMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMe|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Me],[WastewaterSludge]^-[WastewaterSludgeMe],[WastewaterSludge],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Me],[WastewaterSludge]^-[WastewaterSludgeMe],[WastewaterSludge],[QuantityValue],[Me]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,183 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsBa.md b/mixs6/WastewaterSludgeMigsBa.md index c611e1f8..b3a10a64 100644 --- a/mixs6/WastewaterSludgeMigsBa.md +++ b/mixs6/WastewaterSludgeMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with migs_ba URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterSludgeMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsBa|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsBa],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsBa],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge],[QuantityValue],[MigsBa]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,248 @@ URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsEu.md b/mixs6/WastewaterSludgeMigsEu.md index 70a0c1ba..b2a7097d 100644 --- a/mixs6/WastewaterSludgeMigsEu.md +++ b/mixs6/WastewaterSludgeMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with migs_eu URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterSludgeMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsEu|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge],[QuantityValue],[MigsEu]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,248 @@ URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsOrg.md b/mixs6/WastewaterSludgeMigsOrg.md index 932a870f..674f8c01 100644 --- a/mixs6/WastewaterSludgeMigsOrg.md +++ b/mixs6/WastewaterSludgeMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with migs_org URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsOrg|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge],[QuantityValue],[MigsOrg]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,203 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsPl.md b/mixs6/WastewaterSludgeMigsPl.md index e1184e09..816023f0 100644 --- a/mixs6/WastewaterSludgeMigsPl.md +++ b/mixs6/WastewaterSludgeMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with migs_pl URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterSludgeMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsPl|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge],[QuantityValue],[MigsPl]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,218 @@ URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsVi.md b/mixs6/WastewaterSludgeMigsVi.md index 884f9914..ecafa006 100644 --- a/mixs6/WastewaterSludgeMigsVi.md +++ b/mixs6/WastewaterSludgeMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with migs_vi URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterSludgeMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsVi|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge],[QuantityValue],[MigsVi]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,243 @@ URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WastewaterSludgeMimag.md b/mixs6/WastewaterSludgeMimag.md index ac381809..45af03c6 100644 --- a/mixs6/WastewaterSludgeMimag.md +++ b/mixs6/WastewaterSludgeMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with mimag URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSludgeMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimag|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Mimag],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Mimag],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge],[QuantityValue],[Mimag]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,263 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimarksC.md b/mixs6/WastewaterSludgeMimarksC.md index f5971281..8d90d637 100644 --- a/mixs6/WastewaterSludgeMimarksC.md +++ b/mixs6/WastewaterSludgeMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with mimarks_c URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksC|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksC],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksC],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge],[QuantityValue],[MimarksC]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,148 @@ URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/Wastewate * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimarksS.md b/mixs6/WastewaterSludgeMimarksS.md index b088bdb6..d32da042 100644 --- a/mixs6/WastewaterSludgeMimarksS.md +++ b/mixs6/WastewaterSludgeMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with mimarks_s URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksS|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge],[QuantityValue],[MimarksS]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,168 @@ URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/Wastewate * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMisag.md b/mixs6/WastewaterSludgeMisag.md index 87211def..e852dd0f 100644 --- a/mixs6/WastewaterSludgeMisag.md +++ b/mixs6/WastewaterSludgeMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with misag URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSludgeMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMisag|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Misag],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Misag],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge],[QuantityValue],[Misag]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,268 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMiuvig.md b/mixs6/WastewaterSludgeMiuvig.md index 941c3b55..1ed5690c 100644 --- a/mixs6/WastewaterSludgeMiuvig.md +++ b/mixs6/WastewaterSludgeMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for wastewater_sludge with miuvig URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterSludgeMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig|alkalinity(i):string%20%3F;biochem_oxygen_dem(i):string%20%3F;chem_administration(i):string%20%3F;chem_oxygen_dem(i):string%20%3F;efficiency_percent(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;indust_eff_percent(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;nitrate(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;perturbation(i):string%20%3F;phosphate(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;sludge_retent_time(i):string%20%3F;sodium(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;temp(i):string%20%3F;tertiary_treatment(i):string%20%3F;tot_nitro(i):string%20%3F;tot_phosphate(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Miuvig],[WastewaterSludge]^-[WastewaterSludgeMiuvig],[WastewaterSludge],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Miuvig],[WastewaterSludge]^-[WastewaterSludgeMiuvig],[WastewaterSludge],[QuantityValue],[Miuvig]) ## Parents @@ -24,11 +24,15 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -36,35 +40,67 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chem_oxygen_dem](chem_oxygen_dem.md) OPT * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [emulsions](emulsions.md) OPT * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * range: [String](types/String.md) * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [gaseous_substances](gaseous_substances.md) OPT * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances * range: [String](types/String.md) * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [indust_eff_percent](indust_eff_percent.md) OPT * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [inorg_particles](inorg_particles.md) OPT * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles * range: [String](types/String.md) * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [org_particles](org_particles.md) OPT * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. @@ -84,11 +120,11 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [pre_treatment](pre_treatment.md) OPT * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater @@ -104,7 +140,7 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 milligram per liter None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -116,11 +152,11 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [secondary_treatment](secondary_treatment.md) OPT * Description: The process for substantially degrading the biological content of the sewage @@ -132,11 +168,11 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [sludge_retent_time](sludge_retent_time.md) OPT * Description: The time activated sludge remains in reactor - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_inorg_mat](soluble_inorg_mat.md) OPT * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. @@ -152,7 +188,7 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tertiary_treatment](tertiary_treatment.md) OPT * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment @@ -160,13 +196,333 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_phosphate](tot_phosphate.md) OPT * Description: Total amount or concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: None * [wastewater_type](wastewater_type.md) OPT * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. * range: [String](types/String.md) * Example: None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Water.md b/mixs6/Water.md index 1204c230..13f03f4b 100644 --- a/mixs6/Water.md +++ b/mixs6/Water.md @@ -7,7 +7,7 @@ water URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig],[WaterMisag],[WaterMimarksS],[WaterMimarksC],[WaterMimag],[WaterMigsVi],[WaterMigsPl],[WaterMigsOrg],[WaterMigsEu],[WaterMigsBa],[WaterMe],[Water|alkalinity:string%20%3F;alkalinity_method:string%20%3F;alkyl_diethers:string%20%3F;aminopept_act:string%20%3F;ammonium:string%20%3F;atmospheric_data:string%20%3F;bacteria_carb_prod:string%20%3F;bac_prod:string%20%3F;bac_resp:string%20%3F;biomass:string%20%3F;bishomohopanol:string%20%3F;bromide:string%20%3F;calcium:string%20%3F;carb_nitro_ratio:string%20%3F;chem_administration:string%20%3F;chloride:string%20%3F;chlorophyll:string%20%3F;conduc:string%20%3F;density:string%20%3F;diether_lipids:string%20%3F;diss_carb_dioxide:string%20%3F;diss_hydrogen:string%20%3F;diss_inorg_carb:string%20%3F;diss_inorg_nitro:string%20%3F;diss_inorg_phosp:string%20%3F;diss_org_carb:string%20%3F;diss_org_nitro:string%20%3F;diss_oxygen:string%20%3F;down_par:string%20%3F;fluor:string%20%3F;glucosidase_act:string%20%3F;light_intensity:string%20%3F;magnesium:string%20%3F;mean_frict_vel:string%20%3F;mean_peak_frict_vel:string%20%3F;misc_param:string%20%3F;n_alkanes:string%20%3F;nitrate:string%20%3F;nitrite:string%20%3F;nitro:string%20%3F;org_carb:string%20%3F;org_matter:string%20%3F;org_nitro:string%20%3F;organism_count:organism_count_enum%20%3F;oxy_stat_samp:oxy_stat_samp_enum%20%3F;ph:string%20%3F;part_org_carb:string%20%3F;part_org_nitro:string%20%3F;perturbation:string%20%3F;petroleum_hydrocarb:string%20%3F;phaeopigments:string%20%3F;phosphate:string%20%3F;phosplipid_fatt_acid:string%20%3F;photon_flux:string%20%3F;potassium:string%20%3F;pressure:string%20%3F;primary_prod:string%20%3F;redox_potential:string%20%3F;salinity:string%20%3F;samp_store_dur:string%20%3F;samp_store_loc:string%20%3F;samp_store_temp:string%20%3F;samp_vol_we_dna_ext:string%20%3F;silicate:string%20%3F;size_frac_low:string%20%3F;size_frac_up:string%20%3F;sodium:string%20%3F;soluble_react_phosp:string%20%3F;sulfate:string%20%3F;sulfide:string%20%3F;suspend_part_matter:string%20%3F;temp:string%20%3F;tidal_stage:tidal_stage_enum%20%3F;tot_depth_water_col:string%20%3F;tot_diss_nitro:string%20%3F;tot_inorg_nitro:string%20%3F;tot_nitro:string%20%3F;tot_part_carb:string%20%3F;tot_phosp:string%20%3F;turbidity:string%20%3F;water_current:string%20%3F]^-[WaterMiuvig],[Water]^-[WaterMisag],[Water]^-[WaterMimarksS],[Water]^-[WaterMimarksC],[Water]^-[WaterMimag],[Water]^-[WaterMigsVi],[Water]^-[WaterMigsPl],[Water]^-[WaterMigsOrg],[Water]^-[WaterMigsEu],[Water]^-[WaterMigsBa],[Water]^-[WaterMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig],[WaterMisag],[WaterMimarksS],[WaterMimarksC],[WaterMimag],[WaterMigsVi],[WaterMigsPl],[WaterMigsOrg],[WaterMigsEu],[WaterMigsBa],[WaterMe],[QuantityValue]OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -41,15 +41,19 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -57,15 +61,15 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -73,19 +77,19 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -93,83 +97,115 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -181,27 +217,27 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -213,11 +249,11 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -225,11 +261,11 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -237,7 +273,7 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -245,27 +281,27 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -277,47 +313,47 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -325,33 +361,33 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None diff --git a/mixs6/WaterMe.md b/mixs6/WaterMe.md index 3cf4af09..6262db6c 100644 --- a/mixs6/WaterMe.md +++ b/mixs6/WaterMe.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with me URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Me],[Water]^-[WaterMe],[Water],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Me],[Water]^-[WaterMe],[Water],[QuantityValue],[Me]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,203 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from me: + + * [me➞adapters](me_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞annot](me_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_name](me_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞assembly_qual](me_assembly_qual.md) OPT + * range: + +### Mixed in from me: + + * [me➞assembly_software](me_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞env_package](me_env_package.md) OPT + * range: + +### Mixed in from me: + + * [me➞experimental_factor](me_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞feat_pred](me_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞investigation_type](me_investigation_type.md) REQ + * range: + +### Mixed in from me: + + * [me➞lib_layout](me_lib_layout.md) OPT + * range: + +### Mixed in from me: + + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_screen](me_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_size](me_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞lib_vector](me_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞mid](me_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞number_contig](me_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞project_name](me_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞ref_db](me_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * range: + +### Mixed in from me: + + * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞samp_size](me_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from me: + + * [me➞sample_name](me_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞seq_meth](me_seq_meth.md) REQ + * range: + +### Mixed in from me: + + * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞size_frac](me_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞sop](me_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞source_mat_id](me_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞tax_class](me_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from me: + + * [me➞url](me_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsBa.md b/mixs6/WaterMigsBa.md index 0309b2a3..024811eb 100644 --- a/mixs6/WaterMigsBa.md +++ b/mixs6/WaterMigsBa.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with migs_ba URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsBa],[Water]^-[WaterMigsBa],[Water],[MigsBa]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsBa],[Water]^-[WaterMigsBa],[Water],[QuantityValue],[MigsBa]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,268 @@ URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_ba: + + * [migs_ba➞adapters](migs_ba_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞annot](migs_ba_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞env_package](migs_ba_env_package.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞project_name](migs_ba_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞sop](migs_ba_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_ba: + + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT + * range: + +### Mixed in from migs_ba: + + * [migs_ba➞url](migs_ba_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsEu.md b/mixs6/WaterMigsEu.md index 854489cf..b7a697a4 100644 --- a/mixs6/WaterMigsEu.md +++ b/mixs6/WaterMigsEu.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with migs_eu URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsEu],[Water]^-[WaterMigsEu],[Water],[MigsEu]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsEu],[Water]^-[WaterMigsEu],[Water],[QuantityValue],[MigsEu]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,268 @@ URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_eu: + + * [migs_eu➞adapters](migs_eu_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞annot](migs_eu_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞env_package](migs_eu_env_package.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞project_name](migs_eu_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞propagation](migs_eu_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞sop](migs_eu_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_eu: + + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT + * range: + +### Mixed in from migs_eu: + + * [migs_eu➞url](migs_eu_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsOrg.md b/mixs6/WaterMigsOrg.md index dce470a1..edb74005 100644 --- a/mixs6/WaterMigsOrg.md +++ b/mixs6/WaterMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with migs_org URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsOrg],[Water]^-[WaterMigsOrg],[Water],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsOrg],[Water]^-[WaterMigsOrg],[Water],[QuantityValue],[MigsOrg]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,223 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_org: + + * [migs_org➞adapters](migs_org_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞annot](migs_org_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞env_package](migs_org_env_package.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞project_name](migs_org_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_org: + + * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * range: + +### Mixed in from migs_org: + + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞sop](migs_org_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_org: + + * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * range: + +### Mixed in from migs_org: + + * [migs_org➞url](migs_org_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsPl.md b/mixs6/WaterMigsPl.md index 6d93bc90..9e2f8f3d 100644 --- a/mixs6/WaterMigsPl.md +++ b/mixs6/WaterMigsPl.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with migs_pl URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsPl],[Water]^-[WaterMigsPl],[Water],[MigsPl]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsPl],[Water]^-[WaterMigsPl],[Water],[QuantityValue],[MigsPl]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,238 @@ URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_pl: + + * [migs_pl➞adapters](migs_pl_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞annot](migs_pl_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞env_package](migs_pl_env_package.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞project_name](migs_pl_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞propagation](migs_pl_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞sop](migs_pl_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_pl: + + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT + * range: + +### Mixed in from migs_pl: + + * [migs_pl➞url](migs_pl_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMigsVi.md b/mixs6/WaterMigsVi.md index 8909545e..69a67fc7 100644 --- a/mixs6/WaterMigsVi.md +++ b/mixs6/WaterMigsVi.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with migs_vi URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MigsVi],[Water]^-[WaterMigsVi],[Water],[MigsVi]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsVi],[Water]^-[WaterMigsVi],[Water],[QuantityValue],[MigsVi]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,263 @@ URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from migs_vi: + + * [migs_vi➞adapters](migs_vi_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞annot](migs_vi_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞env_package](migs_vi_env_package.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞project_name](migs_vi_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞propagation](migs_vi_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞sop](migs_vi_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT + * range: + +### Mixed in from migs_vi: + + * [migs_vi➞url](migs_vi_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from migs_vi: + + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WaterMimag.md b/mixs6/WaterMimag.md index a61d6060..351a322d 100644 --- a/mixs6/WaterMimag.md +++ b/mixs6/WaterMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with mimag URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Mimag],[Water]^-[WaterMimag],[Water],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Mimag],[Water]^-[WaterMimag],[Water],[QuantityValue],[Mimag]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,283 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimag: + + * [mimag➞adapters](mimag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞annot](mimag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞bin_param](mimag_bin_param.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞bin_software](mimag_bin_software.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞compl_score](mimag_compl_score.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞compl_software](mimag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_score](mimag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞env_package](mimag_env_package.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_size](mimag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞mid](mimag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞number_contig](mimag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞project_name](mimag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞ref_db](mimag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimag: + + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞samp_size](mimag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimag: + + * [mimag➞sample_name](mimag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞size_frac](mimag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞sop](mimag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_class](mimag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * range: + +### Mixed in from mimag: + + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞trnas](mimag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞url](mimag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimag: + + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMimarksC.md b/mixs6/WaterMimarksC.md index 7fed9e00..780713da 100644 --- a/mixs6/WaterMimarksC.md +++ b/mixs6/WaterMimarksC.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with mimarks_c URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksC],[Water]^-[WaterMimarksC],[Water],[MimarksC]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksC],[Water]^-[WaterMimarksC],[Water],[QuantityValue],[MimarksC]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,168 @@ URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimarks_c: + + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞sop](mimarks_c_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_c: + + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT + * range: + +### Mixed in from mimarks_c: + + * [mimarks_c➞url](mimarks_c_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMimarksS.md b/mixs6/WaterMimarksS.md index 500c277c..0d32b1bc 100644 --- a/mixs6/WaterMimarksS.md +++ b/mixs6/WaterMimarksS.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with mimarks_s URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[MimarksS],[Water]^-[WaterMimarksS],[Water],[MimarksS]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksS],[Water]^-[WaterMimarksS],[Water],[QuantityValue],[MimarksS]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,188 @@ URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from mimarks_s: + + * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞mid](mimarks_s_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ + * range: + +### Mixed in from mimarks_s: + + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞sop](mimarks_s_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from mimarks_s: + + * [mimarks_s➞url](mimarks_s_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMisag.md b/mixs6/WaterMisag.md index f02422aa..daf6f06c 100644 --- a/mixs6/WaterMisag.md +++ b/mixs6/WaterMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with misag URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Misag],[Water]^-[WaterMisag],[Water],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Misag],[Water]^-[WaterMisag],[Water],[QuantityValue],[Misag]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,288 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from misag: + + * [misag➞adapters](misag_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞annot](misag_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_name](misag_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞assembly_software](misag_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞compl_appr](misag_compl_appr.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞compl_score](misag_compl_score.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞compl_software](misag_compl_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_score](misag_contam_score.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞decontam_software](misag_decontam_software.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞env_package](misag_env_package.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞feat_pred](misag_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞investigation_type](misag_investigation_type.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞lib_layout](misag_lib_layout.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_screen](misag_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_size](misag_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞lib_vector](misag_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞mid](misag_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞number_contig](misag_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞project_name](misag_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞ref_db](misag_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * range: + +### Mixed in from misag: + + * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞samp_size](misag_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from misag: + + * [misag➞sample_name](misag_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞seq_meth](misag_seq_meth.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞size_frac](misag_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sop](misag_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞sort_tech](misag_sort_tech.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_class](misag_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞tax_ident](misag_tax_ident.md) REQ + * range: + +### Mixed in from misag: + + * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞trnas](misag_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞url](misag_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * range: [String](types/String.md) + +### Mixed in from misag: + + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMiuvig.md b/mixs6/WaterMiuvig.md index e04e19fe..cfa11a1f 100644 --- a/mixs6/WaterMiuvig.md +++ b/mixs6/WaterMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist for water with miuvig URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig|alkalinity(i):string%20%3F;alkalinity_method(i):string%20%3F;alkyl_diethers(i):string%20%3F;aminopept_act(i):string%20%3F;ammonium(i):string%20%3F;atmospheric_data(i):string%20%3F;bacteria_carb_prod(i):string%20%3F;bac_prod(i):string%20%3F;bac_resp(i):string%20%3F;biomass(i):string%20%3F;bishomohopanol(i):string%20%3F;bromide(i):string%20%3F;calcium(i):string%20%3F;carb_nitro_ratio(i):string%20%3F;chem_administration(i):string%20%3F;chloride(i):string%20%3F;chlorophyll(i):string%20%3F;conduc(i):string%20%3F;density(i):string%20%3F;diether_lipids(i):string%20%3F;diss_carb_dioxide(i):string%20%3F;diss_hydrogen(i):string%20%3F;diss_inorg_carb(i):string%20%3F;diss_inorg_nitro(i):string%20%3F;diss_inorg_phosp(i):string%20%3F;diss_org_carb(i):string%20%3F;diss_org_nitro(i):string%20%3F;diss_oxygen(i):string%20%3F;down_par(i):string%20%3F;fluor(i):string%20%3F;glucosidase_act(i):string%20%3F;light_intensity(i):string%20%3F;magnesium(i):string%20%3F;mean_frict_vel(i):string%20%3F;mean_peak_frict_vel(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;nitrate(i):string%20%3F;nitrite(i):string%20%3F;nitro(i):string%20%3F;org_carb(i):string%20%3F;org_matter(i):string%20%3F;org_nitro(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):string%20%3F;part_org_carb(i):string%20%3F;part_org_nitro(i):string%20%3F;perturbation(i):string%20%3F;petroleum_hydrocarb(i):string%20%3F;phaeopigments(i):string%20%3F;phosphate(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;photon_flux(i):string%20%3F;potassium(i):string%20%3F;pressure(i):string%20%3F;primary_prod(i):string%20%3F;redox_potential(i):string%20%3F;salinity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;samp_store_temp(i):string%20%3F;samp_vol_we_dna_ext(i):string%20%3F;silicate(i):string%20%3F;size_frac_low(i):string%20%3F;size_frac_up(i):string%20%3F;sodium(i):string%20%3F;soluble_react_phosp(i):string%20%3F;sulfate(i):string%20%3F;sulfide(i):string%20%3F;suspend_part_matter(i):string%20%3F;temp(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F;tot_depth_water_col(i):string%20%3F;tot_diss_nitro(i):string%20%3F;tot_inorg_nitro(i):string%20%3F;tot_nitro(i):string%20%3F;tot_part_carb(i):string%20%3F;tot_phosp(i):string%20%3F;turbidity(i):string%20%3F;water_current(i):string%20%3F]uses%20-.->[Miuvig],[Water]^-[WaterMiuvig],[Water],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Miuvig],[Water]^-[WaterMiuvig],[Water],[QuantityValue],[Miuvig]) ## Parents @@ -24,7 +24,7 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * [alkalinity](alkalinity.md) OPT * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alkalinity_method](alkalinity_method.md) OPT * Description: Method used for alkalinity measurement @@ -32,15 +32,19 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: titration None * [alkyl_diethers](alkyl_diethers.md) OPT * Description: Concentration of alkyl diethers - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT * Description: Measurement of aminopeptidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.269 mole per liter per hour None * [ammonium](ammonium.md) OPT * Description: Concentration of ammonium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 milligram per liter None * [atmospheric_data](atmospheric_data.md) OPT * Description: Measurement of atmospheric data; can include multiple data @@ -48,15 +52,15 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: wind speed;9 knots None * [bac_prod](bac_prod.md) OPT * Description: Bacterial production in the water column measured by isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter per day None * [bac_resp](bac_resp.md) OPT * Description: Measurement of bacterial respiration in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 micromole oxygen per liter per hour None * [bacteria_carb_prod](bacteria_carb_prod.md) OPT * Description: Measurement of bacterial carbon production - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.53 microgram per liter per hour None * [biomass](biomass.md) OPT * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements @@ -64,19 +68,19 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: total;20 gram None * [bishomohopanol](bishomohopanol.md) OPT * Description: Concentration of bishomohopanol - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 14 microgram per liter None * [bromide](bromide.md) OPT * Description: Concentration of bromide - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 parts per million None * [calcium](calcium.md) OPT * Description: Concentration of calcium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micromole per liter None * [carb_nitro_ratio](carb_nitro_ratio.md) OPT * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.417361111 None * [chem_administration](chem_administration.md) OPT * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi @@ -84,83 +88,115 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [chloride](chloride.md) OPT * Description: Concentration of chloride in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5000 milligram per liter None * [chlorophyll](chlorophyll.md) OPT * Description: Concentration of chlorophyll - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 milliSiemens per centimeter None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None * [diether_lipids](diether_lipids.md) OPT * Description: Concentration of diether lipids; can include multiple types of diether lipids * range: [String](types/String.md) * Example: 0.2 nanogram per liter None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 milligram per liter None * [diss_hydrogen](diss_hydrogen.md) OPT * Description: Concentration of dissolved hydrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [diss_inorg_carb](diss_inorg_carb.md) OPT * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2059 micromole per kilogram None * [diss_inorg_nitro](diss_inorg_nitro.md) OPT * Description: Concentration of dissolved inorganic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 761 micromole per liter None * [diss_inorg_phosp](diss_inorg_phosp.md) OPT * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 56.5 micromole per liter None * [diss_org_carb](diss_org_carb.md) OPT * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 197 micromole per liter None * [diss_org_nitro](diss_org_nitro.md) OPT * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [diss_oxygen](diss_oxygen.md) OPT * Description: Concentration of dissolved oxygen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 175 micromole per kilogram None * [down_par](down_par.md) OPT * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None * [fluor](fluor.md) OPT * Description: Raw or converted fluorescence of water - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None * [glucosidase_act](glucosidase_act.md) OPT * Description: Measurement of glucosidase activity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None * [light_intensity](light_intensity.md) OPT * Description: Measurement of light intensity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 lux None * [magnesium](magnesium.md) OPT * Description: Concentration of magnesium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 52.8 micromole per kilogram None * [mean_frict_vel](mean_frict_vel.md) OPT * Description: Measurement of mean friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 meter per second None * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT * Description: Measurement of mean peak friction velocity - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1 meter per second None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -172,27 +208,27 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: n-hexadecane;100 milligram per liter None * [nitrate](nitrate.md) OPT * Description: Concentration of nitrate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 65 micromole per liter None * [nitrite](nitrite.md) OPT * Description: Concentration of nitrite in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 micromole per liter None * [nitro](nitro.md) OPT * Description: Concentration of nitrogen (total) - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4.2 micromole per liter None * [org_carb](org_carb.md) OPT * Description: Concentration of organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.5 microgram per liter None * [org_matter](org_matter.md) OPT * Description: Concentration of organic matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.75 milligram per cubic meter None * [org_nitro](org_nitro.md) OPT * Description: Concentration of organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 4 micromole per liter None * [organism_count](organism_count.md) OPT * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) @@ -204,11 +240,11 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: aerobic None * [part_org_carb](part_org_carb.md) OPT * Description: Concentration of particulate organic carbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1.92 micromole per liter None * [part_org_nitro](part_org_nitro.md) OPT * Description: Concentration of particulate organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 micromole per liter None * [perturbation](perturbation.md) OPT * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types @@ -216,11 +252,11 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT * Description: Concentration of petroleum hydrocarbon - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [ph](ph.md) OPT * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [String](types/String.md) + * range: [Double](types/Double.md) * Example: 7.2 None * [phaeopigments](phaeopigments.md) OPT * Description: Concentration of phaeopigments; can include multiple phaeopigments @@ -228,7 +264,7 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: 2.5 milligram per cubic meter None * [phosphate](phosphate.md) OPT * Description: Concentration of phosphate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.7 micromole per liter None * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT * Description: Concentration of phospholipid fatty acids; can include multiple values @@ -236,27 +272,27 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: 2.98 milligram per liter None * [photon_flux](photon_flux.md) OPT * Description: Measurement of photon flux - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 3.926 micromole photons per second per square meter None * [potassium](potassium.md) OPT * Description: Concentration of potassium in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 463 milligram per liter None * [pressure](pressure.md) OPT * Description: Pressure to which the sample is subject to, in atmospheres - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 atmosphere None * [primary_prod](primary_prod.md) OPT * Description: Measurement of primary production, generally measured as isotope uptake - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 100 milligram per cubic meter per day None * [redox_potential](redox_potential.md) OPT * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 300 millivolt None * [salinity](salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 practical salinity unit None * [samp_store_dur](samp_store_dur.md) OPT * Description: Duration for which the sample was stored @@ -268,47 +304,47 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: Freezer no:5 None * [samp_store_temp](samp_store_temp.md) OPT * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: -80 degree Celsius None * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 1500 milliliter None * [silicate](silicate.md) OPT * Description: Concentration of silicate - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.05 micromole per liter None * [size_frac_low](size_frac_low.md) OPT * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.2 micrometer None * [size_frac_up](size_frac_up.md) OPT * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 20 micrometer None * [sodium](sodium.md) OPT * Description: Sodium concentration in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10.5 milligram per liter None * [soluble_react_phosp](soluble_react_phosp.md) OPT * Description: Concentration of soluble reactive phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.1 milligram per liter None * [sulfate](sulfate.md) OPT * Description: Concentration of sulfate in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 5 micromole per liter None * [sulfide](sulfide.md) OPT * Description: Concentration of sulfide in the sample - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 2 micromole per liter None * [suspend_part_matter](suspend_part_matter.md) OPT * Description: Concentration of suspended particulate matter - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.5 milligram per liter None * [temp](temp.md) OPT * Description: Temperature of the sample at the time of sampling - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None * [tidal_stage](tidal_stage.md) OPT * Description: Stage of tide @@ -316,33 +352,353 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * Example: high tide None * [tot_depth_water_col](tot_depth_water_col.md) OPT * Description: Measurement of total depth of water column - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 500 meter None * [tot_diss_nitro](tot_diss_nitro.md) OPT * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_inorg_nitro](tot_inorg_nitro.md) OPT * Description: Total inorganic nitrogen content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 40 microgram per liter None * [tot_nitro](tot_nitro.md) OPT * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 50 micromole per liter None * [tot_part_carb](tot_part_carb.md) OPT * Description: Total particulate carbon content - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 35 micromole per liter None * [tot_phosp](tot_phosp.md) OPT * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.03 milligram per liter None * [turbidity](turbidity.md) OPT * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 0.3 nephelometric turbidity units None * [water_current](water_current.md) OPT * Description: Measurement of magnitude and direction of flow within a fluid - * range: [String](types/String.md) + * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None + +### Mixed in from miuvig: + + * [miuvig➞adapters](miuvig_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞annot](miuvig_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞env_package](miuvig_env_package.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞mid](miuvig_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞project_name](miuvig_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from miuvig: + + * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sop](miuvig_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * range: + +### Mixed in from miuvig: + + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞trnas](miuvig_trnas.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞url](miuvig_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * range: + +### Mixed in from miuvig: + + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * range: [String](types/String.md) + +### Mixed in from miuvig: + + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/abs_air_humidity.md b/mixs6/abs_air_humidity.md index ce7d14ab..1c714c79 100644 --- a/mixs6/abs_air_humidity.md +++ b/mixs6/abs_air_humidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:abs_air_humidity](https://w3id.org/mixs/vocab/abs_air_humidity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/adapters.md b/mixs6/adapters.md index 853c935f..58fa9e3f 100644 --- a/mixs6/adapters.md +++ b/mixs6/adapters.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞adapters](me_adapters.md) + * [migs_ba➞adapters](migs_ba_adapters.md) + * [migs_eu➞adapters](migs_eu_adapters.md) + * [migs_org➞adapters](migs_org_adapters.md) + * [migs_pl➞adapters](migs_pl_adapters.md) + * [migs_vi➞adapters](migs_vi_adapters.md) + * [mimag➞adapters](mimag_adapters.md) + * [mimarks_s➞adapters](mimarks_s_adapters.md) + * [misag➞adapters](misag_adapters.md) + * [miuvig➞adapters](miuvig_adapters.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: adapter A and B sequence | | | | Preferred unit: | | | | Position: 48.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT', description=None) | diff --git a/mixs6/air_temp.md b/mixs6/air_temp.md index ecda9ceb..027f9a90 100644 --- a/mixs6/air_temp.md +++ b/mixs6/air_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:air_temp](https://w3id.org/mixs/vocab/air_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/al_sat.md b/mixs6/al_sat.md index 3e0883a7..ba7afe92 100644 --- a/mixs6/al_sat.md +++ b/mixs6/al_sat.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:al_sat](https://w3id.org/mixs/vocab/al_sat) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/alkalinity.md b/mixs6/alkalinity.md index c1b83ff5..33c0158a 100644 --- a/mixs6/alkalinity.md +++ b/mixs6/alkalinity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:alkalinity](https://w3id.org/mixs/vocab/alkalinity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/alkyl_diethers.md b/mixs6/alkyl_diethers.md index 9e510f2c..7de16fae 100644 --- a/mixs6/alkyl_diethers.md +++ b/mixs6/alkyl_diethers.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:alkyl_diethers](https://w3id.org/mixs/vocab/alkyl_diethers) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/alt.md b/mixs6/alt.md index cfb9e50c..ed96c90c 100644 --- a/mixs6/alt.md +++ b/mixs6/alt.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:alt](https://w3id.org/mixs/vocab/alt) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents @@ -20,18 +20,211 @@ None -> OPT [String](types/String.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,17 +234,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: | | | | Position: | -| | | CHECKLIST migs_eu: E | -| | | CHECKLIST migs_ba: E | -| | | CHECKLIST migs_pl: E | -| | | CHECKLIST migs_vi: E | -| | | CHECKLIST migs_org: E | -| | | CHECKLIST me: E | -| | | CHECKLIST mimarks_s: E | -| | | CHECKLIST mimarks_c: E | -| | | CHECKLIST misag: E | -| | | CHECKLIST mimag: E | -| | | CHECKLIST miuvig: E | | | | This field is used in: 3 packages: air, host-associated, miscellaneous natural or artificial environment | | **Examples:** | | Example(value='100 meter', description=None) | diff --git a/mixs6/aminopept_act.md b/mixs6/aminopept_act.md index 18ea2b2e..bf87d253 100644 --- a/mixs6/aminopept_act.md +++ b/mixs6/aminopept_act.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:aminopept_act](https://w3id.org/mixs/vocab/aminopept_act) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ammonium.md b/mixs6/ammonium.md index 79e0fdb8..6964d32d 100644 --- a/mixs6/ammonium.md +++ b/mixs6/ammonium.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ammonium](https://w3id.org/mixs/vocab/ammonium) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/amount_light.md b/mixs6/amount_light.md index 7a5263e5..c5600065 100644 --- a/mixs6/amount_light.md +++ b/mixs6/amount_light.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:amount_light](https://w3id.org/mixs/vocab/amount_light) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/annot.md b/mixs6/annot.md index def42193..c973f9ea 100644 --- a/mixs6/annot.md +++ b/mixs6/annot.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞annot](me_annot.md) + * [migs_ba➞annot](migs_ba_annot.md) + * [migs_eu➞annot](migs_eu_annot.md) + * [migs_org➞annot](migs_org_annot.md) + * [migs_pl➞annot](migs_pl_annot.md) + * [migs_vi➞annot](migs_vi_annot.md) + * [mimag➞annot](mimag_annot.md) + * [misag➞annot](misag_annot.md) + * [miuvig➞annot](miuvig_annot.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name of tool or pipeline used, or annotation source description | | | | Preferred unit: | | | | Position: 57.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='prokka', description=None) | diff --git a/mixs6/annual_precpt.md b/mixs6/annual_precpt.md index e380a5dd..6f10b51f 100644 --- a/mixs6/annual_precpt.md +++ b/mixs6/annual_precpt.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:annual_precpt](https://w3id.org/mixs/vocab/annual_precpt) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/annual_temp.md b/mixs6/annual_temp.md index 209dd2c6..0da57680 100644 --- a/mixs6/annual_temp.md +++ b/mixs6/annual_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:annual_temp](https://w3id.org/mixs/vocab/annual_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/api.md b/mixs6/api.md index 88bf4021..c5bd057a 100644 --- a/mixs6/api.md +++ b/mixs6/api.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:api](https://w3id.org/mixs/vocab/api) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/assembly_name.md b/mixs6/assembly_name.md index 15b59d22..eabd813f 100644 --- a/mixs6/assembly_name.md +++ b/mixs6/assembly_name.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞assembly_name](me_assembly_name.md) + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) + * [migs_org➞assembly_name](migs_org_assembly_name.md) + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) + * [mimag➞assembly_name](mimag_assembly_name.md) + * [misag➞assembly_name](misag_assembly_name.md) + * [miuvig➞assembly_name](miuvig_assembly_name.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name and version of assembly | | | | Preferred unit: | | | | Position: 55.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='HuRef, JCVI_ISG_i3_1.0', description=None) | diff --git a/mixs6/assembly_qual.md b/mixs6/assembly_qual.md index 4a45a974..d74a6e44 100644 --- a/mixs6/assembly_qual.md +++ b/mixs6/assembly_qual.md @@ -17,21 +17,19 @@ None -> OPT ## Children + * [me➞assembly_qual](me_assembly_qual.md) + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) + * [mimag➞assembly_qual](mimag_assembly_qual.md) + * [misag➞assembly_qual](misag_assembly_qual.md) + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 54.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='High-quality draft genome', description=None) | diff --git a/mixs6/assembly_software.md b/mixs6/assembly_software.md index d1baacb2..475c7ade 100644 --- a/mixs6/assembly_software.md +++ b/mixs6/assembly_software.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞assembly_software](me_assembly_software.md) + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) + * [migs_org➞assembly_software](migs_org_assembly_software.md) + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) + * [mimag➞assembly_software](mimag_assembly_software.md) + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) + * [misag➞assembly_software](misag_assembly_software.md) + * [miuvig➞assembly_software](miuvig_assembly_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name and version of software, parameters used | | | | Preferred unit: | | | | Position: 56.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise', description=None) | diff --git a/mixs6/avg_dew_point.md b/mixs6/avg_dew_point.md index 80027415..97359bdd 100644 --- a/mixs6/avg_dew_point.md +++ b/mixs6/avg_dew_point.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:avg_dew_point](https://w3id.org/mixs/vocab/avg_dew_point) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/avg_occup.md b/mixs6/avg_occup.md index 027b8cc7..1c51c4cf 100644 --- a/mixs6/avg_occup.md +++ b/mixs6/avg_occup.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:avg_occup](https://w3id.org/mixs/vocab/avg_occup) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/avg_temp.md b/mixs6/avg_temp.md index b5d8bd95..14ae4ab9 100644 --- a/mixs6/avg_temp.md +++ b/mixs6/avg_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:avg_temp](https://w3id.org/mixs/vocab/avg_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/bac_prod.md b/mixs6/bac_prod.md index 26338540..208216cd 100644 --- a/mixs6/bac_prod.md +++ b/mixs6/bac_prod.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:bac_prod](https://w3id.org/mixs/vocab/bac_prod) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/bac_resp.md b/mixs6/bac_resp.md index 2a2165fd..1786e84b 100644 --- a/mixs6/bac_resp.md +++ b/mixs6/bac_resp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:bac_resp](https://w3id.org/mixs/vocab/bac_resp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/bacteria_carb_prod.md b/mixs6/bacteria_carb_prod.md index bf45a4c4..fa04aa19 100644 --- a/mixs6/bacteria_carb_prod.md +++ b/mixs6/bacteria_carb_prod.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:bacteria_carb_prod](https://w3id.org/mixs/vocab/bacteria_carb_p ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/barometric_press.md b/mixs6/barometric_press.md index 64467fb8..39fb5431 100644 --- a/mixs6/barometric_press.md +++ b/mixs6/barometric_press.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:barometric_press](https://w3id.org/mixs/vocab/barometric_press) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/benzene.md b/mixs6/benzene.md index 89a322bb..4006a265 100644 --- a/mixs6/benzene.md +++ b/mixs6/benzene.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:benzene](https://w3id.org/mixs/vocab/benzene) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/bin_param.md b/mixs6/bin_param.md index de1f06e6..53209920 100644 --- a/mixs6/bin_param.md +++ b/mixs6/bin_param.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [mimag➞bin_param](mimag_bin_param.md) + * [miuvig➞bin_param](miuvig_bin_param.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 79.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='coverage and kmer', description=None) | diff --git a/mixs6/bin_software.md b/mixs6/bin_software.md index 96c0f1e9..0b3e1643 100644 --- a/mixs6/bin_software.md +++ b/mixs6/bin_software.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [mimag➞bin_software](mimag_bin_software.md) + * [miuvig➞bin_software](miuvig_bin_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 80.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='concoct and maxbin', description=None) | diff --git a/mixs6/biochem_oxygen_dem.md b/mixs6/biochem_oxygen_dem.md index 7da1545c..c8c380cb 100644 --- a/mixs6/biochem_oxygen_dem.md +++ b/mixs6/biochem_oxygen_dem.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:biochem_oxygen_dem](https://w3id.org/mixs/vocab/biochem_oxygen_ ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/biotic_relationship.md b/mixs6/biotic_relationship.md index 1bee7867..0afbbafe 100644 --- a/mixs6/biotic_relationship.md +++ b/mixs6/biotic_relationship.md @@ -17,21 +17,15 @@ None -> OPT ## Children + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +35,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 22.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='free living', description=None) | diff --git a/mixs6/bishomohopanol.md b/mixs6/bishomohopanol.md index 198f63ec..62c8bb95 100644 --- a/mixs6/bishomohopanol.md +++ b/mixs6/bishomohopanol.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:bishomohopanol](https://w3id.org/mixs/vocab/bishomohopanol) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/bromide.md b/mixs6/bromide.md index 9690b7b9..c386f9d6 100644 --- a/mixs6/bromide.md +++ b/mixs6/bromide.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:bromide](https://w3id.org/mixs/vocab/bromide) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/built_struc_age.md b/mixs6/built_struc_age.md index f78d56e7..fb1d0e15 100644 --- a/mixs6/built_struc_age.md +++ b/mixs6/built_struc_age.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:built_struc_age](https://w3id.org/mixs/vocab/built_struc_age) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/calcium.md b/mixs6/calcium.md index 91aaf705..6d1230be 100644 --- a/mixs6/calcium.md +++ b/mixs6/calcium.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:calcium](https://w3id.org/mixs/vocab/calcium) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/carb_dioxide.md b/mixs6/carb_dioxide.md index 80042ded..4641ab3d 100644 --- a/mixs6/carb_dioxide.md +++ b/mixs6/carb_dioxide.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:carb_dioxide](https://w3id.org/mixs/vocab/carb_dioxide) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/carb_monoxide.md b/mixs6/carb_monoxide.md index d551078b..a5a2cab9 100644 --- a/mixs6/carb_monoxide.md +++ b/mixs6/carb_monoxide.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:carb_monoxide](https://w3id.org/mixs/vocab/carb_monoxide) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/carb_nitro_ratio.md b/mixs6/carb_nitro_ratio.md index 26a3c3a8..9a61abe1 100644 --- a/mixs6/carb_nitro_ratio.md +++ b/mixs6/carb_nitro_ratio.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:carb_nitro_ratio](https://w3id.org/mixs/vocab/carb_nitro_ratio) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ceil_area.md b/mixs6/ceil_area.md index e960d353..d8e2e2de 100644 --- a/mixs6/ceil_area.md +++ b/mixs6/ceil_area.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ceil_area](https://w3id.org/mixs/vocab/ceil_area) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ceil_thermal_mass.md b/mixs6/ceil_thermal_mass.md index 2491d4f4..2c612407 100644 --- a/mixs6/ceil_thermal_mass.md +++ b/mixs6/ceil_thermal_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ceil_thermal_mass](https://w3id.org/mixs/vocab/ceil_thermal_mas ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/chem_oxygen_dem.md b/mixs6/chem_oxygen_dem.md index f2774536..b1d77d33 100644 --- a/mixs6/chem_oxygen_dem.md +++ b/mixs6/chem_oxygen_dem.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:chem_oxygen_dem](https://w3id.org/mixs/vocab/chem_oxygen_dem) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/chimera_check.md b/mixs6/chimera_check.md index 0c91a466..c882dfa8 100644 --- a/mixs6/chimera_check.md +++ b/mixs6/chimera_check.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name and version of software, parameters used | | | | Preferred unit: | | | | Position: 52.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='uchime;v4.1;default parameters', description=None) | diff --git a/mixs6/chloride.md b/mixs6/chloride.md index ed2320ad..699804b1 100644 --- a/mixs6/chloride.md +++ b/mixs6/chloride.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:chloride](https://w3id.org/mixs/vocab/chloride) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/chlorophyll.md b/mixs6/chlorophyll.md index 5358ce60..5a7854c5 100644 --- a/mixs6/chlorophyll.md +++ b/mixs6/chlorophyll.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:chlorophyll](https://w3id.org/mixs/vocab/chlorophyll) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/collection_date.md b/mixs6/collection_date.md index f5b45268..8f76f286 100644 --- a/mixs6/collection_date.md +++ b/mixs6/collection_date.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞collection_date](me_collection_date.md) + * [migs_ba➞collection_date](migs_ba_collection_date.md) + * [migs_eu➞collection_date](migs_eu_collection_date.md) + * [migs_org➞collection_date](migs_org_collection_date.md) + * [migs_pl➞collection_date](migs_pl_collection_date.md) + * [migs_vi➞collection_date](migs_vi_collection_date.md) + * [mimag➞collection_date](mimag_collection_date.md) + * [mimarks_c➞collection_date](mimarks_c_collection_date.md) + * [mimarks_s➞collection_date](mimarks_s_collection_date.md) + * [misag➞collection_date](misag_collection_date.md) + * [miuvig➞collection_date](miuvig_collection_date.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: date and time | | | | Preferred unit: | | | | Position: 9.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='2018-05-11T10:00:00+01:00', description=None) | diff --git a/mixs6/compl_appr.md b/mixs6/compl_appr.md index 9e612caa..ace92f59 100644 --- a/mixs6/compl_appr.md +++ b/mixs6/compl_appr.md @@ -17,21 +17,13 @@ None -> OPT ## Children + * [mimag➞compl_appr](mimag_compl_appr.md) + * [misag➞compl_appr](misag_compl_appr.md) + * [miuvig➞compl_appr](miuvig_compl_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 69.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)', description=None) | diff --git a/mixs6/compl_score.md b/mixs6/compl_score.md index 9322bcd3..ca2822b8 100644 --- a/mixs6/compl_score.md +++ b/mixs6/compl_score.md @@ -17,21 +17,18 @@ None -> OPT ## Children + * [migs_ba➞compl_score](migs_ba_compl_score.md) + * [migs_eu➞compl_score](migs_eu_compl_score.md) + * [migs_org➞compl_score](migs_org_compl_score.md) + * [migs_pl➞compl_score](migs_pl_compl_score.md) + * [migs_vi➞compl_score](migs_vi_compl_score.md) + * [mimag➞compl_score](mimag_compl_score.md) + * [misag➞compl_score](misag_compl_score.md) + * [miuvig➞compl_score](miuvig_compl_score.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +38,5 @@ None -> OPT | **Comments:** | | Expected value: quality;percent completeness | | | | Preferred unit: | | | | Position: 67.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='med;60%', description=None) | diff --git a/mixs6/compl_software.md b/mixs6/compl_software.md index 834d65d9..105beeae 100644 --- a/mixs6/compl_software.md +++ b/mixs6/compl_software.md @@ -17,21 +17,18 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞compl_software](migs_ba_compl_software.md) + * [migs_eu➞compl_software](migs_eu_compl_software.md) + * [migs_org➞compl_software](migs_org_compl_software.md) + * [migs_pl➞compl_software](migs_pl_compl_software.md) + * [migs_vi➞compl_software](migs_vi_compl_software.md) + * [mimag➞compl_software](mimag_compl_software.md) + * [misag➞compl_software](misag_compl_software.md) + * [miuvig➞compl_software](miuvig_compl_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +38,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names and versions of software(s) used | | | | Preferred unit: | | | | Position: 68.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='checkm', description=None) | diff --git a/mixs6/conduc.md b/mixs6/conduc.md index dfce8e55..453023a0 100644 --- a/mixs6/conduc.md +++ b/mixs6/conduc.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:conduc](https://w3id.org/mixs/vocab/conduc) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/contam_score.md b/mixs6/contam_score.md index 196500ea..a6dcf17f 100644 --- a/mixs6/contam_score.md +++ b/mixs6/contam_score.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞contam_score](mimag_contam_score.md) + * [misag➞contam_score](misag_contam_score.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: value | | | | Preferred unit: | | | | Position: 70.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='1%', description=None) | diff --git a/mixs6/contam_screen_input.md b/mixs6/contam_screen_input.md index 521a7752..66b29ac4 100644 --- a/mixs6/contam_screen_input.md +++ b/mixs6/contam_screen_input.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) + * [misag➞contam_screen_input](misag_contam_screen_input.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 71.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='contigs', description=None) | diff --git a/mixs6/contam_screen_param.md b/mixs6/contam_screen_param.md index 1cf06869..9186ca1f 100644 --- a/mixs6/contam_screen_param.md +++ b/mixs6/contam_screen_param.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) + * [misag➞contam_screen_param](misag_contam_screen_param.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration;value or name | | | | Preferred unit: | | | | Position: 72.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='kmer', description=None) | diff --git a/mixs6/decontam_software.md b/mixs6/decontam_software.md index de9563f7..eb591646 100644 --- a/mixs6/decontam_software.md +++ b/mixs6/decontam_software.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [mimag➞decontam_software](mimag_decontam_software.md) + * [misag➞decontam_software](misag_decontam_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 73.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value="anvi'o", description=None) | diff --git a/mixs6/density.md b/mixs6/density.md index 6cb4096c..f41e5d82 100644 --- a/mixs6/density.md +++ b/mixs6/density.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:density](https://w3id.org/mixs/vocab/density) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/depth.md b/mixs6/depth.md index e919c58c..c30044ad 100644 --- a/mixs6/depth.md +++ b/mixs6/depth.md @@ -20,18 +20,211 @@ None -> OPT [String](types/String.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,17 +234,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: - | | | | Preferred unit: | | | | Position: 6.0 | -| | | CHECKLIST migs_eu: E | -| | | CHECKLIST migs_ba: E | -| | | CHECKLIST migs_pl: E | -| | | CHECKLIST migs_vi: E | -| | | CHECKLIST migs_org: E | -| | | CHECKLIST me: E | -| | | CHECKLIST mimarks_s: E | -| | | CHECKLIST mimarks_c: E | -| | | CHECKLIST misag: E | -| | | CHECKLIST mimag: E | -| | | CHECKLIST miuvig: E | | | | This field is used in: 8 packages: host-associated, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | | **Examples:** | | Example(value='', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/63 | diff --git a/mixs6/detec_type.md b/mixs6/detec_type.md index 053b2d99..e23e2995 100644 --- a/mixs6/detec_type.md +++ b/mixs6/detec_type.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞detec_type](miuvig_detec_type.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 86.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='independent sequence (UViG)', description=None) | diff --git a/mixs6/dew_point.md b/mixs6/dew_point.md index e9a43022..518fc0fd 100644 --- a/mixs6/dew_point.md +++ b/mixs6/dew_point.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:dew_point](https://w3id.org/mixs/vocab/dew_point) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_carb_dioxide.md b/mixs6/diss_carb_dioxide.md index 121a2f88..ae56721d 100644 --- a/mixs6/diss_carb_dioxide.md +++ b/mixs6/diss_carb_dioxide.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_carb_dioxide](https://w3id.org/mixs/vocab/diss_carb_dioxid ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_hydrogen.md b/mixs6/diss_hydrogen.md index 1be01385..bfb38fdd 100644 --- a/mixs6/diss_hydrogen.md +++ b/mixs6/diss_hydrogen.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_hydrogen](https://w3id.org/mixs/vocab/diss_hydrogen) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_inorg_carb.md b/mixs6/diss_inorg_carb.md index 8191e458..612c28bf 100644 --- a/mixs6/diss_inorg_carb.md +++ b/mixs6/diss_inorg_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_inorg_carb](https://w3id.org/mixs/vocab/diss_inorg_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_inorg_nitro.md b/mixs6/diss_inorg_nitro.md index a3ca8758..71fd2597 100644 --- a/mixs6/diss_inorg_nitro.md +++ b/mixs6/diss_inorg_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_inorg_nitro](https://w3id.org/mixs/vocab/diss_inorg_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_inorg_phosp.md b/mixs6/diss_inorg_phosp.md index 28e7180c..723cec6e 100644 --- a/mixs6/diss_inorg_phosp.md +++ b/mixs6/diss_inorg_phosp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_inorg_phosp](https://w3id.org/mixs/vocab/diss_inorg_phosp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_iron.md b/mixs6/diss_iron.md index 63a18f80..2d9684c9 100644 --- a/mixs6/diss_iron.md +++ b/mixs6/diss_iron.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_iron](https://w3id.org/mixs/vocab/diss_iron) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_org_carb.md b/mixs6/diss_org_carb.md index 90a0dbb9..fd9eb0dd 100644 --- a/mixs6/diss_org_carb.md +++ b/mixs6/diss_org_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_org_carb](https://w3id.org/mixs/vocab/diss_org_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_org_nitro.md b/mixs6/diss_org_nitro.md index 659af407..09ff556e 100644 --- a/mixs6/diss_org_nitro.md +++ b/mixs6/diss_org_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_org_nitro](https://w3id.org/mixs/vocab/diss_org_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_oxygen.md b/mixs6/diss_oxygen.md index 5e992c99..a3d1afb3 100644 --- a/mixs6/diss_oxygen.md +++ b/mixs6/diss_oxygen.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_oxygen](https://w3id.org/mixs/vocab/diss_oxygen) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/diss_oxygen_fluid.md b/mixs6/diss_oxygen_fluid.md index bdf9411d..c8b0f036 100644 --- a/mixs6/diss_oxygen_fluid.md +++ b/mixs6/diss_oxygen_fluid.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:diss_oxygen_fluid](https://w3id.org/mixs/vocab/diss_oxygen_flui ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/door_size.md b/mixs6/door_size.md index 768d3f3d..e96360b1 100644 --- a/mixs6/door_size.md +++ b/mixs6/door_size.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:door_size](https://w3id.org/mixs/vocab/door_size) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/down_par.md b/mixs6/down_par.md index bc8727d1..e9acfb0d 100644 --- a/mixs6/down_par.md +++ b/mixs6/down_par.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:down_par](https://w3id.org/mixs/vocab/down_par) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/efficiency_percent.md b/mixs6/efficiency_percent.md index a0a83d5e..61219952 100644 --- a/mixs6/efficiency_percent.md +++ b/mixs6/efficiency_percent.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:efficiency_percent](https://w3id.org/mixs/vocab/efficiency_perc ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/elev.md b/mixs6/elev.md index e76181b9..21b6adc5 100644 --- a/mixs6/elev.md +++ b/mixs6/elev.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:elev](https://w3id.org/mixs/vocab/elev) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents @@ -20,18 +20,211 @@ None -> OPT [String](types/String.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,17 +234,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: | | | | Position: 7.0 | -| | | CHECKLIST migs_eu: E | -| | | CHECKLIST migs_ba: E | -| | | CHECKLIST migs_pl: E | -| | | CHECKLIST migs_vi: E | -| | | CHECKLIST migs_org: E | -| | | CHECKLIST me: E | -| | | CHECKLIST mimarks_s: E | -| | | CHECKLIST mimarks_c: E | -| | | CHECKLIST misag: E | -| | | CHECKLIST mimag: E | -| | | CHECKLIST miuvig: E | | | | This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, water | | **Examples:** | | Example(value='100 meter', description=None) | diff --git a/mixs6/encoded_traits.md b/mixs6/encoded_traits.md index c1cd83aa..e095d968 100644 --- a/mixs6/encoded_traits.md +++ b/mixs6/encoded_traits.md @@ -17,21 +17,13 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: for plasmid: antibiotic resistance; for phage: converting genes | | | | Preferred unit: | | | | Position: 28.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='beta-lactamase class A', description=None) | diff --git a/mixs6/env_broad_scale.md b/mixs6/env_broad_scale.md index 2b8e28a3..946dee0a 100644 --- a/mixs6/env_broad_scale.md +++ b/mixs6/env_broad_scale.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞env_broad_scale](me_env_broad_scale.md) + * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) + * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) + * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) + * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) + * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) + * [mimag➞env_broad_scale](mimag_env_broad_scale.md) + * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) + * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) + * [misag➞env_broad_scale](misag_env_broad_scale.md) + * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] | | | | Preferred unit: | | | | Position: 10.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='forest biome [ENVO:01000174]', description=None) | diff --git a/mixs6/env_local_scale.md b/mixs6/env_local_scale.md index 081df755..cffffbad 100644 --- a/mixs6/env_local_scale.md +++ b/mixs6/env_local_scale.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞env_local_scale](me_env_local_scale.md) + * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) + * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) + * [migs_org➞env_local_scale](migs_org_env_local_scale.md) + * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) + * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) + * [mimag➞env_local_scale](mimag_env_local_scale.md) + * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) + * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) + * [misag➞env_local_scale](misag_env_local_scale.md) + * [miuvig➞env_local_scale](miuvig_env_local_scale.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] | | | | Preferred unit: | | | | Position: 11.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='litter layer [ENVO:01000338]', description=None) | diff --git a/mixs6/env_medium.md b/mixs6/env_medium.md index 195b8eca..16615e78 100644 --- a/mixs6/env_medium.md +++ b/mixs6/env_medium.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞env_medium](me_env_medium.md) + * [migs_ba➞env_medium](migs_ba_env_medium.md) + * [migs_eu➞env_medium](migs_eu_env_medium.md) + * [migs_org➞env_medium](migs_org_env_medium.md) + * [migs_pl➞env_medium](migs_pl_env_medium.md) + * [migs_vi➞env_medium](migs_vi_env_medium.md) + * [mimag➞env_medium](mimag_env_medium.md) + * [mimarks_c➞env_medium](mimarks_c_env_medium.md) + * [mimarks_s➞env_medium](mimarks_s_env_medium.md) + * [misag➞env_medium](misag_env_medium.md) + * [miuvig➞env_medium](miuvig_env_medium.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] | | | | Preferred unit: | | | | Position: 12.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='soil [ENVO:00001998]', description=None) | diff --git a/mixs6/env_package.md b/mixs6/env_package.md index a0a5bb4d..223b5b77 100644 --- a/mixs6/env_package.md +++ b/mixs6/env_package.md @@ -17,21 +17,21 @@ None -> OPT ## Children + * [me➞env_package](me_env_package.md) + * [migs_ba➞env_package](migs_ba_env_package.md) + * [migs_eu➞env_package](migs_eu_env_package.md) + * [migs_org➞env_package](migs_org_env_package.md) + * [migs_pl➞env_package](migs_pl_env_package.md) + * [migs_vi➞env_package](migs_vi_env_package.md) + * [mimag➞env_package](mimag_env_package.md) + * [mimarks_c➞env_package](mimarks_c_env_package.md) + * [mimarks_s➞env_package](mimarks_s_env_package.md) + * [misag➞env_package](misag_env_package.md) + * [miuvig➞env_package](miuvig_env_package.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,6 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 13.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='soil', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/64 | diff --git a/mixs6/estimated_size.md b/mixs6/estimated_size.md index fa88fabe..de2c2f2b 100644 --- a/mixs6/estimated_size.md +++ b/mixs6/estimated_size.md @@ -17,21 +17,16 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) + * [migs_org➞estimated_size](migs_org_estimated_size.md) + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) + * [miuvig➞estimated_size](miuvig_estimated_size.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +36,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: number of base pairs | | | | Preferred unit: | | | | Position: 18.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='300000 bp', description=None) | diff --git a/mixs6/ethylbenzene.md b/mixs6/ethylbenzene.md index 867b685a..7e2e99d9 100644 --- a/mixs6/ethylbenzene.md +++ b/mixs6/ethylbenzene.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ethylbenzene](https://w3id.org/mixs/vocab/ethylbenzene) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/exp_duct.md b/mixs6/exp_duct.md index f2536949..6459e4a3 100644 --- a/mixs6/exp_duct.md +++ b/mixs6/exp_duct.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:exp_duct](https://w3id.org/mixs/vocab/exp_duct) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/experimental_factor.md b/mixs6/experimental_factor.md index 584c1049..b9b12c97 100644 --- a/mixs6/experimental_factor.md +++ b/mixs6/experimental_factor.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞experimental_factor](me_experimental_factor.md) + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) + * [mimag➞experimental_factor](mimag_experimental_factor.md) + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) + * [misag➞experimental_factor](misag_experimental_factor.md) + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: text or EFO and/or OBI | | | | Preferred unit: | | | | Position: 4.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: X | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='time series design [EFO:EFO_0001779]', description=None) | diff --git a/mixs6/extrachrom_elements.md b/mixs6/extrachrom_elements.md index 04cba004..4cd5459c 100644 --- a/mixs6/extrachrom_elements.md +++ b/mixs6/extrachrom_elements.md @@ -17,21 +17,14 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +34,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: number of extrachromosmal elements | | | | Preferred unit: | | | | Position: 17.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: X | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='5', description=None) | diff --git a/mixs6/extreme_salinity.md b/mixs6/extreme_salinity.md index 1c485bb8..796bd326 100644 --- a/mixs6/extreme_salinity.md +++ b/mixs6/extreme_salinity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:extreme_salinity](https://w3id.org/mixs/vocab/extreme_salinity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/feat_pred.md b/mixs6/feat_pred.md index 8f4dea4e..b25e0fea 100644 --- a/mixs6/feat_pred.md +++ b/mixs6/feat_pred.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞feat_pred](me_feat_pred.md) + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) + * [migs_org➞feat_pred](migs_org_feat_pred.md) + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) + * [mimag➞feat_pred](mimag_feat_pred.md) + * [misag➞feat_pred](misag_feat_pred.md) + * [miuvig➞feat_pred](miuvig_feat_pred.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names and versions of software(s), parameters used | | | | Preferred unit: | | | | Position: 59.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='Prodigal;2.6.3;default parameters', description=None) | diff --git a/mixs6/floor_age.md b/mixs6/floor_age.md index 687dedb1..9acf8207 100644 --- a/mixs6/floor_age.md +++ b/mixs6/floor_age.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:floor_age](https://w3id.org/mixs/vocab/floor_age) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/floor_area.md b/mixs6/floor_area.md index cabf5e05..662e03ae 100644 --- a/mixs6/floor_area.md +++ b/mixs6/floor_area.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:floor_area](https://w3id.org/mixs/vocab/floor_area) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/floor_thermal_mass.md b/mixs6/floor_thermal_mass.md index 4951081f..e7ca97de 100644 --- a/mixs6/floor_thermal_mass.md +++ b/mixs6/floor_thermal_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:floor_thermal_mass](https://w3id.org/mixs/vocab/floor_thermal_m ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/fluor.md b/mixs6/fluor.md index e026726e..c4d2ef80 100644 --- a/mixs6/fluor.md +++ b/mixs6/fluor.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:fluor](https://w3id.org/mixs/vocab/fluor) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/geo_loc_name.md b/mixs6/geo_loc_name.md index 23fd975f..4a83654f 100644 --- a/mixs6/geo_loc_name.md +++ b/mixs6/geo_loc_name.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞geo_loc_name](me_geo_loc_name.md) + * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) + * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) + * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) + * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) + * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) + * [mimag➞geo_loc_name](mimag_geo_loc_name.md) + * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) + * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) + * [misag➞geo_loc_name](misag_geo_loc_name.md) + * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location name | | | | Preferred unit: | | | | Position: 8.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='Germany;North Rhine-Westphalia;Eifel National Park', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/17 | diff --git a/mixs6/glucosidase_act.md b/mixs6/glucosidase_act.md index ae3570aa..e95340b6 100644 --- a/mixs6/glucosidase_act.md +++ b/mixs6/glucosidase_act.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:glucosidase_act](https://w3id.org/mixs/vocab/glucosidase_act) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/hcr_fw_salinity.md b/mixs6/hcr_fw_salinity.md index 72cfdc8d..88563d61 100644 --- a/mixs6/hcr_fw_salinity.md +++ b/mixs6/hcr_fw_salinity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:hcr_fw_salinity](https://w3id.org/mixs/vocab/hcr_fw_salinity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/health_disease_stat.md b/mixs6/health_disease_stat.md index 99770ae0..7e6669f1 100644 --- a/mixs6/health_disease_stat.md +++ b/mixs6/health_disease_stat.md @@ -17,21 +17,13 @@ None -> OPT ## Children + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 25.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='dead', description=None) | diff --git a/mixs6/height_carper_fiber.md b/mixs6/height_carper_fiber.md index f724f3f0..00346395 100644 --- a/mixs6/height_carper_fiber.md +++ b/mixs6/height_carper_fiber.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:height_carper_fiber](https://w3id.org/mixs/vocab/height_carper_ ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_age.md b/mixs6/host_age.md index a7b358de..72a6309e 100644 --- a/mixs6/host_age.md +++ b/mixs6/host_age.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_age](https://w3id.org/mixs/vocab/host_age) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_blood_press_diast.md b/mixs6/host_blood_press_diast.md index 251ca0b4..cc8e73a1 100644 --- a/mixs6/host_blood_press_diast.md +++ b/mixs6/host_blood_press_diast.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_blood_press_diast](https://w3id.org/mixs/vocab/host_blood_ ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_blood_press_syst.md b/mixs6/host_blood_press_syst.md index 18c249c2..913bbfde 100644 --- a/mixs6/host_blood_press_syst.md +++ b/mixs6/host_blood_press_syst.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_blood_press_syst](https://w3id.org/mixs/vocab/host_blood_p ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_body_mass_index.md b/mixs6/host_body_mass_index.md index 1a61d559..eeeba402 100644 --- a/mixs6/host_body_mass_index.md +++ b/mixs6/host_body_mass_index.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_body_mass_index](https://w3id.org/mixs/vocab/host_body_mas ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_body_temp.md b/mixs6/host_body_temp.md index a96e6ad5..f0613e63 100644 --- a/mixs6/host_body_temp.md +++ b/mixs6/host_body_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_body_temp](https://w3id.org/mixs/vocab/host_body_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_dry_mass.md b/mixs6/host_dry_mass.md index 10f1b65e..7a0b3644 100644 --- a/mixs6/host_dry_mass.md +++ b/mixs6/host_dry_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_dry_mass](https://w3id.org/mixs/vocab/host_dry_mass) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_height.md b/mixs6/host_height.md index 4c496e2c..f1223f2e 100644 --- a/mixs6/host_height.md +++ b/mixs6/host_height.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_height](https://w3id.org/mixs/vocab/host_height) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_length.md b/mixs6/host_length.md index 9443bc9b..f1b3506b 100644 --- a/mixs6/host_length.md +++ b/mixs6/host_length.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_length](https://w3id.org/mixs/vocab/host_length) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_pred_appr.md b/mixs6/host_pred_appr.md index 39e5d40d..8ae50929 100644 --- a/mixs6/host_pred_appr.md +++ b/mixs6/host_pred_appr.md @@ -17,21 +17,11 @@ None -> OPT ## Children + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 90.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='CRISPR spacer match', description=None) | diff --git a/mixs6/host_pred_est_acc.md b/mixs6/host_pred_est_acc.md index 2cce1cba..3edf10c6 100644 --- a/mixs6/host_pred_est_acc.md +++ b/mixs6/host_pred_est_acc.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: false discovery rate | | | | Preferred unit: | | | | Position: 91.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)', description=None) | diff --git a/mixs6/host_pulse.md b/mixs6/host_pulse.md index 60291e7f..211698b9 100644 --- a/mixs6/host_pulse.md +++ b/mixs6/host_pulse.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_pulse](https://w3id.org/mixs/vocab/host_pulse) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_spec_range.md b/mixs6/host_spec_range.md index 29ba2ee5..5543fa70 100644 --- a/mixs6/host_spec_range.md +++ b/mixs6/host_spec_range.md @@ -17,21 +17,15 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +35,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: NCBI taxid | | | | Preferred unit: | | | | Position: 24.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='9606', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/66 | diff --git a/mixs6/host_tot_mass.md b/mixs6/host_tot_mass.md index 9ed641da..6c014e6c 100644 --- a/mixs6/host_tot_mass.md +++ b/mixs6/host_tot_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_tot_mass](https://w3id.org/mixs/vocab/host_tot_mass) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/host_wet_mass.md b/mixs6/host_wet_mass.md index fe7a5b64..9b149d0a 100644 --- a/mixs6/host_wet_mass.md +++ b/mixs6/host_wet_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:host_wet_mass](https://w3id.org/mixs/vocab/host_wet_mass) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/humidity.md b/mixs6/humidity.md index ecee61f9..c7058a60 100644 --- a/mixs6/humidity.md +++ b/mixs6/humidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:humidity](https://w3id.org/mixs/vocab/humidity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/index.md b/mixs6/index.md index 1dfea2e6..5e65871a 100644 --- a/mixs6/index.md +++ b/mixs6/index.md @@ -31,18 +31,7 @@ MIxS 6 linkml rendering * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - Combinatorial checklist for built environment with mimarks_s * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - Combinatorial checklist for built environment with misag * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) - Combinatorial checklist for built environment with miuvig - * [Core](Core.md) - core package - * [CoreMe](CoreMe.md) - Combinatorial checklist for core with me - * [CoreMigsBa](CoreMigsBa.md) - Combinatorial checklist for core with migs_ba - * [CoreMigsEu](CoreMigsEu.md) - Combinatorial checklist for core with migs_eu - * [CoreMigsOrg](CoreMigsOrg.md) - Combinatorial checklist for core with migs_org - * [CoreMigsPl](CoreMigsPl.md) - Combinatorial checklist for core with migs_pl - * [CoreMigsVi](CoreMigsVi.md) - Combinatorial checklist for core with migs_vi - * [CoreMimag](CoreMimag.md) - Combinatorial checklist for core with mimag - * [CoreMimarksC](CoreMimarksC.md) - Combinatorial checklist for core with mimarks_c - * [CoreMimarksS](CoreMimarksS.md) - Combinatorial checklist for core with mimarks_s - * [CoreMisag](CoreMisag.md) - Combinatorial checklist for core with misag - * [CoreMiuvig](CoreMiuvig.md) - Combinatorial checklist for core with miuvig + * [Core](Core.md) - Core package. Do not use this directly, this is used to build other packages * [Host-associated](Host-associated.md) - host-associated * [Host-associatedMe](Host-associatedMe.md) - Combinatorial checklist for host-associated with me * [Host-associatedMigsBa](Host-associatedMigsBa.md) - Combinatorial checklist for host-associated with migs_ba @@ -175,6 +164,7 @@ MIxS 6 linkml rendering * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - Combinatorial checklist for plant-associated with mimarks_s * [Plant-associatedMisag](Plant-associatedMisag.md) - Combinatorial checklist for plant-associated with misag * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) - Combinatorial checklist for plant-associated with miuvig + * [QuantityValue](QuantityValue.md) - used to record a measurement * [Sediment](Sediment.md) - sediment * [SedimentMe](SedimentMe.md) - Combinatorial checklist for sediment with me * [SedimentMigsBa](SedimentMigsBa.md) - Combinatorial checklist for sediment with migs_ba @@ -242,6 +232,17 @@ MIxS 6 linkml rendering * [core field](core_field.md) - basic fields * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * [me➞sample_name](me_sample_name.md) + * [migs_ba➞sample_name](migs_ba_sample_name.md) + * [migs_eu➞sample_name](migs_eu_sample_name.md) + * [migs_org➞sample_name](migs_org_sample_name.md) + * [migs_pl➞sample_name](migs_pl_sample_name.md) + * [migs_vi➞sample_name](migs_vi_sample_name.md) + * [mimag➞sample_name](mimag_sample_name.md) + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) + * [misag➞sample_name](misag_sample_name.md) + * [miuvig➞sample_name](miuvig_sample_name.md) * [environment field](environment_field.md) - field describing environmental aspect of a sample * [abs_air_humidity](abs_air_humidity.md) - Actual mass of water vapor - mh20 - present in the air water vapor mixture * [add_recov_method](add_recov_method.md) - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field @@ -319,6 +320,17 @@ MIxS 6 linkml rendering * [chlorophyll](chlorophyll.md) - Concentration of chlorophyll * [climate_environment](climate_environment.md) - Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * [collection_date](collection_date.md) - The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * [me➞collection_date](me_collection_date.md) + * [migs_ba➞collection_date](migs_ba_collection_date.md) + * [migs_eu➞collection_date](migs_eu_collection_date.md) + * [migs_org➞collection_date](migs_org_collection_date.md) + * [migs_pl➞collection_date](migs_pl_collection_date.md) + * [migs_vi➞collection_date](migs_vi_collection_date.md) + * [mimag➞collection_date](mimag_collection_date.md) + * [mimarks_c➞collection_date](mimarks_c_collection_date.md) + * [mimarks_s➞collection_date](mimarks_s_collection_date.md) + * [misag➞collection_date](misag_collection_date.md) + * [miuvig➞collection_date](miuvig_collection_date.md) * [conduc](conduc.md) - Electrical conductivity of water * [cool_syst_id](cool_syst_id.md) - The cooling system identifier * [crop_rotation](crop_rotation.md) - Whether or not crop is rotated, and if yes, rotation schedule @@ -366,8 +378,41 @@ MIxS 6 linkml rendering * [elevator](elevator.md) - The number of elevators within the built structure * [emulsions](emulsions.md) - Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * [env_broad_scale](env_broad_scale.md) - In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [me➞env_broad_scale](me_env_broad_scale.md) + * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) + * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) + * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) + * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) + * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) + * [mimag➞env_broad_scale](mimag_env_broad_scale.md) + * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) + * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) + * [misag➞env_broad_scale](misag_env_broad_scale.md) + * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) * [env_local_scale](env_local_scale.md) - In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [me➞env_local_scale](me_env_local_scale.md) + * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) + * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) + * [migs_org➞env_local_scale](migs_org_env_local_scale.md) + * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) + * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) + * [mimag➞env_local_scale](mimag_env_local_scale.md) + * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) + * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) + * [misag➞env_local_scale](misag_env_local_scale.md) + * [miuvig➞env_local_scale](miuvig_env_local_scale.md) * [env_medium](env_medium.md) - In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * [me➞env_medium](me_env_medium.md) + * [migs_ba➞env_medium](migs_ba_env_medium.md) + * [migs_eu➞env_medium](migs_eu_env_medium.md) + * [migs_org➞env_medium](migs_org_env_medium.md) + * [migs_pl➞env_medium](migs_pl_env_medium.md) + * [migs_vi➞env_medium](migs_vi_env_medium.md) + * [mimag➞env_medium](mimag_env_medium.md) + * [mimarks_c➞env_medium](mimarks_c_env_medium.md) + * [mimarks_s➞env_medium](mimarks_s_env_medium.md) + * [misag➞env_medium](misag_env_medium.md) + * [miuvig➞env_medium](miuvig_env_medium.md) * [escalator](escalator.md) - The number of escalators within the built structure * [ethylbenzene](ethylbenzene.md) - Concentration of ethylbenzene in the sample * [exp_duct](exp_duct.md) - The amount of exposed ductwork in the room @@ -404,6 +449,17 @@ MIxS 6 linkml rendering * [gender_restroom](gender_restroom.md) - The gender type of the restroom * [genetic_mod](genetic_mod.md) - Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * [geo_loc_name](geo_loc_name.md) - The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * [me➞geo_loc_name](me_geo_loc_name.md) + * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) + * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) + * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) + * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) + * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) + * [mimag➞geo_loc_name](mimag_geo_loc_name.md) + * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) + * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) + * [misag➞geo_loc_name](misag_geo_loc_name.md) + * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) * [gestation_state](gestation_state.md) - Specification of the gestation state * [glucosidase_act](glucosidase_act.md) - Measurement of glucosidase activity * [gravidity](gravidity.md) - Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used @@ -479,6 +535,17 @@ MIxS 6 linkml rendering * [iwf](iwf.md) - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) * [last_clean](last_clean.md) - The last time the floor was cleaned (swept, mopped, vacuumed) * [lat_lon](lat_lon.md) - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * [me➞lat_lon](me_lat_lon.md) + * [migs_ba➞lat_lon](migs_ba_lat_lon.md) + * [migs_eu➞lat_lon](migs_eu_lat_lon.md) + * [migs_org➞lat_lon](migs_org_lat_lon.md) + * [migs_pl➞lat_lon](migs_pl_lat_lon.md) + * [migs_vi➞lat_lon](migs_vi_lat_lon.md) + * [mimag➞lat_lon](mimag_lat_lon.md) + * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) + * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) + * [misag➞lat_lon](misag_lat_lon.md) + * [miuvig➞lat_lon](miuvig_lat_lon.md) * [light_intensity](light_intensity.md) - Measurement of light intensity * [light_regm](light_regm.md) - Information about treatment(s) involving exposure to light, including both light intensity and quality. * [light_type](light_type.md) - Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light @@ -759,93 +826,561 @@ MIxS 6 linkml rendering * [xylene](xylene.md) - Concentration of xylene in the sample * [investigation field](investigation_field.md) - field describing aspect of the investigation/study to which the sample belongs * [experimental_factor](experimental_factor.md) - Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [me➞experimental_factor](me_experimental_factor.md) + * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) + * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) + * [migs_org➞experimental_factor](migs_org_experimental_factor.md) + * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) + * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) + * [mimag➞experimental_factor](mimag_experimental_factor.md) + * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) + * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) + * [misag➞experimental_factor](misag_experimental_factor.md) + * [miuvig➞experimental_factor](miuvig_experimental_factor.md) * [investigation_type](investigation_type.md) - Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome + * [me➞investigation_type](me_investigation_type.md) + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) + * [migs_org➞investigation_type](migs_org_investigation_type.md) + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) + * [mimag➞investigation_type](mimag_investigation_type.md) + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) + * [misag➞investigation_type](misag_investigation_type.md) + * [miuvig➞investigation_type](miuvig_investigation_type.md) * [project_name](project_name.md) - Name of the project within which the sequencing was organized + * [me➞project_name](me_project_name.md) + * [migs_ba➞project_name](migs_ba_project_name.md) + * [migs_eu➞project_name](migs_eu_project_name.md) + * [migs_org➞project_name](migs_org_project_name.md) + * [migs_pl➞project_name](migs_pl_project_name.md) + * [migs_vi➞project_name](migs_vi_project_name.md) + * [mimag➞project_name](mimag_project_name.md) + * [mimarks_c➞project_name](mimarks_c_project_name.md) + * [mimarks_s➞project_name](mimarks_s_project_name.md) + * [misag➞project_name](misag_project_name.md) + * [miuvig➞project_name](miuvig_project_name.md) * [submitted_to_insdc](submitted_to_insdc.md) - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) * [mixs extension field](mixs_extension_field.md) * [env_package](env_package.md) - MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + * [me➞env_package](me_env_package.md) + * [migs_ba➞env_package](migs_ba_env_package.md) + * [migs_eu➞env_package](migs_eu_env_package.md) + * [migs_org➞env_package](migs_org_env_package.md) + * [migs_pl➞env_package](migs_pl_env_package.md) + * [migs_vi➞env_package](migs_vi_env_package.md) + * [mimag➞env_package](mimag_env_package.md) + * [mimarks_c➞env_package](mimarks_c_env_package.md) + * [mimarks_s➞env_package](mimarks_s_env_package.md) + * [misag➞env_package](misag_env_package.md) + * [miuvig➞env_package](miuvig_env_package.md) * [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) * [biotic_relationship](biotic_relationship.md) - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) + * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) + * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) + * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) + * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) * [encoded_traits](encoded_traits.md) - Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) + * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) + * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) * [estimated_size](estimated_size.md) - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + * [migs_ba➞estimated_size](migs_ba_estimated_size.md) + * [migs_eu➞estimated_size](migs_eu_estimated_size.md) + * [migs_org➞estimated_size](migs_org_estimated_size.md) + * [migs_pl➞estimated_size](migs_pl_estimated_size.md) + * [migs_vi➞estimated_size](migs_vi_estimated_size.md) + * [miuvig➞estimated_size](miuvig_estimated_size.md) * [extrachrom_elements](extrachrom_elements.md) - Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) + * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) + * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) + * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) * [health_disease_stat](health_disease_stat.md) - Health or disease status of specific host at time of collection + * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) + * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) + * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) * [host_spec_range](host_spec_range.md) - The NCBI taxonomy identifier of the specific host if it is known + * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) + * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) + * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) + * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) + * [miuvig➞host_spec_range](miuvig_host_spec_range.md) * [isol_growth_condt](isol_growth_condt.md) - Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) * [num_replicons](num_replicons.md) - Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) * [pathogenicity](pathogenicity.md) - To what is the entity pathogenic + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) * [ploidy](ploidy.md) - The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + * [migs_eu➞ploidy](migs_eu_ploidy.md) * [propagation](propagation.md) - This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice + * [migs_eu➞propagation](migs_eu_propagation.md) + * [migs_pl➞propagation](migs_pl_propagation.md) + * [migs_vi➞propagation](migs_vi_propagation.md) * [ref_biomaterial](ref_biomaterial.md) - Primary publication if isolated before genome publication; otherwise, primary genome report + * [me➞ref_biomaterial](me_ref_biomaterial.md) + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) * [rel_to_oxygen](rel_to_oxygen.md) - Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) * [samp_collect_device](samp_collect_device.md) - The method or device employed for collecting the sample + * [me➞samp_collect_device](me_samp_collect_device.md) + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) + * [misag➞samp_collect_device](misag_samp_collect_device.md) + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) * [samp_mat_process](samp_mat_process.md) - Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [me➞samp_mat_process](me_samp_mat_process.md) + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) + * [misag➞samp_mat_process](misag_samp_mat_process.md) + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) * [samp_size](samp_size.md) - Amount or size of sample (volume, mass or area) that was collected + * [me➞samp_size](me_samp_size.md) + * [migs_ba➞samp_size](migs_ba_samp_size.md) + * [migs_eu➞samp_size](migs_eu_samp_size.md) + * [migs_org➞samp_size](migs_org_samp_size.md) + * [migs_pl➞samp_size](migs_pl_samp_size.md) + * [migs_vi➞samp_size](migs_vi_samp_size.md) + * [mimag➞samp_size](mimag_samp_size.md) + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) + * [misag➞samp_size](misag_samp_size.md) + * [miuvig➞samp_size](miuvig_samp_size.md) * [size_frac](size_frac.md) - Filtering pore size used in sample preparation + * [me➞size_frac](me_size_frac.md) + * [mimag➞size_frac](mimag_size_frac.md) + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) + * [misag➞size_frac](misag_size_frac.md) + * [miuvig➞size_frac](miuvig_size_frac.md) * [source_mat_id](source_mat_id.md) - A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + * [me➞source_mat_id](me_source_mat_id.md) + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) + * [mimag➞source_mat_id](mimag_source_mat_id.md) + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) + * [misag➞source_mat_id](misag_source_mat_id.md) + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) * [source_uvig](source_uvig.md) - Type of dataset from which the UViG was obtained + * [miuvig➞source_uvig](miuvig_source_uvig.md) * [specific_host](specific_host.md) - If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) + * [migs_ba➞specific_host](migs_ba_specific_host.md) + * [migs_eu➞specific_host](migs_eu_specific_host.md) + * [migs_pl➞specific_host](migs_pl_specific_host.md) + * [migs_vi➞specific_host](migs_vi_specific_host.md) + * [miuvig➞specific_host](miuvig_specific_host.md) * [subspecf_gen_lin](subspecf_gen_lin.md) - This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) * [trophic_level](trophic_level.md) - Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) * [virus_enrich_appr](virus_enrich_appr.md) - List of approaches used to enrich the sample for viruses, if any + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) + * [➞has numeric value](quantityValue__has_numeric_value.md) + * [➞has raw value](quantityValue__has_raw_value.md) + * [➞has unit](quantityValue__has_unit.md) - Example "m" * [sequencing field](sequencing_field.md) * [adapters](adapters.md) - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + * [me➞adapters](me_adapters.md) + * [migs_ba➞adapters](migs_ba_adapters.md) + * [migs_eu➞adapters](migs_eu_adapters.md) + * [migs_org➞adapters](migs_org_adapters.md) + * [migs_pl➞adapters](migs_pl_adapters.md) + * [migs_vi➞adapters](migs_vi_adapters.md) + * [mimag➞adapters](mimag_adapters.md) + * [mimarks_s➞adapters](mimarks_s_adapters.md) + * [misag➞adapters](misag_adapters.md) + * [miuvig➞adapters](miuvig_adapters.md) * [annot](annot.md) - Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + * [me➞annot](me_annot.md) + * [migs_ba➞annot](migs_ba_annot.md) + * [migs_eu➞annot](migs_eu_annot.md) + * [migs_org➞annot](migs_org_annot.md) + * [migs_pl➞annot](migs_pl_annot.md) + * [migs_vi➞annot](migs_vi_annot.md) + * [mimag➞annot](mimag_annot.md) + * [misag➞annot](misag_annot.md) + * [miuvig➞annot](miuvig_annot.md) * [assembly_name](assembly_name.md) - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + * [me➞assembly_name](me_assembly_name.md) + * [migs_ba➞assembly_name](migs_ba_assembly_name.md) + * [migs_eu➞assembly_name](migs_eu_assembly_name.md) + * [migs_org➞assembly_name](migs_org_assembly_name.md) + * [migs_pl➞assembly_name](migs_pl_assembly_name.md) + * [migs_vi➞assembly_name](migs_vi_assembly_name.md) + * [mimag➞assembly_name](mimag_assembly_name.md) + * [misag➞assembly_name](misag_assembly_name.md) + * [miuvig➞assembly_name](miuvig_assembly_name.md) * [assembly_qual](assembly_qual.md) - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated + * [me➞assembly_qual](me_assembly_qual.md) + * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) + * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) + * [migs_org➞assembly_qual](migs_org_assembly_qual.md) + * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) + * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) + * [mimag➞assembly_qual](mimag_assembly_qual.md) + * [misag➞assembly_qual](misag_assembly_qual.md) + * [miuvig➞assembly_qual](miuvig_assembly_qual.md) * [assembly_software](assembly_software.md) - Tool(s) used for assembly, including version number and parameters + * [me➞assembly_software](me_assembly_software.md) + * [migs_ba➞assembly_software](migs_ba_assembly_software.md) + * [migs_eu➞assembly_software](migs_eu_assembly_software.md) + * [migs_org➞assembly_software](migs_org_assembly_software.md) + * [migs_pl➞assembly_software](migs_pl_assembly_software.md) + * [migs_vi➞assembly_software](migs_vi_assembly_software.md) + * [mimag➞assembly_software](mimag_assembly_software.md) + * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) + * [misag➞assembly_software](misag_assembly_software.md) + * [miuvig➞assembly_software](miuvig_assembly_software.md) * [bin_param](bin_param.md) - The parameters that have been applied during the extraction of genomes from metagenomic datasets + * [mimag➞bin_param](mimag_bin_param.md) + * [miuvig➞bin_param](miuvig_bin_param.md) * [bin_software](bin_software.md) - Tool(s) used for the extraction of genomes from metagenomic datasets + * [mimag➞bin_software](mimag_bin_software.md) + * [miuvig➞bin_software](miuvig_bin_software.md) * [chimera_check](chimera_check.md) - A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point + * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) + * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) * [compl_appr](compl_appr.md) - The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + * [mimag➞compl_appr](mimag_compl_appr.md) + * [misag➞compl_appr](misag_compl_appr.md) + * [miuvig➞compl_appr](miuvig_compl_appr.md) * [compl_score](compl_score.md) - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores + * [migs_ba➞compl_score](migs_ba_compl_score.md) + * [migs_eu➞compl_score](migs_eu_compl_score.md) + * [migs_org➞compl_score](migs_org_compl_score.md) + * [migs_pl➞compl_score](migs_pl_compl_score.md) + * [migs_vi➞compl_score](migs_vi_compl_score.md) + * [mimag➞compl_score](mimag_compl_score.md) + * [misag➞compl_score](misag_compl_score.md) + * [miuvig➞compl_score](miuvig_compl_score.md) * [compl_software](compl_software.md) - Tools used for completion estimate, i.e. checkm, anvi'o, busco + * [migs_ba➞compl_software](migs_ba_compl_software.md) + * [migs_eu➞compl_software](migs_eu_compl_software.md) + * [migs_org➞compl_software](migs_org_compl_software.md) + * [migs_pl➞compl_software](migs_pl_compl_software.md) + * [migs_vi➞compl_software](migs_vi_compl_software.md) + * [mimag➞compl_software](mimag_compl_software.md) + * [misag➞compl_software](misag_compl_software.md) + * [miuvig➞compl_software](miuvig_compl_software.md) * [contam_score](contam_score.md) - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + * [mimag➞contam_score](mimag_contam_score.md) + * [misag➞contam_score](misag_contam_score.md) * [contam_screen_input](contam_screen_input.md) - The type of sequence data used as input + * [mimag➞contam_screen_input](mimag_contam_screen_input.md) + * [misag➞contam_screen_input](misag_contam_screen_input.md) * [contam_screen_param](contam_screen_param.md) - Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + * [mimag➞contam_screen_param](mimag_contam_screen_param.md) + * [misag➞contam_screen_param](misag_contam_screen_param.md) * [decontam_software](decontam_software.md) - Tool(s) used in contamination screening + * [mimag➞decontam_software](mimag_decontam_software.md) + * [misag➞decontam_software](misag_decontam_software.md) * [detec_type](detec_type.md) - Type of UViG detection + * [miuvig➞detec_type](miuvig_detec_type.md) * [feat_pred](feat_pred.md) - Method used to predict UViGs features such as ORFs, integration site, etc. + * [me➞feat_pred](me_feat_pred.md) + * [migs_ba➞feat_pred](migs_ba_feat_pred.md) + * [migs_eu➞feat_pred](migs_eu_feat_pred.md) + * [migs_org➞feat_pred](migs_org_feat_pred.md) + * [migs_pl➞feat_pred](migs_pl_feat_pred.md) + * [migs_vi➞feat_pred](migs_vi_feat_pred.md) + * [mimag➞feat_pred](mimag_feat_pred.md) + * [misag➞feat_pred](misag_feat_pred.md) + * [miuvig➞feat_pred](miuvig_feat_pred.md) * [host_pred_appr](host_pred_appr.md) - Tool or approach used for host prediction + * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) * [host_pred_est_acc](host_pred_est_acc.md) - For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) * [lib_layout](lib_layout.md) - Specify whether to expect single, paired, or other configuration of reads + * [me➞lib_layout](me_lib_layout.md) + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) + * [migs_org➞lib_layout](migs_org_lib_layout.md) + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) + * [mimag➞lib_layout](mimag_lib_layout.md) + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) + * [misag➞lib_layout](misag_lib_layout.md) + * [miuvig➞lib_layout](miuvig_lib_layout.md) * [lib_reads_seqd](lib_reads_seqd.md) - Total number of clones sequenced from the library + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) * [lib_screen](lib_screen.md) - Specific enrichment or screening methods applied before and/or after creating libraries + * [me➞lib_screen](me_lib_screen.md) + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) + * [migs_org➞lib_screen](migs_org_lib_screen.md) + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) + * [mimag➞lib_screen](mimag_lib_screen.md) + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) + * [misag➞lib_screen](misag_lib_screen.md) + * [miuvig➞lib_screen](miuvig_lib_screen.md) * [lib_size](lib_size.md) - Total number of clones in the library prepared for the project + * [me➞lib_size](me_lib_size.md) + * [migs_ba➞lib_size](migs_ba_lib_size.md) + * [migs_eu➞lib_size](migs_eu_lib_size.md) + * [migs_org➞lib_size](migs_org_lib_size.md) + * [migs_pl➞lib_size](migs_pl_lib_size.md) + * [migs_vi➞lib_size](migs_vi_lib_size.md) + * [mimag➞lib_size](mimag_lib_size.md) + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) + * [misag➞lib_size](misag_lib_size.md) + * [miuvig➞lib_size](miuvig_lib_size.md) * [lib_vector](lib_vector.md) - Cloning vector type(s) used in construction of libraries + * [me➞lib_vector](me_lib_vector.md) + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) + * [migs_org➞lib_vector](migs_org_lib_vector.md) + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) + * [mimag➞lib_vector](mimag_lib_vector.md) + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) + * [misag➞lib_vector](misag_lib_vector.md) + * [miuvig➞lib_vector](miuvig_lib_vector.md) * [mag_cov_software](mag_cov_software.md) - Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) * [mid](mid.md) - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + * [me➞mid](me_mid.md) + * [mimag➞mid](mimag_mid.md) + * [mimarks_s➞mid](mimarks_s_mid.md) + * [misag➞mid](misag_mid.md) + * [miuvig➞mid](miuvig_mid.md) * [nucl_acid_amp](nucl_acid_amp.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) * [nucl_acid_ext](nucl_acid_ext.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) * [number_contig](number_contig.md) - Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + * [me➞number_contig](me_number_contig.md) + * [migs_ba➞number_contig](migs_ba_number_contig.md) + * [migs_eu➞number_contig](migs_eu_number_contig.md) + * [migs_org➞number_contig](migs_org_number_contig.md) + * [migs_pl➞number_contig](migs_pl_number_contig.md) + * [migs_vi➞number_contig](migs_vi_number_contig.md) + * [mimag➞number_contig](mimag_number_contig.md) + * [misag➞number_contig](misag_number_contig.md) + * [miuvig➞number_contig](miuvig_number_contig.md) * [pcr_cond](pcr_cond.md) - Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) * [pcr_primers](pcr_primers.md) - PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) * [pred_genome_struc](pred_genome_struc.md) - Expected structure of the viral genome + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) * [pred_genome_type](pred_genome_type.md) - Type of genome predicted for the UViG + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) * [reassembly_bin](reassembly_bin.md) - Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) * [ref_db](ref_db.md) - List of database(s) used for ORF annotation, along with version number and reference to website or publication + * [me➞ref_db](me_ref_db.md) + * [migs_ba➞ref_db](migs_ba_ref_db.md) + * [migs_eu➞ref_db](migs_eu_ref_db.md) + * [migs_org➞ref_db](migs_org_ref_db.md) + * [migs_pl➞ref_db](migs_pl_ref_db.md) + * [migs_vi➞ref_db](migs_vi_ref_db.md) + * [mimag➞ref_db](mimag_ref_db.md) + * [misag➞ref_db](misag_ref_db.md) + * [miuvig➞ref_db](miuvig_ref_db.md) * [seq_meth](seq_meth.md) - Sequencing method used; e.g. Sanger, ABI-solid + * [me➞seq_meth](me_seq_meth.md) + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) + * [migs_org➞seq_meth](migs_org_seq_meth.md) + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) + * [mimag➞seq_meth](mimag_seq_meth.md) + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) + * [misag➞seq_meth](misag_seq_meth.md) + * [miuvig➞seq_meth](miuvig_seq_meth.md) * [seq_quality_check](seq_quality_check.md) - Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) * [sim_search_meth](sim_search_meth.md) - Tool used to compare ORFs with database, along with version and cutoffs used + * [me➞sim_search_meth](me_sim_search_meth.md) + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) + * [misag➞sim_search_meth](misag_sim_search_meth.md) + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) * [single_cell_lysis_appr](single_cell_lysis_appr.md) - Method used to free DNA from interior of the cell(s) or particle(s) + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) * [single_cell_lysis_prot](single_cell_lysis_prot.md) - Name of the kit or standard protocol used for cell(s) or particle(s) lysis + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) * [sop](sop.md) - Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + * [me➞sop](me_sop.md) + * [migs_ba➞sop](migs_ba_sop.md) + * [migs_eu➞sop](migs_eu_sop.md) + * [migs_org➞sop](migs_org_sop.md) + * [migs_pl➞sop](migs_pl_sop.md) + * [migs_vi➞sop](migs_vi_sop.md) + * [mimag➞sop](mimag_sop.md) + * [mimarks_c➞sop](mimarks_c_sop.md) + * [mimarks_s➞sop](mimarks_s_sop.md) + * [misag➞sop](misag_sop.md) + * [miuvig➞sop](miuvig_sop.md) * [sort_tech](sort_tech.md) - Method used to sort/isolate cells or particles of interest + * [misag➞sort_tech](misag_sort_tech.md) + * [miuvig➞sort_tech](miuvig_sort_tech.md) * [target_gene](target_gene.md) - Targeted gene or locus name for marker gene studies + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) * [target_subfragment](target_subfragment.md) - Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) * [tax_class](tax_class.md) - Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + * [me➞tax_class](me_tax_class.md) + * [migs_ba➞tax_class](migs_ba_tax_class.md) + * [migs_eu➞tax_class](migs_eu_tax_class.md) + * [migs_org➞tax_class](migs_org_tax_class.md) + * [migs_pl➞tax_class](migs_pl_tax_class.md) + * [migs_vi➞tax_class](migs_vi_tax_class.md) + * [mimag➞tax_class](mimag_tax_class.md) + * [misag➞tax_class](misag_tax_class.md) + * [miuvig➞tax_class](miuvig_tax_class.md) * [tax_ident](tax_ident.md) - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) + * [migs_org➞tax_ident](migs_org_tax_ident.md) + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) + * [mimag➞tax_ident](mimag_tax_ident.md) + * [misag➞tax_ident](misag_tax_ident.md) + * [miuvig➞tax_ident](miuvig_tax_ident.md) * [trna_ext_software](trna_ext_software.md) - Tools used for tRNA identification + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) + * [misag➞trna_ext_software](misag_trna_ext_software.md) + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) * [trnas](trnas.md) - The total number of tRNAs identified from the SAG or MAG + * [mimag➞trnas](mimag_trnas.md) + * [misag➞trnas](misag_trnas.md) + * [miuvig➞trnas](miuvig_trnas.md) * [url](url.md) + * [me➞url](me_url.md) + * [migs_ba➞url](migs_ba_url.md) + * [migs_eu➞url](migs_eu_url.md) + * [migs_org➞url](migs_org_url.md) + * [migs_pl➞url](migs_pl_url.md) + * [migs_vi➞url](migs_vi_url.md) + * [mimag➞url](mimag_url.md) + * [mimarks_c➞url](mimarks_c_url.md) + * [mimarks_s➞url](mimarks_s_url.md) + * [misag➞url](misag_url.md) + * [miuvig➞url](miuvig_url.md) * [vir_ident_software](vir_ident_software.md) - Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) * [votu_class_appr](votu_class_appr.md) - Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) * [votu_db](votu_db.md) - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any + * [miuvig➞votu_db](miuvig_votu_db.md) * [votu_seq_comp_appr](votu_seq_comp_appr.md) - Tool and thresholds used to compare sequences when computing "species-level" vOTUs + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) * [wga_amp_appr](wga_amp_appr.md) - Method used to amplify genomic DNA in preparation for sequencing + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) * [wga_amp_kit](wga_amp_kit.md) - Kit used to amplify genomic DNA in preparation for sequencing + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) * [x_16s_recover](x_16s_recover.md) - Can a 16S gene be recovered from the submitted SAG or MAG? + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) + * [misag➞x_16s_recover](misag_x_16s_recover.md) * [x_16s_recover_software](x_16s_recover_software.md) - Tools used for 16S rRNA gene extraction + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) ### Types diff --git a/mixs6/indust_eff_percent.md b/mixs6/indust_eff_percent.md index 7529dc36..fc9b9352 100644 --- a/mixs6/indust_eff_percent.md +++ b/mixs6/indust_eff_percent.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:indust_eff_percent](https://w3id.org/mixs/vocab/indust_eff_perc ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/inside_lux.md b/mixs6/inside_lux.md index b6b723ca..2c22b8bc 100644 --- a/mixs6/inside_lux.md +++ b/mixs6/inside_lux.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:inside_lux](https://w3id.org/mixs/vocab/inside_lux) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/investigation_type.md b/mixs6/investigation_type.md index 10dd698e..8a7ae30d 100644 --- a/mixs6/investigation_type.md +++ b/mixs6/investigation_type.md @@ -17,21 +17,21 @@ None -> OPT ## Children + * [me➞investigation_type](me_investigation_type.md) + * [migs_ba➞investigation_type](migs_ba_investigation_type.md) + * [migs_eu➞investigation_type](migs_eu_investigation_type.md) + * [migs_org➞investigation_type](migs_org_investigation_type.md) + * [migs_pl➞investigation_type](migs_pl_investigation_type.md) + * [migs_vi➞investigation_type](migs_vi_investigation_type.md) + * [mimag➞investigation_type](mimag_investigation_type.md) + * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) + * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) + * [misag➞investigation_type](misag_investigation_type.md) + * [miuvig➞investigation_type](miuvig_investigation_type.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,6 @@ None -> OPT | **Comments:** | | Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genomes | | | | Preferred unit: | | | | Position: 2.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='metagenome', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/60 | diff --git a/mixs6/isol_growth_condt.md b/mixs6/isol_growth_condt.md index 914b5acf..5113ed09 100644 --- a/mixs6/isol_growth_condt.md +++ b/mixs6/isol_growth_condt.md @@ -17,21 +17,16 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) + * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) + * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) + * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) + * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) + * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +36,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: PMID,DOI or URL | | | | Preferred unit: | | | | Position: 30.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='doi: 10.1016/j.syapm.2018.01.009', description=None) | diff --git a/mixs6/iwf.md b/mixs6/iwf.md index f2478681..39f690b5 100644 --- a/mixs6/iwf.md +++ b/mixs6/iwf.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:iwf](https://w3id.org/mixs/vocab/iwf) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/lat_lon.md b/mixs6/lat_lon.md index 0089620d..d6c931b5 100644 --- a/mixs6/lat_lon.md +++ b/mixs6/lat_lon.md @@ -17,21 +17,225 @@ None -> OPT [String](types/String.md) ## Children + * [me➞lat_lon](me_lat_lon.md) + * [migs_ba➞lat_lon](migs_ba_lat_lon.md) + * [migs_eu➞lat_lon](migs_eu_lat_lon.md) + * [migs_org➞lat_lon](migs_org_lat_lon.md) + * [migs_pl➞lat_lon](migs_pl_lat_lon.md) + * [migs_vi➞lat_lon](migs_vi_lat_lon.md) + * [mimag➞lat_lon](mimag_lat_lon.md) + * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) + * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) + * [misag➞lat_lon](misag_lat_lon.md) + * [miuvig➞lat_lon](miuvig_lat_lon.md) ## Used by + * [Air](Air.md) + * [AirMe](AirMe.md) + * [AirMigsBa](AirMigsBa.md) + * [AirMigsEu](AirMigsEu.md) + * [AirMigsOrg](AirMigsOrg.md) + * [AirMigsPl](AirMigsPl.md) + * [AirMigsVi](AirMigsVi.md) + * [AirMimag](AirMimag.md) + * [AirMimarksC](AirMimarksC.md) + * [AirMimarksS](AirMimarksS.md) + * [AirMisag](AirMisag.md) + * [AirMiuvig](AirMiuvig.md) + * [BuiltEnvironment](BuiltEnvironment.md) + * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) + * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) + * [Host-associated](Host-associated.md) + * [Host-associatedMe](Host-associatedMe.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Host-associatedMimag](Host-associatedMimag.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Host-associatedMisag](Host-associatedMisag.md) + * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Human-associated](Human-associated.md) + * [Human-associatedMe](Human-associatedMe.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-associatedMimag](Human-associatedMimag.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-associatedMisag](Human-associatedMisag.md) + * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-gut](Human-gut.md) + * [Human-gutMe](Human-gutMe.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-gutMigsOrg](Human-gutMigsOrg.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-gutMimag](Human-gutMimag.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-gutMisag](Human-gutMisag.md) + * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-oral](Human-oral.md) + * [Human-oralMe](Human-oralMe.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-oralMigsOrg](Human-oralMigsOrg.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-oralMimag](Human-oralMimag.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-oralMisag](Human-oralMisag.md) + * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-skin](Human-skin.md) + * [Human-skinMe](Human-skinMe.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-skinMigsOrg](Human-skinMigsOrg.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-skinMimag](Human-skinMimag.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-skinMisag](Human-skinMisag.md) + * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalMe](Human-vaginalMe.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [Human-vaginalMimag](Human-vaginalMimag.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [Human-vaginalMisag](Human-vaginalMisag.md) + * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) + * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) + * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) + * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) + * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) + * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) + * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedMe](Plant-associatedMe.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [Plant-associatedMimag](Plant-associatedMimag.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [Plant-associatedMisag](Plant-associatedMisag.md) + * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Sediment](Sediment.md) + * [SedimentMe](SedimentMe.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SedimentMigsOrg](SedimentMigsOrg.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SedimentMimag](SedimentMimag.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SedimentMisag](SedimentMisag.md) + * [SedimentMiuvig](SedimentMiuvig.md) + * [Soil](Soil.md) + * [SoilMe](SoilMe.md) + * [SoilMigsBa](SoilMigsBa.md) + * [SoilMigsEu](SoilMigsEu.md) + * [SoilMigsOrg](SoilMigsOrg.md) + * [SoilMigsPl](SoilMigsPl.md) + * [SoilMigsVi](SoilMigsVi.md) + * [SoilMimag](SoilMimag.md) + * [SoilMimarksC](SoilMimarksC.md) + * [SoilMimarksS](SoilMimarksS.md) + * [SoilMisag](SoilMisag.md) + * [SoilMiuvig](SoilMiuvig.md) + * [WastewaterSludge](WastewaterSludge.md) + * [WastewaterSludgeMe](WastewaterSludgeMe.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) + * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [Water](Water.md) + * [WaterMe](WaterMe.md) + * [WaterMigsBa](WaterMigsBa.md) + * [WaterMigsEu](WaterMigsEu.md) + * [WaterMigsOrg](WaterMigsOrg.md) + * [WaterMigsPl](WaterMigsPl.md) + * [WaterMigsVi](WaterMigsVi.md) + * [WaterMimag](WaterMimag.md) + * [WaterMimarksC](WaterMimarksC.md) + * [WaterMimarksS](WaterMimarksS.md) + * [WaterMisag](WaterMisag.md) + * [WaterMiuvig](WaterMiuvig.md) ## Other properties @@ -41,16 +245,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: decimal degrees | | | | Preferred unit: | | | | Position: 5.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='50.586825 6.408977', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/62 | diff --git a/mixs6/lib_layout.md b/mixs6/lib_layout.md index 12613448..5932a10c 100644 --- a/mixs6/lib_layout.md +++ b/mixs6/lib_layout.md @@ -17,21 +17,20 @@ None -> OPT ## Children + * [me➞lib_layout](me_lib_layout.md) + * [migs_ba➞lib_layout](migs_ba_lib_layout.md) + * [migs_eu➞lib_layout](migs_eu_lib_layout.md) + * [migs_org➞lib_layout](migs_org_lib_layout.md) + * [migs_pl➞lib_layout](migs_pl_lib_layout.md) + * [migs_vi➞lib_layout](migs_vi_lib_layout.md) + * [mimag➞lib_layout](mimag_lib_layout.md) + * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) + * [misag➞lib_layout](misag_lib_layout.md) + * [miuvig➞lib_layout](miuvig_lib_layout.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 41.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='paired', description=None) | diff --git a/mixs6/lib_reads_seqd.md b/mixs6/lib_reads_seqd.md index 521c38f7..c9b29727 100644 --- a/mixs6/lib_reads_seqd.md +++ b/mixs6/lib_reads_seqd.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞lib_reads_seqd](me_lib_reads_seqd.md) + * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) + * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) + * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) + * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) + * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) + * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) + * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) + * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) + * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: number of reads sequenced | | | | Preferred unit: | | | | Position: 40.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='20', description=None) | diff --git a/mixs6/lib_screen.md b/mixs6/lib_screen.md index 0d4d7286..64c65f62 100644 --- a/mixs6/lib_screen.md +++ b/mixs6/lib_screen.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞lib_screen](me_lib_screen.md) + * [migs_ba➞lib_screen](migs_ba_lib_screen.md) + * [migs_eu➞lib_screen](migs_eu_lib_screen.md) + * [migs_org➞lib_screen](migs_org_lib_screen.md) + * [migs_pl➞lib_screen](migs_pl_lib_screen.md) + * [migs_vi➞lib_screen](migs_vi_lib_screen.md) + * [mimag➞lib_screen](mimag_lib_screen.md) + * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) + * [misag➞lib_screen](misag_lib_screen.md) + * [miuvig➞lib_screen](miuvig_lib_screen.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: screening strategy name | | | | Preferred unit: | | | | Position: 43.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='enriched, screened, normalized', description=None) | diff --git a/mixs6/lib_size.md b/mixs6/lib_size.md index b0f81a53..38355583 100644 --- a/mixs6/lib_size.md +++ b/mixs6/lib_size.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞lib_size](me_lib_size.md) + * [migs_ba➞lib_size](migs_ba_lib_size.md) + * [migs_eu➞lib_size](migs_eu_lib_size.md) + * [migs_org➞lib_size](migs_org_lib_size.md) + * [migs_pl➞lib_size](migs_pl_lib_size.md) + * [migs_vi➞lib_size](migs_vi_lib_size.md) + * [mimag➞lib_size](mimag_lib_size.md) + * [mimarks_s➞lib_size](mimarks_s_lib_size.md) + * [misag➞lib_size](misag_lib_size.md) + * [miuvig➞lib_size](miuvig_lib_size.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: number of clones | | | | Preferred unit: | | | | Position: 39.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='50', description=None) | diff --git a/mixs6/lib_vector.md b/mixs6/lib_vector.md index 558e3f57..dc09b669 100644 --- a/mixs6/lib_vector.md +++ b/mixs6/lib_vector.md @@ -17,21 +17,20 @@ None -> OPT [String](types/String.md) ## Children + * [me➞lib_vector](me_lib_vector.md) + * [migs_ba➞lib_vector](migs_ba_lib_vector.md) + * [migs_eu➞lib_vector](migs_eu_lib_vector.md) + * [migs_org➞lib_vector](migs_org_lib_vector.md) + * [migs_pl➞lib_vector](migs_pl_lib_vector.md) + * [migs_vi➞lib_vector](migs_vi_lib_vector.md) + * [mimag➞lib_vector](mimag_lib_vector.md) + * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) + * [misag➞lib_vector](misag_lib_vector.md) + * [miuvig➞lib_vector](miuvig_lib_vector.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +40,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: vector | | | | Preferred unit: | | | | Position: 42.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='Bacteriophage P1', description=None) | diff --git a/mixs6/light_intensity.md b/mixs6/light_intensity.md index 47fcd68c..297d8254 100644 --- a/mixs6/light_intensity.md +++ b/mixs6/light_intensity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:light_intensity](https://w3id.org/mixs/vocab/light_intensity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/mag_cov_software.md b/mixs6/mag_cov_software.md index 62fbb265..1f1af192 100644 --- a/mixs6/mag_cov_software.md +++ b/mixs6/mag_cov_software.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [mimag➞mag_cov_software](mimag_mag_cov_software.md) + * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 82.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='bbmap', description=None) | diff --git a/mixs6/magnesium.md b/mixs6/magnesium.md index c211f549..b19e9519 100644 --- a/mixs6/magnesium.md +++ b/mixs6/magnesium.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:magnesium](https://w3id.org/mixs/vocab/magnesium) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/mean_frict_vel.md b/mixs6/mean_frict_vel.md index 6f47a556..784a13ce 100644 --- a/mixs6/mean_frict_vel.md +++ b/mixs6/mean_frict_vel.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:mean_frict_vel](https://w3id.org/mixs/vocab/mean_frict_vel) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/mean_peak_frict_vel.md b/mixs6/mean_peak_frict_vel.md index 914d11f0..f3a1808a 100644 --- a/mixs6/mean_peak_frict_vel.md +++ b/mixs6/mean_peak_frict_vel.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:mean_peak_frict_vel](https://w3id.org/mixs/vocab/mean_peak_fric ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/methane.md b/mixs6/methane.md index 29e7431c..31a055da 100644 --- a/mixs6/methane.md +++ b/mixs6/methane.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:methane](https://w3id.org/mixs/vocab/methane) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/microbial_biomass.md b/mixs6/microbial_biomass.md index a694ed9c..064693f0 100644 --- a/mixs6/microbial_biomass.md +++ b/mixs6/microbial_biomass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:microbial_biomass](https://w3id.org/mixs/vocab/microbial_biomas ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/mid.md b/mixs6/mid.md index ee45b56c..93462abf 100644 --- a/mixs6/mid.md +++ b/mixs6/mid.md @@ -17,21 +17,15 @@ None -> OPT [String](types/String.md) ## Children + * [me➞mid](me_mid.md) + * [mimag➞mid](mimag_mid.md) + * [mimarks_s➞mid](mimarks_s_mid.md) + * [misag➞mid](misag_mid.md) + * [miuvig➞mid](miuvig_mid.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +35,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: multiplex identifier sequence | | | | Preferred unit: | | | | Position: 47.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='GTGAATAT', description=None) | diff --git a/mixs6/nitrate.md b/mixs6/nitrate.md index c29e1a50..5294fc32 100644 --- a/mixs6/nitrate.md +++ b/mixs6/nitrate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:nitrate](https://w3id.org/mixs/vocab/nitrate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/nitrite.md b/mixs6/nitrite.md index fab7a30d..4b8270fb 100644 --- a/mixs6/nitrite.md +++ b/mixs6/nitrite.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:nitrite](https://w3id.org/mixs/vocab/nitrite) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/nitro.md b/mixs6/nitro.md index e6f70aea..ae6b4849 100644 --- a/mixs6/nitro.md +++ b/mixs6/nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:nitro](https://w3id.org/mixs/vocab/nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/nucl_acid_amp.md b/mixs6/nucl_acid_amp.md index 5f739c15..00d60643 100644 --- a/mixs6/nucl_acid_amp.md +++ b/mixs6/nucl_acid_amp.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞nucl_acid_amp](me_nucl_acid_amp.md) + * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) + * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) + * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) + * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) + * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) + * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) + * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) + * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) + * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) + * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: PMID, DOI or URL | | | | Preferred unit: | | | | Position: 38.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='https://phylogenomics.me/protocols/16s-pcr-protocol/', description=None) | diff --git a/mixs6/nucl_acid_ext.md b/mixs6/nucl_acid_ext.md index 4c7237fd..b49b4624 100644 --- a/mixs6/nucl_acid_ext.md +++ b/mixs6/nucl_acid_ext.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞nucl_acid_ext](me_nucl_acid_ext.md) + * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) + * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) + * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) + * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) + * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) + * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) + * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) + * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) + * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) + * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: PMID, DOI or URL | | | | Preferred unit: | | | | Position: 37.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf', description=None) | diff --git a/mixs6/num_replicons.md b/mixs6/num_replicons.md index 240dff21..35ba25c8 100644 --- a/mixs6/num_replicons.md +++ b/mixs6/num_replicons.md @@ -17,21 +17,13 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞num_replicons](migs_ba_num_replicons.md) + * [migs_eu➞num_replicons](migs_eu_num_replicons.md) + * [migs_vi➞num_replicons](migs_vi_num_replicons.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments | | | | Preferred unit: | | | | Position: 16.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='2', description=None) | diff --git a/mixs6/number_contig.md b/mixs6/number_contig.md index c141d738..bbbef608 100644 --- a/mixs6/number_contig.md +++ b/mixs6/number_contig.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞number_contig](me_number_contig.md) + * [migs_ba➞number_contig](migs_ba_number_contig.md) + * [migs_eu➞number_contig](migs_eu_number_contig.md) + * [migs_org➞number_contig](migs_org_number_contig.md) + * [migs_pl➞number_contig](migs_pl_number_contig.md) + * [migs_vi➞number_contig](migs_vi_number_contig.md) + * [mimag➞number_contig](mimag_number_contig.md) + * [misag➞number_contig](misag_number_contig.md) + * [miuvig➞number_contig](miuvig_number_contig.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: value | | | | Preferred unit: | | | | Position: 58.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='40', description=None) | diff --git a/mixs6/occup_density_samp.md b/mixs6/occup_density_samp.md index f6deb0b9..9f21d64b 100644 --- a/mixs6/occup_density_samp.md +++ b/mixs6/occup_density_samp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:occup_density_samp](https://w3id.org/mixs/vocab/occup_density_s ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/org_carb.md b/mixs6/org_carb.md index bf68047e..363eaa9c 100644 --- a/mixs6/org_carb.md +++ b/mixs6/org_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:org_carb](https://w3id.org/mixs/vocab/org_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/org_matter.md b/mixs6/org_matter.md index 131b55fd..acbf7cf4 100644 --- a/mixs6/org_matter.md +++ b/mixs6/org_matter.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:org_matter](https://w3id.org/mixs/vocab/org_matter) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/org_nitro.md b/mixs6/org_nitro.md index 654dd377..9ac7700b 100644 --- a/mixs6/org_nitro.md +++ b/mixs6/org_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:org_nitro](https://w3id.org/mixs/vocab/org_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/owc_tvdss.md b/mixs6/owc_tvdss.md index bb0c5628..95d4d1e0 100644 --- a/mixs6/owc_tvdss.md +++ b/mixs6/owc_tvdss.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:owc_tvdss](https://w3id.org/mixs/vocab/owc_tvdss) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/oxygen.md b/mixs6/oxygen.md index aff04179..925ab518 100644 --- a/mixs6/oxygen.md +++ b/mixs6/oxygen.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:oxygen](https://w3id.org/mixs/vocab/oxygen) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/part_org_carb.md b/mixs6/part_org_carb.md index 17801662..ff9307ed 100644 --- a/mixs6/part_org_carb.md +++ b/mixs6/part_org_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:part_org_carb](https://w3id.org/mixs/vocab/part_org_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/part_org_nitro.md b/mixs6/part_org_nitro.md index 15fa76c5..3782755d 100644 --- a/mixs6/part_org_nitro.md +++ b/mixs6/part_org_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:part_org_nitro](https://w3id.org/mixs/vocab/part_org_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/pathogenicity.md b/mixs6/pathogenicity.md index 8661f343..b277a4b7 100644 --- a/mixs6/pathogenicity.md +++ b/mixs6/pathogenicity.md @@ -17,21 +17,14 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) + * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) + * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) + * [miuvig➞pathogenicity](miuvig_pathogenicity.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +34,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names of organisms that the entity is pathogenic to | | | | Preferred unit: | | | | Position: 21.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='human, animal, plant, fungi, bacteria', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/65 | diff --git a/mixs6/pcr_cond.md b/mixs6/pcr_cond.md index eb55d623..28aed573 100644 --- a/mixs6/pcr_cond.md +++ b/mixs6/pcr_cond.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) + * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles | | | | Preferred unit: | | | | Position: 49.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35', description=None) | diff --git a/mixs6/pcr_primers.md b/mixs6/pcr_primers.md index 1ca7877c..df23eee3 100644 --- a/mixs6/pcr_primers.md +++ b/mixs6/pcr_primers.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) + * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: FWD: forward primer sequence;REV:reverse primer sequence | | | | Preferred unit: | | | | Position: 46.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT', description=None) | diff --git a/mixs6/petroleum_hydrocarb.md b/mixs6/petroleum_hydrocarb.md index 6bd7441f..81c49fc8 100644 --- a/mixs6/petroleum_hydrocarb.md +++ b/mixs6/petroleum_hydrocarb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:petroleum_hydrocarb](https://w3id.org/mixs/vocab/petroleum_hydr ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ph.md b/mixs6/ph.md index 2bf00497..cb1e4755 100644 --- a/mixs6/ph.md +++ b/mixs6/ph.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ph](https://w3id.org/mixs/vocab/ph) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/phosphate.md b/mixs6/phosphate.md index 6b593edb..1aa68564 100644 --- a/mixs6/phosphate.md +++ b/mixs6/phosphate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:phosphate](https://w3id.org/mixs/vocab/phosphate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/photon_flux.md b/mixs6/photon_flux.md index 4077b70d..3f18247f 100644 --- a/mixs6/photon_flux.md +++ b/mixs6/photon_flux.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:photon_flux](https://w3id.org/mixs/vocab/photon_flux) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ploidy.md b/mixs6/ploidy.md index f1594aa1..853e5d03 100644 --- a/mixs6/ploidy.md +++ b/mixs6/ploidy.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [migs_eu➞ploidy](migs_eu_ploidy.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: PATO | | | | Preferred unit: | | | | Position: 15.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='allopolyploidy [PATO:0001379]', description=None) | diff --git a/mixs6/potassium.md b/mixs6/potassium.md index bae598aa..e4b5249f 100644 --- a/mixs6/potassium.md +++ b/mixs6/potassium.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:potassium](https://w3id.org/mixs/vocab/potassium) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/pour_point.md b/mixs6/pour_point.md index c25634ce..32f0c656 100644 --- a/mixs6/pour_point.md +++ b/mixs6/pour_point.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:pour_point](https://w3id.org/mixs/vocab/pour_point) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/pred_genome_struc.md b/mixs6/pred_genome_struc.md index 45d11946..7cabd459 100644 --- a/mixs6/pred_genome_struc.md +++ b/mixs6/pred_genome_struc.md @@ -17,21 +17,11 @@ None -> OPT ## Children + * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 85.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='non-segmented', description=None) | diff --git a/mixs6/pred_genome_type.md b/mixs6/pred_genome_type.md index 5af23f27..cca7ecda 100644 --- a/mixs6/pred_genome_type.md +++ b/mixs6/pred_genome_type.md @@ -17,21 +17,11 @@ None -> OPT ## Children + * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 84.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='dsDNA', description=None) | diff --git a/mixs6/pressure.md b/mixs6/pressure.md index ec66800a..f50109f9 100644 --- a/mixs6/pressure.md +++ b/mixs6/pressure.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:pressure](https://w3id.org/mixs/vocab/pressure) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/primary_prod.md b/mixs6/primary_prod.md index 01855825..1777c31f 100644 --- a/mixs6/primary_prod.md +++ b/mixs6/primary_prod.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:primary_prod](https://w3id.org/mixs/vocab/primary_prod) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/prod_rate.md b/mixs6/prod_rate.md index 18ca9191..10096100 100644 --- a/mixs6/prod_rate.md +++ b/mixs6/prod_rate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:prod_rate](https://w3id.org/mixs/vocab/prod_rate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/project_name.md b/mixs6/project_name.md index 0df86d42..5646099e 100644 --- a/mixs6/project_name.md +++ b/mixs6/project_name.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞project_name](me_project_name.md) + * [migs_ba➞project_name](migs_ba_project_name.md) + * [migs_eu➞project_name](migs_eu_project_name.md) + * [migs_org➞project_name](migs_org_project_name.md) + * [migs_pl➞project_name](migs_pl_project_name.md) + * [migs_vi➞project_name](migs_vi_project_name.md) + * [mimag➞project_name](mimag_project_name.md) + * [mimarks_c➞project_name](mimarks_c_project_name.md) + * [mimarks_s➞project_name](mimarks_s_project_name.md) + * [misag➞project_name](misag_project_name.md) + * [miuvig➞project_name](miuvig_project_name.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: | | | | Preferred unit: | | | | Position: 3.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='Forest soil metagenome', description=None) | diff --git a/mixs6/propagation.md b/mixs6/propagation.md index 1a4b8ca0..07b0e37e 100644 --- a/mixs6/propagation.md +++ b/mixs6/propagation.md @@ -17,21 +17,13 @@ None -> OPT [String](types/String.md) ## Children + * [migs_eu➞propagation](migs_eu_propagation.md) + * [migs_pl➞propagation](migs_pl_propagation.md) + * [migs_vi➞propagation](migs_vi_propagation.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual | | | | Preferred unit: | | | | Position: 27.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='lytic', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/88 | diff --git a/mixs6/reassembly_bin.md b/mixs6/reassembly_bin.md index e12ede21..09474c6f 100644 --- a/mixs6/reassembly_bin.md +++ b/mixs6/reassembly_bin.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞reassembly_bin](mimag_reassembly_bin.md) + * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: boolean | | | | Preferred unit: | | | | Position: 81.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='no', description=None) | diff --git a/mixs6/redox_potential.md b/mixs6/redox_potential.md index db022351..3202d774 100644 --- a/mixs6/redox_potential.md +++ b/mixs6/redox_potential.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:redox_potential](https://w3id.org/mixs/vocab/redox_potential) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/ref_biomaterial.md b/mixs6/ref_biomaterial.md index eb708476..0fd61e7b 100644 --- a/mixs6/ref_biomaterial.md +++ b/mixs6/ref_biomaterial.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞ref_biomaterial](me_ref_biomaterial.md) + * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) + * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) + * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) + * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) + * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) + * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) + * [misag➞ref_biomaterial](misag_ref_biomaterial.md) + * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: PMID, DOI or URL | | | | Preferred unit: | | | | Position: 19.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='doi:10.1016/j.syapm.2018.01.009', description=None) | diff --git a/mixs6/ref_db.md b/mixs6/ref_db.md index d1450d49..88ca55a1 100644 --- a/mixs6/ref_db.md +++ b/mixs6/ref_db.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞ref_db](me_ref_db.md) + * [migs_ba➞ref_db](migs_ba_ref_db.md) + * [migs_eu➞ref_db](migs_eu_ref_db.md) + * [migs_org➞ref_db](migs_org_ref_db.md) + * [migs_pl➞ref_db](migs_pl_ref_db.md) + * [migs_vi➞ref_db](migs_vi_ref_db.md) + * [mimag➞ref_db](mimag_ref_db.md) + * [misag➞ref_db](misag_ref_db.md) + * [miuvig➞ref_db](miuvig_ref_db.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names, versions, and references of databases | | | | Preferred unit: | | | | Position: 60.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975', description=None) | diff --git a/mixs6/rel_air_humidity.md b/mixs6/rel_air_humidity.md index 9ebd00a6..02f129ef 100644 --- a/mixs6/rel_air_humidity.md +++ b/mixs6/rel_air_humidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:rel_air_humidity](https://w3id.org/mixs/vocab/rel_air_humidity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/rel_humidity_out.md b/mixs6/rel_humidity_out.md index 50e8665d..c42e7033 100644 --- a/mixs6/rel_humidity_out.md +++ b/mixs6/rel_humidity_out.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:rel_humidity_out](https://w3id.org/mixs/vocab/rel_humidity_out) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/rel_to_oxygen.md b/mixs6/rel_to_oxygen.md index 0eb4968e..689c6d7c 100644 --- a/mixs6/rel_to_oxygen.md +++ b/mixs6/rel_to_oxygen.md @@ -17,21 +17,16 @@ None -> OPT ## Children + * [me➞rel_to_oxygen](me_rel_to_oxygen.md) + * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) + * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) + * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) + * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) + * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +36,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 29.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: X | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='aerobe', description=None) | diff --git a/mixs6/room_air_exch_rate.md b/mixs6/room_air_exch_rate.md index 9aea04d2..975ab88a 100644 --- a/mixs6/room_air_exch_rate.md +++ b/mixs6/room_air_exch_rate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:room_air_exch_rate](https://w3id.org/mixs/vocab/room_air_exch_r ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/root_med_ph.md b/mixs6/root_med_ph.md index ba42760a..6afbdd2d 100644 --- a/mixs6/root_med_ph.md +++ b/mixs6/root_med_ph.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:root_med_ph](https://w3id.org/mixs/vocab/root_med_ph) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/salinity.md b/mixs6/salinity.md index e45db0af..ba3905b4 100644 --- a/mixs6/salinity.md +++ b/mixs6/salinity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:salinity](https://w3id.org/mixs/vocab/salinity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/samp_collect_device.md b/mixs6/samp_collect_device.md index c00d5059..f3f98719 100644 --- a/mixs6/samp_collect_device.md +++ b/mixs6/samp_collect_device.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞samp_collect_device](me_samp_collect_device.md) + * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) + * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) + * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) + * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) + * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) + * [mimag➞samp_collect_device](mimag_samp_collect_device.md) + * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) + * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) + * [misag➞samp_collect_device](misag_samp_collect_device.md) + * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: type name | | | | Preferred unit: | | | | Position: 31.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: X | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='environmental swab sampling, biopsy, niskin bottle, push core', description=None) | diff --git a/mixs6/samp_mat_process.md b/mixs6/samp_mat_process.md index 96a3bae2..9d7dc8f7 100644 --- a/mixs6/samp_mat_process.md +++ b/mixs6/samp_mat_process.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞samp_mat_process](me_samp_mat_process.md) + * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) + * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) + * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) + * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) + * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) + * [mimag➞samp_mat_process](mimag_samp_mat_process.md) + * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) + * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) + * [misag➞samp_mat_process](misag_samp_mat_process.md) + * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: text or OBI | | | | Preferred unit: | | | | Position: 32.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='filtering of seawater, storing samples in ethanol', description=None) | diff --git a/mixs6/samp_salinity.md b/mixs6/samp_salinity.md index 297340dc..792a9a14 100644 --- a/mixs6/samp_salinity.md +++ b/mixs6/samp_salinity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_salinity](https://w3id.org/mixs/vocab/samp_salinity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/samp_size.md b/mixs6/samp_size.md index 95a1ffa6..bd390b51 100644 --- a/mixs6/samp_size.md +++ b/mixs6/samp_size.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_size](https://w3id.org/mixs/vocab/samp_size) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞samp_size](me_samp_size.md) + * [migs_ba➞samp_size](migs_ba_samp_size.md) + * [migs_eu➞samp_size](migs_eu_samp_size.md) + * [migs_org➞samp_size](migs_org_samp_size.md) + * [migs_pl➞samp_size](migs_pl_samp_size.md) + * [migs_vi➞samp_size](migs_vi_samp_size.md) + * [mimag➞samp_size](mimag_samp_size.md) + * [mimarks_c➞samp_size](mimarks_c_samp_size.md) + * [mimarks_s➞samp_size](mimarks_s_samp_size.md) + * [misag➞samp_size](misag_samp_size.md) + * [miuvig➞samp_size](miuvig_samp_size.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millliter, gram, milligram, liter | | | | Position: 34.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: X | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='5 liter', description=None) | diff --git a/mixs6/samp_store_temp.md b/mixs6/samp_store_temp.md index 1066a15e..e9af5a45 100644 --- a/mixs6/samp_store_temp.md +++ b/mixs6/samp_store_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_store_temp](https://w3id.org/mixs/vocab/samp_store_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/samp_time_out.md b/mixs6/samp_time_out.md index 4262dc73..476a879c 100644 --- a/mixs6/samp_time_out.md +++ b/mixs6/samp_time_out.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_time_out](https://w3id.org/mixs/vocab/samp_time_out) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/samp_vol_we_dna_ext.md b/mixs6/samp_vol_we_dna_ext.md index d2e98a32..684a23ca 100644 --- a/mixs6/samp_vol_we_dna_ext.md +++ b/mixs6/samp_vol_we_dna_ext.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_vol_we_dna_ext](https://w3id.org/mixs/vocab/samp_vol_we_dn ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sample_name.md b/mixs6/sample_name.md index 30a30ebe..fa336154 100644 --- a/mixs6/sample_name.md +++ b/mixs6/sample_name.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞sample_name](me_sample_name.md) + * [migs_ba➞sample_name](migs_ba_sample_name.md) + * [migs_eu➞sample_name](migs_eu_sample_name.md) + * [migs_org➞sample_name](migs_org_sample_name.md) + * [migs_pl➞sample_name](migs_pl_sample_name.md) + * [migs_vi➞sample_name](migs_vi_sample_name.md) + * [mimag➞sample_name](mimag_sample_name.md) + * [mimarks_c➞sample_name](mimarks_c_sample_name.md) + * [mimarks_s➞sample_name](mimarks_s_sample_name.md) + * [misag➞sample_name](misag_sample_name.md) + * [miuvig➞sample_name](miuvig_sample_name.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: | | | | Preferred unit: | | | | Position: | -| | | CHECKLIST migs_eu: | -| | | CHECKLIST migs_ba: | -| | | CHECKLIST migs_pl: | -| | | CHECKLIST migs_vi: | -| | | CHECKLIST migs_org: | -| | | CHECKLIST me: | -| | | CHECKLIST mimarks_s: | -| | | CHECKLIST mimarks_c: | -| | | CHECKLIST misag: | -| | | CHECKLIST mimag: | -| | | CHECKLIST miuvig: | | **Examples:** | | Example(value='', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/78 | diff --git a/mixs6/season_precpt.md b/mixs6/season_precpt.md index 345b211e..53b4bd4d 100644 --- a/mixs6/season_precpt.md +++ b/mixs6/season_precpt.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:season_precpt](https://w3id.org/mixs/vocab/season_precpt) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/season_temp.md b/mixs6/season_temp.md index 1195a4b3..e5279f06 100644 --- a/mixs6/season_temp.md +++ b/mixs6/season_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:season_temp](https://w3id.org/mixs/vocab/season_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/seq_meth.md b/mixs6/seq_meth.md index aa474909..369317d4 100644 --- a/mixs6/seq_meth.md +++ b/mixs6/seq_meth.md @@ -17,21 +17,21 @@ None -> OPT ## Children + * [me➞seq_meth](me_seq_meth.md) + * [migs_ba➞seq_meth](migs_ba_seq_meth.md) + * [migs_eu➞seq_meth](migs_eu_seq_meth.md) + * [migs_org➞seq_meth](migs_org_seq_meth.md) + * [migs_pl➞seq_meth](migs_pl_seq_meth.md) + * [migs_vi➞seq_meth](migs_vi_seq_meth.md) + * [mimag➞seq_meth](mimag_seq_meth.md) + * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) + * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) + * [misag➞seq_meth](misag_seq_meth.md) + * [miuvig➞seq_meth](miuvig_seq_meth.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 50.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='Illumina HiSeq 1500', description=None) | diff --git a/mixs6/seq_quality_check.md b/mixs6/seq_quality_check.md index 77e5500f..4531334e 100644 --- a/mixs6/seq_quality_check.md +++ b/mixs6/seq_quality_check.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) + * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: none or manually edited | | | | Preferred unit: | | | | Position: 51.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='none', description=None) | diff --git a/mixs6/silicate.md b/mixs6/silicate.md index dff17edc..7a7208de 100644 --- a/mixs6/silicate.md +++ b/mixs6/silicate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:silicate](https://w3id.org/mixs/vocab/silicate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sim_search_meth.md b/mixs6/sim_search_meth.md index 36457ce7..741cf252 100644 --- a/mixs6/sim_search_meth.md +++ b/mixs6/sim_search_meth.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞sim_search_meth](me_sim_search_meth.md) + * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) + * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) + * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) + * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) + * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) + * [mimag➞sim_search_meth](mimag_sim_search_meth.md) + * [misag➞sim_search_meth](misag_sim_search_meth.md) + * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names and versions of software(s), parameters used | | | | Preferred unit: | | | | Position: 61.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='HMMER3;3.1b2;hmmsearch, cutoff of 50 on score', description=None) | diff --git a/mixs6/single_cell_lysis_appr.md b/mixs6/single_cell_lysis_appr.md index 626203c3..4462fd34 100644 --- a/mixs6/single_cell_lysis_appr.md +++ b/mixs6/single_cell_lysis_appr.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) + * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 75.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='enzymatic', description=None) | diff --git a/mixs6/single_cell_lysis_prot.md b/mixs6/single_cell_lysis_prot.md index e1abf739..a7bbc9c6 100644 --- a/mixs6/single_cell_lysis_prot.md +++ b/mixs6/single_cell_lysis_prot.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) + * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: kit, protocol name | | | | Preferred unit: | | | | Position: 76.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='ambion single cell lysis kit', description=None) | diff --git a/mixs6/size_frac.md b/mixs6/size_frac.md index f2604800..7dd3c8cd 100644 --- a/mixs6/size_frac.md +++ b/mixs6/size_frac.md @@ -17,21 +17,15 @@ None -> OPT [String](types/String.md) ## Children + * [me➞size_frac](me_size_frac.md) + * [mimag➞size_frac](mimag_size_frac.md) + * [mimarks_s➞size_frac](mimarks_s_size_frac.md) + * [misag➞size_frac](misag_size_frac.md) + * [miuvig➞size_frac](miuvig_size_frac.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +35,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: filter size value range | | | | Preferred unit: | | | | Position: 33.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: X | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='0-0.22 micrometer', description=None) | diff --git a/mixs6/size_frac_low.md b/mixs6/size_frac_low.md index ea597466..e2e3c833 100644 --- a/mixs6/size_frac_low.md +++ b/mixs6/size_frac_low.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:size_frac_low](https://w3id.org/mixs/vocab/size_frac_low) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/size_frac_up.md b/mixs6/size_frac_up.md index 18765b27..69efe33f 100644 --- a/mixs6/size_frac_up.md +++ b/mixs6/size_frac_up.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:size_frac_up](https://w3id.org/mixs/vocab/size_frac_up) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/slope_aspect.md b/mixs6/slope_aspect.md index 6f664fe0..43d68877 100644 --- a/mixs6/slope_aspect.md +++ b/mixs6/slope_aspect.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:slope_aspect](https://w3id.org/mixs/vocab/slope_aspect) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/slope_gradient.md b/mixs6/slope_gradient.md index 69cd1df9..21ca0a3e 100644 --- a/mixs6/slope_gradient.md +++ b/mixs6/slope_gradient.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:slope_gradient](https://w3id.org/mixs/vocab/slope_gradient) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sludge_retent_time.md b/mixs6/sludge_retent_time.md index 57a9189c..616cb0ca 100644 --- a/mixs6/sludge_retent_time.md +++ b/mixs6/sludge_retent_time.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:sludge_retent_time](https://w3id.org/mixs/vocab/sludge_retent_t ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sodium.md b/mixs6/sodium.md index 5f2a2f9c..751948b1 100644 --- a/mixs6/sodium.md +++ b/mixs6/sodium.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:sodium](https://w3id.org/mixs/vocab/sodium) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/solar_irradiance.md b/mixs6/solar_irradiance.md index 9630b3d0..4bfcb31c 100644 --- a/mixs6/solar_irradiance.md +++ b/mixs6/solar_irradiance.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:solar_irradiance](https://w3id.org/mixs/vocab/solar_irradiance) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/soluble_react_phosp.md b/mixs6/soluble_react_phosp.md index 5bba34f5..865148b0 100644 --- a/mixs6/soluble_react_phosp.md +++ b/mixs6/soluble_react_phosp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:soluble_react_phosp](https://w3id.org/mixs/vocab/soluble_react_ ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sop.md b/mixs6/sop.md index 9df0caa5..4f6400cf 100644 --- a/mixs6/sop.md +++ b/mixs6/sop.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞sop](me_sop.md) + * [migs_ba➞sop](migs_ba_sop.md) + * [migs_eu➞sop](migs_eu_sop.md) + * [migs_org➞sop](migs_org_sop.md) + * [migs_pl➞sop](migs_pl_sop.md) + * [migs_vi➞sop](migs_vi_sop.md) + * [mimag➞sop](mimag_sop.md) + * [mimarks_c➞sop](mimarks_c_sop.md) + * [mimarks_s➞sop](mimarks_s_sop.md) + * [misag➞sop](misag_sop.md) + * [miuvig➞sop](miuvig_sop.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: reference to SOP | | | | Preferred unit: | | | | Position: 93.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/', description=None) | diff --git a/mixs6/sort_tech.md b/mixs6/sort_tech.md index f7bf8c35..8804b9f8 100644 --- a/mixs6/sort_tech.md +++ b/mixs6/sort_tech.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [misag➞sort_tech](misag_sort_tech.md) + * [miuvig➞sort_tech](miuvig_sort_tech.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 74.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='optical manipulation', description=None) | diff --git a/mixs6/source_mat_id.md b/mixs6/source_mat_id.md index 54519094..d7dad879 100644 --- a/mixs6/source_mat_id.md +++ b/mixs6/source_mat_id.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞source_mat_id](me_source_mat_id.md) + * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) + * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) + * [migs_org➞source_mat_id](migs_org_source_mat_id.md) + * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) + * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) + * [mimag➞source_mat_id](mimag_source_mat_id.md) + * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) + * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) + * [misag➞source_mat_id](misag_source_mat_id.md) + * [miuvig➞source_mat_id](miuvig_source_mat_id.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer | | | | Preferred unit: | | | | Position: 20.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='MPI012345', description=None) | diff --git a/mixs6/source_uvig.md b/mixs6/source_uvig.md index a545013c..b2d4ffc1 100644 --- a/mixs6/source_uvig.md +++ b/mixs6/source_uvig.md @@ -17,21 +17,11 @@ None -> OPT ## Children + * [miuvig➞source_uvig](miuvig_source_uvig.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 35.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='viral fraction metagenome (virome)', description=None) | diff --git a/mixs6/specific_host.md b/mixs6/specific_host.md index 73ee2288..8cc9dd09 100644 --- a/mixs6/specific_host.md +++ b/mixs6/specific_host.md @@ -17,21 +17,15 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞specific_host](migs_ba_specific_host.md) + * [migs_eu➞specific_host](migs_eu_specific_host.md) + * [migs_pl➞specific_host](migs_pl_specific_host.md) + * [migs_vi➞specific_host](migs_vi_specific_host.md) + * [miuvig➞specific_host](miuvig_specific_host.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +35,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: host taxid, unknown, environmental | | | | Preferred unit: | | | | Position: 23.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='9606', description=None) | diff --git a/mixs6/specific_humidity.md b/mixs6/specific_humidity.md index ebc14a64..2d5fa209 100644 --- a/mixs6/specific_humidity.md +++ b/mixs6/specific_humidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:specific_humidity](https://w3id.org/mixs/vocab/specific_humidit ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/submitted_to_insdc.md b/mixs6/submitted_to_insdc.md index cff6d74e..cf65f882 100644 --- a/mixs6/submitted_to_insdc.md +++ b/mixs6/submitted_to_insdc.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞submitted_to_insdc](me_submitted_to_insdc.md) + * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) + * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) + * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) + * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) + * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) + * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) + * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) + * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) + * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) + * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: boolean | | | | Preferred unit: | | | | Position: 1.0 | -| | | CHECKLIST migs_eu: M | -| | | CHECKLIST migs_ba: M | -| | | CHECKLIST migs_pl: M | -| | | CHECKLIST migs_vi: M | -| | | CHECKLIST migs_org: M | -| | | CHECKLIST me: M | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/subspecf_gen_lin.md b/mixs6/subspecf_gen_lin.md index e86bf8b4..eba108cb 100644 --- a/mixs6/subspecf_gen_lin.md +++ b/mixs6/subspecf_gen_lin.md @@ -17,21 +17,16 @@ None -> OPT [String](types/String.md) ## Children + * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) + * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) + * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) + * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) + * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) + * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +36,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype | | | | Preferred unit: | | | | Position: 14.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='serovar:Newport', description=None) | diff --git a/mixs6/sulfate.md b/mixs6/sulfate.md index 6443288f..582d1d90 100644 --- a/mixs6/sulfate.md +++ b/mixs6/sulfate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:sulfate](https://w3id.org/mixs/vocab/sulfate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sulfate_fw.md b/mixs6/sulfate_fw.md index 4e776bf4..e6b4afb1 100644 --- a/mixs6/sulfate_fw.md +++ b/mixs6/sulfate_fw.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:sulfate_fw](https://w3id.org/mixs/vocab/sulfate_fw) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/sulfide.md b/mixs6/sulfide.md index 03d3e550..d73fe895 100644 --- a/mixs6/sulfide.md +++ b/mixs6/sulfide.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:sulfide](https://w3id.org/mixs/vocab/sulfide) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/surf_humidity.md b/mixs6/surf_humidity.md index 85ef1c33..c700404e 100644 --- a/mixs6/surf_humidity.md +++ b/mixs6/surf_humidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:surf_humidity](https://w3id.org/mixs/vocab/surf_humidity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/surf_moisture.md b/mixs6/surf_moisture.md index ac51ab2d..1d0f6d00 100644 --- a/mixs6/surf_moisture.md +++ b/mixs6/surf_moisture.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:surf_moisture](https://w3id.org/mixs/vocab/surf_moisture) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/surf_moisture_ph.md b/mixs6/surf_moisture_ph.md index 801a5714..300f4fa4 100644 --- a/mixs6/surf_moisture_ph.md +++ b/mixs6/surf_moisture_ph.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:surf_moisture_ph](https://w3id.org/mixs/vocab/surf_moisture_ph) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/surf_temp.md b/mixs6/surf_temp.md index 1b9dc1c6..f8c67ef2 100644 --- a/mixs6/surf_temp.md +++ b/mixs6/surf_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:surf_temp](https://w3id.org/mixs/vocab/surf_temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/suspend_part_matter.md b/mixs6/suspend_part_matter.md index e3dc4793..a149ccb9 100644 --- a/mixs6/suspend_part_matter.md +++ b/mixs6/suspend_part_matter.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:suspend_part_matter](https://w3id.org/mixs/vocab/suspend_part_m ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tan.md b/mixs6/tan.md index c28cc21b..c5975086 100644 --- a/mixs6/tan.md +++ b/mixs6/tan.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tan](https://w3id.org/mixs/vocab/tan) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/target_gene.md b/mixs6/target_gene.md index 864490b9..c3c9906f 100644 --- a/mixs6/target_gene.md +++ b/mixs6/target_gene.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞target_gene](mimarks_c_target_gene.md) + * [mimarks_s➞target_gene](mimarks_s_target_gene.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gene name | | | | Preferred unit: | | | | Position: 44.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: M | -| | | CHECKLIST mimarks_c: M | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='16S rRNA, 18S rRNA, nif, amoA, rpo', description=None) | diff --git a/mixs6/target_subfragment.md b/mixs6/target_subfragment.md index 02cc401c..f2a5a97f 100644 --- a/mixs6/target_subfragment.md +++ b/mixs6/target_subfragment.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) + * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gene fragment name | | | | Preferred unit: | | | | Position: 45.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='V6, V9, ITS', description=None) | diff --git a/mixs6/tax_class.md b/mixs6/tax_class.md index 48a9c22d..7c862b71 100644 --- a/mixs6/tax_class.md +++ b/mixs6/tax_class.md @@ -17,21 +17,19 @@ None -> OPT [String](types/String.md) ## Children + * [me➞tax_class](me_tax_class.md) + * [migs_ba➞tax_class](migs_ba_tax_class.md) + * [migs_eu➞tax_class](migs_eu_tax_class.md) + * [migs_org➞tax_class](migs_org_tax_class.md) + * [migs_pl➞tax_class](migs_pl_tax_class.md) + * [migs_vi➞tax_class](migs_vi_tax_class.md) + * [mimag➞tax_class](mimag_tax_class.md) + * [misag➞tax_class](misag_tax_class.md) + * [miuvig➞tax_class](miuvig_tax_class.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +39,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: classification method, database name, and other parameters | | | | Preferred unit: | | | | Position: 62.0 | -| | | CHECKLIST migs_eu: X | -| | | CHECKLIST migs_ba: X | -| | | CHECKLIST migs_pl: X | -| | | CHECKLIST migs_vi: X | -| | | CHECKLIST migs_org: X | -| | | CHECKLIST me: X | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)', description=None) | diff --git a/mixs6/tax_ident.md b/mixs6/tax_ident.md index 21c7a4d0..e5cf175f 100644 --- a/mixs6/tax_ident.md +++ b/mixs6/tax_ident.md @@ -17,21 +17,18 @@ None -> OPT ## Children + * [migs_ba➞tax_ident](migs_ba_tax_ident.md) + * [migs_eu➞tax_ident](migs_eu_tax_ident.md) + * [migs_org➞tax_ident](migs_org_tax_ident.md) + * [migs_pl➞tax_ident](migs_pl_tax_ident.md) + * [migs_vi➞tax_ident](migs_vi_tax_ident.md) + * [mimag➞tax_ident](mimag_tax_ident.md) + * [misag➞tax_ident](misag_tax_ident.md) + * [miuvig➞tax_ident](miuvig_tax_ident.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +38,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 53.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: M | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='other: rpoB gene', description=None) | diff --git a/mixs6/temp.md b/mixs6/temp.md index 80501f4b..371f6e50 100644 --- a/mixs6/temp.md +++ b/mixs6/temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:temp](https://w3id.org/mixs/vocab/temp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/temp_out.md b/mixs6/temp_out.md index 7d2cf27a..2d8298b9 100644 --- a/mixs6/temp_out.md +++ b/mixs6/temp_out.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:temp_out](https://w3id.org/mixs/vocab/temp_out) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/texture.md b/mixs6/texture.md index ea9f7a8e..6fdd69cf 100644 --- a/mixs6/texture.md +++ b/mixs6/texture.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:texture](https://w3id.org/mixs/vocab/texture) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/toluene.md b/mixs6/toluene.md index 2243078c..997a3cf5 100644 --- a/mixs6/toluene.md +++ b/mixs6/toluene.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:toluene](https://w3id.org/mixs/vocab/toluene) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_carb.md b/mixs6/tot_carb.md index 7ba6f8e3..20e3cf32 100644 --- a/mixs6/tot_carb.md +++ b/mixs6/tot_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_carb](https://w3id.org/mixs/vocab/tot_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_depth_water_col.md b/mixs6/tot_depth_water_col.md index 8de8c90d..df45c1d9 100644 --- a/mixs6/tot_depth_water_col.md +++ b/mixs6/tot_depth_water_col.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_depth_water_col](https://w3id.org/mixs/vocab/tot_depth_wate ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_diss_nitro.md b/mixs6/tot_diss_nitro.md index 37c49b31..8300503f 100644 --- a/mixs6/tot_diss_nitro.md +++ b/mixs6/tot_diss_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_diss_nitro](https://w3id.org/mixs/vocab/tot_diss_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_inorg_nitro.md b/mixs6/tot_inorg_nitro.md index 976d47a7..fdfb23f9 100644 --- a/mixs6/tot_inorg_nitro.md +++ b/mixs6/tot_inorg_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_inorg_nitro](https://w3id.org/mixs/vocab/tot_inorg_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_iron.md b/mixs6/tot_iron.md index 08386946..11156c61 100644 --- a/mixs6/tot_iron.md +++ b/mixs6/tot_iron.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_iron](https://w3id.org/mixs/vocab/tot_iron) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_nitro.md b/mixs6/tot_nitro.md index 565e282e..884d3649 100644 --- a/mixs6/tot_nitro.md +++ b/mixs6/tot_nitro.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_nitro](https://w3id.org/mixs/vocab/tot_nitro) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_nitro_content.md b/mixs6/tot_nitro_content.md index 3e287979..71c210c1 100644 --- a/mixs6/tot_nitro_content.md +++ b/mixs6/tot_nitro_content.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_nitro_content](https://w3id.org/mixs/vocab/tot_nitro_conten ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_org_carb.md b/mixs6/tot_org_carb.md index 18a46583..3e42f25f 100644 --- a/mixs6/tot_org_carb.md +++ b/mixs6/tot_org_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_org_carb](https://w3id.org/mixs/vocab/tot_org_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_part_carb.md b/mixs6/tot_part_carb.md index 0c92d522..240cf5f7 100644 --- a/mixs6/tot_part_carb.md +++ b/mixs6/tot_part_carb.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_part_carb](https://w3id.org/mixs/vocab/tot_part_carb) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_phosp.md b/mixs6/tot_phosp.md index 97314e15..848ab347 100644 --- a/mixs6/tot_phosp.md +++ b/mixs6/tot_phosp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_phosp](https://w3id.org/mixs/vocab/tot_phosp) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_phosphate.md b/mixs6/tot_phosphate.md index 48546f13..7b9836ab 100644 --- a/mixs6/tot_phosphate.md +++ b/mixs6/tot_phosphate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_phosphate](https://w3id.org/mixs/vocab/tot_phosphate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tot_sulfur.md b/mixs6/tot_sulfur.md index 335f5de9..8bbd4698 100644 --- a/mixs6/tot_sulfur.md +++ b/mixs6/tot_sulfur.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tot_sulfur](https://w3id.org/mixs/vocab/tot_sulfur) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/trna_ext_software.md b/mixs6/trna_ext_software.md index 49683728..1942d7df 100644 --- a/mixs6/trna_ext_software.md +++ b/mixs6/trna_ext_software.md @@ -17,21 +17,13 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞trna_ext_software](mimag_trna_ext_software.md) + * [misag➞trna_ext_software](misag_trna_ext_software.md) + * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names and versions of software(s), parameters used | | | | Preferred unit: | | | | Position: 66.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='infernal;v2;default parameters', description=None) | diff --git a/mixs6/trnas.md b/mixs6/trnas.md index 398bb910..d0cc9724 100644 --- a/mixs6/trnas.md +++ b/mixs6/trnas.md @@ -17,21 +17,13 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞trnas](mimag_trnas.md) + * [misag➞trnas](misag_trnas.md) + * [miuvig➞trnas](miuvig_trnas.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: value from 0-21 | | | | Preferred unit: | | | | Position: 65.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: X | | **Examples:** | | Example(value='18', description=None) | diff --git a/mixs6/trophic_level.md b/mixs6/trophic_level.md index bf95829b..19702600 100644 --- a/mixs6/trophic_level.md +++ b/mixs6/trophic_level.md @@ -17,21 +17,13 @@ None -> OPT ## Children + * [migs_ba➞trophic_level](migs_ba_trophic_level.md) + * [migs_eu➞trophic_level](migs_eu_trophic_level.md) + * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +33,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 26.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='heterotroph', description=None) | diff --git a/mixs6/turbidity.md b/mixs6/turbidity.md index 1c1de5b3..435c99c2 100644 --- a/mixs6/turbidity.md +++ b/mixs6/turbidity.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:turbidity](https://w3id.org/mixs/vocab/turbidity) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tvdss_of_hcr_pressure.md b/mixs6/tvdss_of_hcr_pressure.md index f146c44a..92e7d0b7 100644 --- a/mixs6/tvdss_of_hcr_pressure.md +++ b/mixs6/tvdss_of_hcr_pressure.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tvdss_of_hcr_pressure](https://w3id.org/mixs/vocab/tvdss_of_hcr ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/tvdss_of_hcr_temp.md b/mixs6/tvdss_of_hcr_temp.md index 682fac52..37cfc857 100644 --- a/mixs6/tvdss_of_hcr_temp.md +++ b/mixs6/tvdss_of_hcr_temp.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:tvdss_of_hcr_temp](https://w3id.org/mixs/vocab/tvdss_of_hcr_tem ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/typ_occup_density.md b/mixs6/typ_occup_density.md index 35be40c3..77d128a4 100644 --- a/mixs6/typ_occup_density.md +++ b/mixs6/typ_occup_density.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:typ_occup_density](https://w3id.org/mixs/vocab/typ_occup_densit ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Double](types/Double.md) ## Parents diff --git a/mixs6/url.md b/mixs6/url.md index 0dfa22e0..6b71dc6b 100644 --- a/mixs6/url.md +++ b/mixs6/url.md @@ -17,21 +17,21 @@ None -> OPT [String](types/String.md) ## Children + * [me➞url](me_url.md) + * [migs_ba➞url](migs_ba_url.md) + * [migs_eu➞url](migs_eu_url.md) + * [migs_org➞url](migs_org_url.md) + * [migs_pl➞url](migs_pl_url.md) + * [migs_vi➞url](migs_vi_url.md) + * [mimag➞url](mimag_url.md) + * [mimarks_c➞url](mimarks_c_url.md) + * [mimarks_s➞url](mimarks_s_url.md) + * [misag➞url](misag_url.md) + * [miuvig➞url](miuvig_url.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +41,6 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: URL | | | | Preferred unit: | | | | Position: 92.0 | -| | | CHECKLIST migs_eu: C | -| | | CHECKLIST migs_ba: C | -| | | CHECKLIST migs_pl: C | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: C | -| | | CHECKLIST me: C | -| | | CHECKLIST mimarks_s: C | -| | | CHECKLIST mimarks_c: C | -| | | CHECKLIST misag: C | -| | | CHECKLIST mimag: C | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='http://www.earthmicrobiome.org/', description=None) | +| **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/67 | diff --git a/mixs6/ventilation_rate.md b/mixs6/ventilation_rate.md index 4bdecf2b..2254e025 100644 --- a/mixs6/ventilation_rate.md +++ b/mixs6/ventilation_rate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ventilation_rate](https://w3id.org/mixs/vocab/ventilation_rate) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/vfa.md b/mixs6/vfa.md index 4914d32d..6e5c71d8 100644 --- a/mixs6/vfa.md +++ b/mixs6/vfa.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:vfa](https://w3id.org/mixs/vocab/vfa) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/vfa_fw.md b/mixs6/vfa_fw.md index 9194aa70..d9e6691f 100644 --- a/mixs6/vfa_fw.md +++ b/mixs6/vfa_fw.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:vfa_fw](https://w3id.org/mixs/vocab/vfa_fw) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/vir_ident_software.md b/mixs6/vir_ident_software.md index 47cb8637..218bd29f 100644 --- a/mixs6/vir_ident_software.md +++ b/mixs6/vir_ident_software.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: software name, version and relevant parameters | | | | Preferred unit: | | | | Position: 83.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='VirSorter; 1.0.4; Virome database, category 2', description=None) | diff --git a/mixs6/virus_enrich_appr.md b/mixs6/virus_enrich_appr.md index a021c28c..f59db6e3 100644 --- a/mixs6/virus_enrich_appr.md +++ b/mixs6/virus_enrich_appr.md @@ -17,21 +17,12 @@ None -> OPT ## Children + * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) + * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 36.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: C | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: M | | **Examples:** | | Example(value='filtration + FeCl Precipitation + ultracentrifugation + DNAse', description=None) | diff --git a/mixs6/votu_class_appr.md b/mixs6/votu_class_appr.md index 0240f9fd..29913ae5 100644 --- a/mixs6/votu_class_appr.md +++ b/mixs6/votu_class_appr.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: cutoffs and method used | | | | Preferred unit: | | | | Position: 87.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='95% ANI;85% AF; greedy incremental clustering', description=None) | diff --git a/mixs6/votu_db.md b/mixs6/votu_db.md index 0bf67ee2..54ae02ba 100644 --- a/mixs6/votu_db.md +++ b/mixs6/votu_db.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞votu_db](miuvig_votu_db.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: database and version | | | | Preferred unit: | | | | Position: 89.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='NCBI Viral RefSeq;83', description=None) | diff --git a/mixs6/votu_seq_comp_appr.md b/mixs6/votu_seq_comp_appr.md index 4719341b..e57af414 100644 --- a/mixs6/votu_seq_comp_appr.md +++ b/mixs6/votu_seq_comp_appr.md @@ -17,21 +17,11 @@ None -> OPT [String](types/String.md) ## Children + * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +31,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: software name, version and relevant parameters | | | | Preferred unit: | | | | Position: 88.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: - | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='blastn;2.6.0+;e-value cutoff: 0.001', description=None) | diff --git a/mixs6/wall_area.md b/mixs6/wall_area.md index 7e5a2395..1663f1cb 100644 --- a/mixs6/wall_area.md +++ b/mixs6/wall_area.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:wall_area](https://w3id.org/mixs/vocab/wall_area) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/wall_height.md b/mixs6/wall_height.md index 79e4a6cd..fe489ce3 100644 --- a/mixs6/wall_height.md +++ b/mixs6/wall_height.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:wall_height](https://w3id.org/mixs/vocab/wall_height) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/wall_thermal_mass.md b/mixs6/wall_thermal_mass.md index fdcfcd6a..952b1a3c 100644 --- a/mixs6/wall_thermal_mass.md +++ b/mixs6/wall_thermal_mass.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:wall_thermal_mass](https://w3id.org/mixs/vocab/wall_thermal_mas ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/water_content.md b/mixs6/water_content.md index 5f93f11e..ff89bd39 100644 --- a/mixs6/water_content.md +++ b/mixs6/water_content.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:water_content](https://w3id.org/mixs/vocab/water_content) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/water_current.md b/mixs6/water_current.md index fdffd7f1..370b63d7 100644 --- a/mixs6/water_current.md +++ b/mixs6/water_current.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:water_current](https://w3id.org/mixs/vocab/water_current) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/water_cut.md b/mixs6/water_cut.md index d6e1b7f4..83013323 100644 --- a/mixs6/water_cut.md +++ b/mixs6/water_cut.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:water_cut](https://w3id.org/mixs/vocab/water_cut) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/water_feat_size.md b/mixs6/water_feat_size.md index 79f91383..ae2cf4f0 100644 --- a/mixs6/water_feat_size.md +++ b/mixs6/water_feat_size.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:water_feat_size](https://w3id.org/mixs/vocab/water_feat_size) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/water_production_rate.md b/mixs6/water_production_rate.md index 02b022a0..de178af3 100644 --- a/mixs6/water_production_rate.md +++ b/mixs6/water_production_rate.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:water_production_rate](https://w3id.org/mixs/vocab/water_produc ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/wga_amp_appr.md b/mixs6/wga_amp_appr.md index 90170ae6..7f9264d8 100644 --- a/mixs6/wga_amp_appr.md +++ b/mixs6/wga_amp_appr.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [misag➞wga_amp_appr](misag_wga_amp_appr.md) + * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: enumeration | | | | Preferred unit: | | | | Position: 77.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: M | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='mda based', description=None) | diff --git a/mixs6/wga_amp_kit.md b/mixs6/wga_amp_kit.md index b2990e73..3aae5df4 100644 --- a/mixs6/wga_amp_kit.md +++ b/mixs6/wga_amp_kit.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [misag➞wga_amp_kit](misag_wga_amp_kit.md) + * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: kit name | | | | Preferred unit: | | | | Position: 78.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: - | -| | | CHECKLIST miuvig: C | | **Examples:** | | Example(value='qiagen repli-g', description=None) | diff --git a/mixs6/wind_speed.md b/mixs6/wind_speed.md index 1afeea98..fd08e0e5 100644 --- a/mixs6/wind_speed.md +++ b/mixs6/wind_speed.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:wind_speed](https://w3id.org/mixs/vocab/wind_speed) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents diff --git a/mixs6/x_16s_recover.md b/mixs6/x_16s_recover.md index 509515be..efcceb87 100644 --- a/mixs6/x_16s_recover.md +++ b/mixs6/x_16s_recover.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞x_16s_recover](mimag_x_16s_recover.md) + * [misag➞x_16s_recover](misag_x_16s_recover.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: boolean | | | | Preferred unit: | | | | Position: 63.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/x_16s_recover_software.md b/mixs6/x_16s_recover_software.md index 34c2a9fa..2e8aa95f 100644 --- a/mixs6/x_16s_recover_software.md +++ b/mixs6/x_16s_recover_software.md @@ -17,21 +17,12 @@ None -> OPT [String](types/String.md) ## Children + * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) + * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) ## Used by * [Core](Core.md) - * [CoreMe](CoreMe.md) - * [CoreMigsBa](CoreMigsBa.md) - * [CoreMigsEu](CoreMigsEu.md) - * [CoreMigsOrg](CoreMigsOrg.md) - * [CoreMigsPl](CoreMigsPl.md) - * [CoreMigsVi](CoreMigsVi.md) - * [CoreMimag](CoreMimag.md) - * [CoreMimarksC](CoreMimarksC.md) - * [CoreMimarksS](CoreMimarksS.md) - * [CoreMisag](CoreMisag.md) - * [CoreMiuvig](CoreMiuvig.md) ## Other properties @@ -41,16 +32,5 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: names and versions of software(s), parameters used | | | | Preferred unit: | | | | Position: 64.0 | -| | | CHECKLIST migs_eu: - | -| | | CHECKLIST migs_ba: - | -| | | CHECKLIST migs_pl: - | -| | | CHECKLIST migs_vi: - | -| | | CHECKLIST migs_org: - | -| | | CHECKLIST me: - | -| | | CHECKLIST mimarks_s: - | -| | | CHECKLIST mimarks_c: - | -| | | CHECKLIST misag: X | -| | | CHECKLIST mimag: X | -| | | CHECKLIST miuvig: - | | **Examples:** | | Example(value='rambl;v2;default parameters', description=None) | diff --git a/mixs6/xylene.md b/mixs6/xylene.md index 97ee680d..30c6a247 100644 --- a/mixs6/xylene.md +++ b/mixs6/xylene.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:xylene](https://w3id.org/mixs/vocab/xylene) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [QuantityValue](QuantityValue.md) ## Parents From e364a884f0733884d6854e0ef138978e679ae4c8 Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 15:11:59 -0700 Subject: [PATCH 5/7] regen --- src/schema/mixs.yaml | 5178 ++++++++++++++++++++++++++---------------- 1 file changed, 3202 insertions(+), 1976 deletions(-) diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index 5c5bb293..28f20e38 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -1,5 +1,5 @@ id: http://w3id.org/mixs6 -description: MIxS 6 linkml rendering (experimental) +description: MIxS 6 linkml rendering imports: - biolinkml:types prefixes: @@ -28,24 +28,14 @@ slots: systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - pattern: '{boolean}' + range: string examples: - value: 'yes' comments: - 'Expected value: boolean' - 'Preferred unit: ' - 'Position: 1.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{boolean}' investigation_type: is_a: investigation field aliases: @@ -55,7 +45,7 @@ slots: is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - pattern: '[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig]' + range: investigation_type_enum examples: - value: metagenome comments: @@ -64,18 +54,8 @@ slots: genome, or uncultivated viral genomes' - 'Preferred unit: ' - 'Position: 2.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' - range: investigation_type_enum + pattern: '[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig]' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/60 sample_name: is_a: core field aliases: @@ -84,47 +64,28 @@ slots: any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. ' - pattern: '' + range: string examples: - value: '' comments: - 'Expected value: ' - 'Preferred unit: ' - 'Position: ' - - 'CHECKLIST migs_eu: ' - - 'CHECKLIST migs_ba: ' - - 'CHECKLIST migs_pl: ' - - 'CHECKLIST migs_vi: ' - - 'CHECKLIST migs_org: ' - - 'CHECKLIST me: ' - - 'CHECKLIST mimarks_s: ' - - 'CHECKLIST mimarks_c: ' - - 'CHECKLIST misag: ' - - 'CHECKLIST mimag: ' - - 'CHECKLIST miuvig: ' + pattern: '' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/78 project_name: is_a: investigation field aliases: - project name description: Name of the project within which the sequencing was organized - pattern: '{text}' + range: string examples: - value: Forest soil metagenome comments: - 'Expected value: ' - 'Preferred unit: ' - 'Position: 3.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{text}' experimental_factor: is_a: investigation field aliases: @@ -135,74 +96,46 @@ slots: Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - pattern: '{termLabel} {[termID]}|{text}' + range: string examples: - value: time series design [EFO:EFO_0001779] comments: - 'Expected value: text or EFO and/or OBI' - 'Preferred unit: ' - 'Position: 4.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: X' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{termLabel} {[termID]}|{text}' lat_lon: is_a: environment field aliases: - geographic location (latitude and longitude) description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - pattern: '{float} {float}' + range: string examples: - value: 50.586825 6.408977 comments: - 'Expected value: decimal degrees' - 'Preferred unit: ' - 'Position: 5.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{float} {float}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/62 depth: is_a: environment field aliases: - geographic location (depth) description: Please refer to the definitions of depth in the environmental packages - pattern: '-' + range: string examples: - value: '' comments: - 'Expected value: -' - 'Preferred unit: ' - 'Position: 6.0' - - 'CHECKLIST migs_eu: E' - - 'CHECKLIST migs_ba: E' - - 'CHECKLIST migs_pl: E' - - 'CHECKLIST migs_vi: E' - - 'CHECKLIST migs_org: E' - - 'CHECKLIST me: E' - - 'CHECKLIST mimarks_s: E' - - 'CHECKLIST mimarks_c: E' - - 'CHECKLIST misag: E' - - 'CHECKLIST mimag: E' - - 'CHECKLIST miuvig: E' - 'This field is used in: 8 packages: host-associated, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water' + pattern: '-' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/63 alt: is_a: environment field aliases: @@ -213,24 +146,13 @@ slots: \ which is above the earth\u201A\xC4\xF4s surface. In this context, the altitude\ \ measurement is the vertical distance between the earth's surface above sea\ \ level and the sampled position in the air" - pattern: '{float} {unit}' + range: quantity value examples: - value: 100 meter comments: - 'Expected value: measurement value' - 'Preferred unit: ' - 'Position: ' - - 'CHECKLIST migs_eu: E' - - 'CHECKLIST migs_ba: E' - - 'CHECKLIST migs_pl: E' - - 'CHECKLIST migs_vi: E' - - 'CHECKLIST migs_org: E' - - 'CHECKLIST me: E' - - 'CHECKLIST mimarks_s: E' - - 'CHECKLIST mimarks_c: E' - - 'CHECKLIST misag: E' - - 'CHECKLIST mimag: E' - - 'CHECKLIST miuvig: E' - 'This field is used in: 3 packages: air, host-associated, miscellaneous natural or artificial environment' elev: @@ -241,24 +163,13 @@ slots: point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - pattern: '{float} {unit}' + range: quantity value examples: - value: 100 meter comments: - 'Expected value: measurement value' - 'Preferred unit: ' - 'Position: 7.0' - - 'CHECKLIST migs_eu: E' - - 'CHECKLIST migs_ba: E' - - 'CHECKLIST migs_pl: E' - - 'CHECKLIST migs_vi: E' - - 'CHECKLIST migs_org: E' - - 'CHECKLIST me: E' - - 'CHECKLIST mimarks_s: E' - - 'CHECKLIST mimarks_c: E' - - 'CHECKLIST misag: E' - - 'CHECKLIST mimag: E' - - 'CHECKLIST miuvig: E' - 'This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, water' @@ -270,7 +181,7 @@ slots: sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - pattern: '{term};{term};{text}' + range: string examples: - value: Germany;North Rhine-Westphalia;Eifel National Park comments: @@ -278,17 +189,8 @@ slots: name' - 'Preferred unit: ' - 'Position: 8.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{term};{term};{text}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/17 collection_date: is_a: environment field aliases: @@ -297,24 +199,14 @@ slots: or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11T10:00:00+01:00' comments: - 'Expected value: date and time' - 'Preferred unit: ' - 'Position: 9.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{timestamp}' env_broad_scale: is_a: environment field aliases: @@ -330,7 +222,7 @@ slots: \ epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the\ \ Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228].\ \ If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" - pattern: '{termLabel} {[termID]}' + range: string examples: - value: forest biome [ENVO:01000174] comments: @@ -340,17 +232,7 @@ slots: biome [ENVO:01000020]' - 'Preferred unit: ' - 'Position: 10.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{termLabel} {[termID]}' env_local_scale: is_a: environment field aliases: @@ -365,7 +247,7 @@ slots: \ and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub\ \ layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified\ \ here: http://www.obofoundry.org/ontology/envo.html" - pattern: '{termLabel} {[termID]}' + range: string examples: - value: litter layer [ENVO:01000338] comments: @@ -374,17 +256,7 @@ slots: by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]' - 'Preferred unit: ' - 'Position: 11.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{termLabel} {[termID]}' env_medium: is_a: environment field aliases: @@ -398,7 +270,7 @@ slots: \ Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on\ \ a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed,\ \ request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" - pattern: '{termLabel} {[termID]}' + range: string examples: - value: soil [ENVO:00001998] comments: @@ -408,17 +280,7 @@ slots: mud [ENVO:00002160]' - 'Preferred unit: ' - 'Position: 12.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{termLabel} {[termID]}' env_package: is_a: mixs extension field aliases: @@ -428,27 +290,17 @@ slots: packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - pattern: '[air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon - resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc - environment|plant-associated|sediment|soil|wastewater/sludge|water]' + range: env_package_enum examples: - value: soil comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 13.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' - range: env_package_enum + pattern: '[air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon + resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc + environment|plant-associated|sediment|soil|wastewater/sludge|water]' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/64 subspecf_gen_lin: is_a: nucleic acid sequence source field aliases: @@ -458,7 +310,7 @@ slots: serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - pattern: '{rank name}:{text}' + range: string examples: - value: serovar:Newport comments: @@ -466,17 +318,7 @@ slots: subspecies, e.g. serovar, biotype, ecotype' - 'Preferred unit: ' - 'Position: 14.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{rank name}:{text}' ploidy: is_a: nucleic acid sequence source field aliases: @@ -487,24 +329,14 @@ slots: For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - pattern: '{termLabel} {[termID]}' + range: string examples: - value: allopolyploidy [PATO:0001379] comments: - 'Expected value: PATO' - 'Preferred unit: ' - 'Position: 15.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{termLabel} {[termID]}' num_replicons: is_a: nucleic acid sequence source field aliases: @@ -512,7 +344,7 @@ slots: description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - pattern: '{integer}' + range: string examples: - value: '2' comments: @@ -520,17 +352,7 @@ slots: viruses: segments' - 'Preferred unit: ' - 'Position: 16.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{integer}' extrachrom_elements: is_a: nucleic acid sequence source field aliases: @@ -538,24 +360,14 @@ slots: description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - pattern: '{integer}' + range: string examples: - value: '5' comments: - 'Expected value: number of extrachromosmal elements' - 'Preferred unit: ' - 'Position: 17.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: X' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{integer}' estimated_size: is_a: nucleic acid sequence source field aliases: @@ -563,48 +375,28 @@ slots: description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - pattern: '{integer} bp' + range: string examples: - value: 300000 bp comments: - 'Expected value: number of base pairs' - 'Preferred unit: ' - 'Position: 18.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: X' + pattern: '{integer} bp' ref_biomaterial: is_a: nucleic acid sequence source field aliases: - reference for biomaterial description: Primary publication if isolated before genome publication; otherwise, primary genome report - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: doi:10.1016/j.syapm.2018.01.009 comments: - 'Expected value: PMID, DOI or URL' - 'Preferred unit: ' - 'Position: 19.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: X' + pattern: '{PMID}|{DOI}|{URL}' source_mat_id: is_a: nucleic acid sequence source field aliases: @@ -621,7 +413,7 @@ slots: may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - pattern: '{text}' + range: string examples: - value: MPI012345 comments: @@ -629,40 +421,21 @@ slots: collections; for other material a unique arbitrary identifer' - 'Preferred unit: ' - 'Position: 20.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text}' pathogenicity: is_a: nucleic acid sequence source field aliases: - known pathogenicity description: To what is the entity pathogenic - pattern: '{text}' + range: string examples: - value: human, animal, plant, fungi, bacteria comments: - 'Expected value: names of organisms that the entity is pathogenic to' - 'Preferred unit: ' - 'Position: 21.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: X' + pattern: '{text}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/65 biotic_relationship: is_a: nucleic acid sequence source field aliases: @@ -671,25 +444,14 @@ slots: organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - pattern: '[free living|parasitism|commensalism|symbiotic|mutualism]' + range: biotic_relationship_enum examples: - value: free living comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 22.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: X' - range: biotic_relationship_enum + pattern: '[free living|parasitism|commensalism|symbiotic|mutualism]' specific_host: is_a: nucleic acid sequence source field aliases: @@ -698,97 +460,56 @@ slots: if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - pattern: '{NCBI taxid}|{text}' + range: string examples: - value: '9606' comments: - 'Expected value: host taxid, unknown, environmental' - 'Preferred unit: ' - 'Position: 23.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: X' + pattern: '{NCBI taxid}|{text}' host_spec_range: is_a: nucleic acid sequence source field aliases: - host specificity or range description: The NCBI taxonomy identifier of the specific host if it is known - pattern: '{integer}' + range: string examples: - value: '9606' comments: - 'Expected value: NCBI taxid' - 'Preferred unit: ' - 'Position: 24.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: X' + pattern: '{integer}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/66 health_disease_stat: is_a: nucleic acid sequence source field aliases: - health or disease status of specific host at time of collection description: Health or disease status of specific host at time of collection - pattern: '[healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing - condition|pathological|life threatening|congenital]' + range: health_disease_stat_enum examples: - value: dead comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 25.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' - range: health_disease_stat_enum + pattern: '[healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing + condition|pathological|life threatening|congenital]' trophic_level: is_a: nucleic acid sequence source field aliases: - trophic level description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - pattern: '[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]' + range: trophic_level_enum examples: - value: heterotroph comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 26.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' - range: trophic_level_enum + pattern: '[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]' propagation: is_a: nucleic acid sequence source field aliases: @@ -797,7 +518,7 @@ slots: for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice' - pattern: '{text}' + range: string examples: - value: lytic comments: @@ -805,67 +526,37 @@ slots: plasmid: incompatibility group; for eukaryote: asexual, sexual' - 'Preferred unit: ' - 'Position: 27.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{text}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/88 encoded_traits: is_a: nucleic acid sequence source field aliases: - encoded traits description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - pattern: '{text}' + range: string examples: - value: beta-lactamase class A comments: - 'Expected value: for plasmid: antibiotic resistance; for phage: converting genes' - 'Preferred unit: ' - 'Position: 28.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{text}' rel_to_oxygen: is_a: nucleic acid sequence source field aliases: - relationship to oxygen description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - pattern: '[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate - aerobe|obligate anaerobe]' + range: rel_to_oxygen_enum examples: - value: aerobe comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 29.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: X' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' - range: rel_to_oxygen_enum + pattern: '[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate + aerobe|obligate anaerobe]' isol_growth_condt: is_a: nucleic acid sequence source field aliases: @@ -873,47 +564,27 @@ slots: description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: 'doi: 10.1016/j.syapm.2018.01.009' comments: - 'Expected value: PMID,DOI or URL' - 'Preferred unit: ' - 'Position: 30.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{PMID}|{DOI}|{URL}' samp_collect_device: is_a: nucleic acid sequence source field aliases: - sample collection device or method description: The method or device employed for collecting the sample - pattern: '{text}' + range: string examples: - value: environmental swab sampling, biopsy, niskin bottle, push core comments: - 'Expected value: type name' - 'Preferred unit: ' - 'Position: 31.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: X' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text}' samp_mat_process: is_a: nucleic acid sequence source field aliases: @@ -921,122 +592,69 @@ slots: description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - pattern: '{text}|{termLabel} {[termID]}' + range: string examples: - value: filtering of seawater, storing samples in ethanol comments: - 'Expected value: text or OBI' - 'Preferred unit: ' - 'Position: 32.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text}|{termLabel} {[termID]}' size_frac: is_a: nucleic acid sequence source field aliases: - size fraction selected description: Filtering pore size used in sample preparation - pattern: '{float}-{float} {unit}' + range: string examples: - value: 0-0.22 micrometer comments: - 'Expected value: filter size value range' - 'Preferred unit: ' - 'Position: 33.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: X' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{float}-{float} {unit}' samp_size: is_a: nucleic acid sequence source field aliases: - amount or size of sample collected description: Amount or size of sample (volume, mass or area) that was collected - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 liter comments: - 'Expected value: measurement value' - 'Preferred unit: millliter, gram, milligram, liter' - 'Position: 34.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: X' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' source_uvig: is_a: nucleic acid sequence source field aliases: - source of UViGs description: Type of dataset from which the UViG was obtained - pattern: '[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted - metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome - (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome - (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]' + range: source_uvig_enum examples: - value: viral fraction metagenome (virome) comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 35.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' - range: source_uvig_enum + pattern: '[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted + metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome + (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome + (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]' virus_enrich_appr: is_a: nucleic acid sequence source field aliases: - virus enrichment approach description: List of approaches used to enrich the sample for viruses, if any - pattern: '[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl - Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]' + range: virus_enrich_appr_enum examples: - value: filtration + FeCl Precipitation + ultracentrifugation + DNAse comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 36.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' - range: virus_enrich_appr_enum + pattern: '[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl + Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]' nucl_acid_ext: is_a: sequencing field aliases: @@ -1044,24 +662,14 @@ slots: description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf comments: - 'Expected value: PMID, DOI or URL' - 'Preferred unit: ' - 'Position: 37.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{PMID}|{DOI}|{URL}' nucl_acid_amp: is_a: sequencing field aliases: @@ -1069,189 +677,108 @@ slots: description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ comments: - 'Expected value: PMID, DOI or URL' - 'Preferred unit: ' - 'Position: 38.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{PMID}|{DOI}|{URL}' lib_size: is_a: sequencing field aliases: - library size description: Total number of clones in the library prepared for the project - pattern: '{integer}' + range: string examples: - value: '50' comments: - 'Expected value: number of clones' - 'Preferred unit: ' - 'Position: 39.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{integer}' lib_reads_seqd: is_a: sequencing field aliases: - library reads sequenced description: Total number of clones sequenced from the library - pattern: '{integer}' + range: string examples: - value: '20' comments: - 'Expected value: number of reads sequenced' - 'Preferred unit: ' - 'Position: 40.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{integer}' lib_layout: is_a: sequencing field aliases: - library layout description: Specify whether to expect single, paired, or other configuration of reads - pattern: '[paired|single|vector|other]' + range: lib_layout_enum examples: - value: paired comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 41.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' - range: lib_layout_enum + pattern: '[paired|single|vector|other]' lib_vector: is_a: sequencing field aliases: - library vector description: Cloning vector type(s) used in construction of libraries - pattern: '{text}' + range: string examples: - value: Bacteriophage P1 comments: - 'Expected value: vector' - 'Preferred unit: ' - 'Position: 42.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text}' lib_screen: is_a: sequencing field aliases: - library screening strategy description: Specific enrichment or screening methods applied before and/or after creating libraries - pattern: '{text}' + range: string examples: - value: enriched, screened, normalized comments: - 'Expected value: screening strategy name' - 'Preferred unit: ' - 'Position: 43.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text}' target_gene: is_a: sequencing field aliases: - target gene description: Targeted gene or locus name for marker gene studies - pattern: '{text}' + range: string examples: - value: 16S rRNA, 18S rRNA, nif, amoA, rpo comments: - 'Expected value: gene name' - 'Preferred unit: ' - 'Position: 44.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{text}' target_subfragment: is_a: sequencing field aliases: - target subfragment description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - pattern: '{text}' + range: string examples: - value: V6, V9, ITS comments: - 'Expected value: gene fragment name' - 'Preferred unit: ' - 'Position: 45.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{text}' pcr_primers: is_a: sequencing field aliases: @@ -1260,24 +787,14 @@ slots: gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - pattern: FWD:{dna};REV:{dna} + range: string examples: - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT comments: - 'Expected value: FWD: forward primer sequence;REV:reverse primer sequence' - 'Preferred unit: ' - 'Position: 46.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: FWD:{dna};REV:{dna} mid: is_a: sequencing field aliases: @@ -1285,24 +802,14 @@ slots: description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - pattern: '{dna}' + range: string examples: - value: GTGAATAT comments: - 'Expected value: multiplex identifier sequence' - 'Preferred unit: ' - 'Position: 47.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{dna}' adapters: is_a: sequencing field aliases: @@ -1310,32 +817,21 @@ slots: description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - pattern: '{dna};{dna}' + range: string examples: - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT comments: - 'Expected value: adapter A and B sequence' - 'Preferred unit: ' - 'Position: 48.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{dna};{dna}' pcr_cond: is_a: sequencing field aliases: - pcr conditions description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - pattern: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles + range: string examples: - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 comments: @@ -1343,22 +839,20 @@ slots: elongation:degrees_minutes;total cycles' - 'Preferred unit: ' - 'Position: 49.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes;total cycles seq_meth: is_a: sequencing field aliases: - sequencing method description: Sequencing method used; e.g. Sanger, ABI-solid + range: seq_meth_enum + examples: + - value: Illumina HiSeq 1500 + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Position: 50.0' pattern: '[454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|AB 310 Genetic Analyzer|AB 3130 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB @@ -1371,24 +865,6 @@ slots: HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|MinION|PacBio RS|PacBio RS II|PromethION|Sequel]' - examples: - - value: Illumina HiSeq 1500 - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 50.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: M' - - 'CHECKLIST mimarks_s: M' - - 'CHECKLIST mimarks_c: M' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' - range: seq_meth_enum seq_quality_check: is_a: sequencing field aliases: @@ -1397,24 +873,14 @@ slots: or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - pattern: '[none|manually edited]' + range: string examples: - value: none comments: - 'Expected value: none or manually edited' - 'Preferred unit: ' - 'Position: 51.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '[none|manually edited]' chimera_check: is_a: sequencing field aliases: @@ -1425,49 +891,28 @@ slots: to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - pattern: '{software};{version};{parameters}' + range: string examples: - value: uchime;v4.1;default parameters comments: - 'Expected value: name and version of software, parameters used' - 'Preferred unit: ' - 'Position: 52.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: -' + pattern: '{software};{version};{parameters}' tax_ident: is_a: sequencing field aliases: - taxonomic identity marker description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - pattern: '[16S rRNA gene|multi-marker approach|other]' + range: tax_ident_enum examples: - value: 'other: rpoB gene' comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 53.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: X' - range: tax_ident_enum + pattern: '[16S rRNA gene|multi-marker approach|other]' assembly_qual: is_a: sequencing field aliases: @@ -1489,73 +934,42 @@ slots: \ of the expected genome or replicon sequence or predicted complete. Genome\ \ fragment(s): One or multiple fragments, totalling < 90% of the expected genome\ \ or replicon sequence, or for which no genome size could be estimated" - pattern: '[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality - draft genome|Genome fragment(s)]' + range: assembly_qual_enum examples: - value: High-quality draft genome comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 54.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' - range: assembly_qual_enum + pattern: '[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality + draft genome|Genome fragment(s)]' assembly_name: is_a: sequencing field aliases: - assembly name description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - pattern: '{text} {text}' + range: string examples: - value: HuRef, JCVI_ISG_i3_1.0 comments: - 'Expected value: name and version of assembly' - 'Preferred unit: ' - 'Position: 55.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{text} {text}' assembly_software: is_a: sequencing field aliases: - assembly software description: Tool(s) used for assembly, including version number and parameters - pattern: '{software};{version};{parameters}' + range: string examples: - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise comments: - 'Expected value: name and version of software, parameters used' - 'Preferred unit: ' - 'Position: 56.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: M' - - 'CHECKLIST migs_vi: M' - - 'CHECKLIST migs_org: M' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: M' + pattern: '{software};{version};{parameters}' annot: is_a: sequencing field aliases: @@ -1563,79 +977,49 @@ slots: description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - pattern: '{text}' + range: string examples: - value: prokka comments: - 'Expected value: name of tool or pipeline used, or annotation source description' - 'Preferred unit: ' - 'Position: 57.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: X' + pattern: '{text}' number_contig: is_a: sequencing field aliases: - number of contigs description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - pattern: '{integer}' + range: string examples: - value: '40' comments: - 'Expected value: value' - 'Preferred unit: ' - 'Position: 58.0' - - 'CHECKLIST migs_eu: M' - - 'CHECKLIST migs_ba: M' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: M' + pattern: '{integer}' feat_pred: is_a: sequencing field aliases: - feature prediction description: Method used to predict UViGs features such as ORFs, integration site, etc. - pattern: '{software};{version};{parameters}' + range: string examples: - value: Prodigal;2.6.3;default parameters comments: - 'Expected value: names and versions of software(s), parameters used' - 'Preferred unit: ' - 'Position: 59.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{software};{version};{parameters}' ref_db: is_a: sequencing field aliases: - reference database(s) description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - pattern: '{database};{version};{reference}' + range: string examples: - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 @@ -1643,48 +1027,28 @@ slots: - 'Expected value: names, versions, and references of databases' - 'Preferred unit: ' - 'Position: 60.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{database};{version};{reference}' sim_search_meth: is_a: sequencing field aliases: - similarity search method description: Tool used to compare ORFs with database, along with version and cutoffs used - pattern: '{software};{version};{parameters}' + range: string examples: - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score comments: - 'Expected value: names and versions of software(s), parameters used' - 'Preferred unit: ' - 'Position: 61.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{software};{version};{parameters}' tax_class: is_a: sequencing field aliases: - taxonomic classification description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - pattern: '{text}' + range: string examples: - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) @@ -1692,109 +1056,59 @@ slots: - 'Expected value: classification method, database name, and other parameters' - 'Preferred unit: ' - 'Position: 62.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: X' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{text}' x_16s_recover: is_a: sequencing field aliases: - 16S recovered description: Can a 16S gene be recovered from the submitted SAG or MAG? - pattern: '{boolean}' + range: string examples: - value: 'yes' comments: - 'Expected value: boolean' - 'Preferred unit: ' - 'Position: 63.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' + pattern: '{boolean}' x_16s_recover_software: is_a: sequencing field aliases: - 16S recovery software description: Tools used for 16S rRNA gene extraction - pattern: '{software};{version};{parameters}' + range: string examples: - value: rambl;v2;default parameters comments: - 'Expected value: names and versions of software(s), parameters used' - 'Preferred unit: ' - 'Position: 64.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' + pattern: '{software};{version};{parameters}' trnas: is_a: sequencing field aliases: - number of standard tRNAs extracted description: The total number of tRNAs identified from the SAG or MAG - pattern: '{integer}' + range: string examples: - value: '18' comments: - 'Expected value: value from 0-21' - 'Preferred unit: ' - 'Position: 65.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: X' + pattern: '{integer}' trna_ext_software: is_a: sequencing field aliases: - tRNA extraction software description: Tools used for tRNA identification - pattern: '{software};{version};{parameters}' + range: string examples: - value: infernal;v2;default parameters comments: - 'Expected value: names and versions of software(s), parameters used' - 'Preferred unit: ' - 'Position: 66.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: X' + pattern: '{software};{version};{parameters}' compl_score: is_a: sequencing field aliases: @@ -1804,48 +1118,27 @@ slots: compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores' - pattern: '[high|med|low];{percentage}' + range: compl_score_enum examples: - value: med;60% comments: - 'Expected value: quality;percent completeness' - 'Preferred unit: ' - 'Position: 67.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: C' - range: compl_score_enum + pattern: '[high|med|low];{percentage}' compl_software: is_a: sequencing field aliases: - completeness software description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - pattern: '{software};{version}' + range: string examples: - value: checkm comments: - 'Expected value: names and versions of software(s) used' - 'Preferred unit: ' - 'Position: 68.0' - - 'CHECKLIST migs_eu: X' - - 'CHECKLIST migs_ba: X' - - 'CHECKLIST migs_pl: X' - - 'CHECKLIST migs_vi: X' - - 'CHECKLIST migs_org: X' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: X' + pattern: '{software};{version}' compl_appr: is_a: sequencing field aliases: @@ -1854,7 +1147,7 @@ slots: MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - pattern: '[marker gene|reference based|other]' + range: compl_appr_enum examples: - value: 'other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)' @@ -1862,18 +1155,7 @@ slots: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 69.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' - range: compl_appr_enum + pattern: '[marker gene|reference based|other]' contam_score: is_a: sequencing field aliases: @@ -1883,47 +1165,27 @@ slots: are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases' - pattern: '{float} percentage' + range: string examples: - value: 1% comments: - 'Expected value: value' - 'Preferred unit: ' - 'Position: 70.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: -' + pattern: '{float} percentage' contam_screen_input: is_a: sequencing field aliases: - contamination screening input description: The type of sequence data used as input - pattern: '[reads| contigs]' + range: string examples: - value: contigs comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 71.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' + pattern: '[reads| contigs]' contam_screen_param: is_a: sequencing field aliases: @@ -1931,360 +1193,201 @@ slots: description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - pattern: '[ref db|kmer|coverage|combination];{text|integer}' + range: contam_screen_param_enum examples: - value: kmer comments: - 'Expected value: enumeration;value or name' - 'Preferred unit: ' - 'Position: 72.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' - range: contam_screen_param_enum + pattern: '[ref db|kmer|coverage|combination];{text|integer}' decontam_software: is_a: sequencing field aliases: - decontamination software description: Tool(s) used in contamination screening - pattern: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' + range: decontam_software_enum examples: - value: anvi'o comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 73.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: -' - range: decontam_software_enum + pattern: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' sort_tech: is_a: sequencing field aliases: - sorting technology description: Method used to sort/isolate cells or particles of interest - pattern: '[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]' + range: sort_tech_enum examples: - value: optical manipulation comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 74.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' - range: sort_tech_enum + pattern: '[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]' single_cell_lysis_appr: is_a: sequencing field aliases: - single cell or viral particle lysis approach description: Method used to free DNA from interior of the cell(s) or particle(s) - pattern: '[chemical|enzymatic|physical|combination]' + range: single_cell_lysis_appr_enum examples: - value: enzymatic comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 75.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' - range: single_cell_lysis_appr_enum + pattern: '[chemical|enzymatic|physical|combination]' single_cell_lysis_prot: is_a: sequencing field aliases: - single cell or viral particle lysis kit protocol description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - pattern: '{text}' + range: string examples: - value: ambion single cell lysis kit comments: - 'Expected value: kit, protocol name' - 'Preferred unit: ' - 'Position: 76.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{text}' wga_amp_appr: is_a: sequencing field aliases: - WGA amplification approach description: Method used to amplify genomic DNA in preparation for sequencing - pattern: '[pcr based|mda based]' + range: string examples: - value: mda based comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 77.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: M' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '[pcr based|mda based]' wga_amp_kit: is_a: sequencing field aliases: - WGA amplification kit description: Kit used to amplify genomic DNA in preparation for sequencing - pattern: '{text}' + range: string examples: - value: qiagen repli-g comments: - 'Expected value: kit name' - 'Preferred unit: ' - 'Position: 78.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: X' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{text}' bin_param: is_a: sequencing field aliases: - binning parameters description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - pattern: '[homology search|kmer|coverage|codon usage|combination]' + range: bin_param_enum examples: - value: coverage and kmer comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 79.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: C' - range: bin_param_enum + pattern: '[homology search|kmer|coverage|codon usage|combination]' bin_software: is_a: sequencing field aliases: - binning software description: Tool(s) used for the extraction of genomes from metagenomic datasets - pattern: '[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]' + range: bin_software_enum examples: - value: concoct and maxbin comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 80.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: M' - - 'CHECKLIST miuvig: C' - range: bin_software_enum + pattern: '[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]' reassembly_bin: is_a: sequencing field aliases: - reassembly post binning description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - pattern: '{boolean}' + range: string examples: - value: 'no' comments: - 'Expected value: boolean' - 'Preferred unit: ' - 'Position: 81.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: C' + pattern: '{boolean}' mag_cov_software: is_a: sequencing field aliases: - MAG coverage software description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - pattern: '[bwa|bbmap|bowtie|other]' + range: mag_cov_software_enum examples: - value: bbmap comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 82.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: X' - - 'CHECKLIST miuvig: X' - range: mag_cov_software_enum + pattern: '[bwa|bbmap|bowtie|other]' vir_ident_software: is_a: sequencing field aliases: - viral identification software description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - pattern: '{software};{version};{parameters}' + range: string examples: - value: VirSorter; 1.0.4; Virome database, category 2 comments: - 'Expected value: software name, version and relevant parameters' - 'Preferred unit: ' - 'Position: 83.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' + pattern: '{software};{version};{parameters}' pred_genome_type: is_a: sequencing field aliases: - predicted genome type description: Type of genome predicted for the UViG - pattern: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' + range: pred_genome_type_enum examples: - value: dsDNA comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 84.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' - range: pred_genome_type_enum + pattern: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' pred_genome_struc: is_a: sequencing field aliases: - predicted genome structure description: Expected structure of the viral genome - pattern: '[segmented|non-segmented|undetermined]' + range: pred_genome_struc_enum examples: - value: non-segmented comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 85.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' - range: pred_genome_struc_enum + pattern: '[segmented|non-segmented|undetermined]' detec_type: is_a: sequencing field aliases: - detection type description: Type of UViG detection - pattern: '[independent sequence (UViG)|provirus (UpViG)]' + range: string examples: - value: independent sequence (UViG) comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 86.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: M' + pattern: '[independent sequence (UViG)|provirus (UpViG)]' votu_class_appr: is_a: sequencing field aliases: @@ -2293,103 +1396,62 @@ slots: \ vOTUs. Note that results from standard 95% ANI / 85% AF clustering should\ \ be provided alongside vOTUS defined from another set of thresholds, even if\ \ the latter are the ones primarily used during the analysis" - pattern: '{ANI cutoff};{AF cutoff};{clustering method}' + range: string examples: - value: 95% ANI;85% AF; greedy incremental clustering comments: - 'Expected value: cutoffs and method used' - 'Preferred unit: ' - 'Position: 87.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{ANI cutoff};{AF cutoff};{clustering method}' votu_seq_comp_appr: is_a: sequencing field aliases: - vOTU sequence comparison approach description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - pattern: '{software};{version};{parameters}' + range: string examples: - value: 'blastn;2.6.0+;e-value cutoff: 0.001' comments: - 'Expected value: software name, version and relevant parameters' - 'Preferred unit: ' - 'Position: 88.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{software};{version};{parameters}' votu_db: is_a: sequencing field aliases: - vOTU database description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - pattern: '{database};{version}' + range: string examples: - value: NCBI Viral RefSeq;83 comments: - 'Expected value: database and version' - 'Preferred unit: ' - 'Position: 89.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{database};{version}' host_pred_appr: is_a: sequencing field aliases: - host prediction approach description: Tool or approach used for host prediction - pattern: '[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co-occurrence|combination|other]' + range: host_pred_appr_enum examples: - value: CRISPR spacer match comments: - 'Expected value: enumeration' - 'Preferred unit: ' - 'Position: 90.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' - range: host_pred_appr_enum + pattern: '[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co-occurrence|combination|other]' host_pred_est_acc: is_a: sequencing field aliases: - host prediction estimated accuracy description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - pattern: '{text}' + range: string examples: - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' @@ -2397,71 +1459,42 @@ slots: - 'Expected value: false discovery rate' - 'Preferred unit: ' - 'Position: 91.0' - - 'CHECKLIST migs_eu: -' - - 'CHECKLIST migs_ba: -' - - 'CHECKLIST migs_pl: -' - - 'CHECKLIST migs_vi: -' - - 'CHECKLIST migs_org: -' - - 'CHECKLIST me: -' - - 'CHECKLIST mimarks_s: -' - - 'CHECKLIST mimarks_c: -' - - 'CHECKLIST misag: -' - - 'CHECKLIST mimag: -' - - 'CHECKLIST miuvig: C' + pattern: '{text}' url: is_a: sequencing field aliases: - relevant electronic resources description: '' - pattern: '{URL}' + range: string examples: - value: http://www.earthmicrobiome.org/ comments: - 'Expected value: URL' - 'Preferred unit: ' - 'Position: 92.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{URL}' + see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/67 sop: is_a: sequencing field aliases: - relevant standard operating procedures description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ comments: - 'Expected value: reference to SOP' - 'Preferred unit: ' - 'Position: 93.0' - - 'CHECKLIST migs_eu: C' - - 'CHECKLIST migs_ba: C' - - 'CHECKLIST migs_pl: C' - - 'CHECKLIST migs_vi: C' - - 'CHECKLIST migs_org: C' - - 'CHECKLIST me: C' - - 'CHECKLIST mimarks_s: C' - - 'CHECKLIST mimarks_c: C' - - 'CHECKLIST misag: C' - - 'CHECKLIST mimag: C' - - 'CHECKLIST miuvig: C' + pattern: '{PMID}|{DOI}|{URL}' barometric_press: is_a: environment field aliases: - barometric pressure description: Force per unit area exerted against a surface by the weight of air above that surface - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 millibar comments: @@ -2476,7 +1509,7 @@ slots: aliases: - carbon dioxide description: Carbon dioxide (gas) amount or concentration at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 410 parts per million comments: @@ -2491,7 +1524,7 @@ slots: aliases: - carbon monoxide description: Carbon monoxide (gas) amount or concentration at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.1 parts per million comments: @@ -2509,7 +1542,7 @@ slots: sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - pattern: '{termLabel} {[termID]};{timestamp}' + range: string examples: - value: agar [CHEBI:2509];2018-05-11T20:00Z comments: @@ -2521,13 +1554,14 @@ slots: human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' + pattern: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 humidity: is_a: environment field aliases: - humidity description: Amount of water vapour in the air, at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 25 gram per cubic meter comments: @@ -2542,7 +1576,7 @@ slots: aliases: - methane description: Methane (gas) amount or concentration at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 1800 parts per billion comments: @@ -2558,7 +1592,7 @@ slots: - miscellaneous parameter description: Any other measurement performed or parameter collected, that is not listed here - pattern: '{text};{float} {unit}' + range: string examples: - value: Bicarbonate ion concentration;2075 micromole per kilogram comments: @@ -2571,6 +1605,7 @@ slots: hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000752 organism_count: is_a: environment field @@ -2580,7 +1615,7 @@ slots: volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' - pattern: '{text};{float} {unit};[qPCR|ATP|MPN|other]' + range: organism_count_enum examples: - value: total prokaryotes;3.5e7 cells per milliliter;qPCR comments: @@ -2594,14 +1629,14 @@ slots: resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' - range: organism_count_enum + pattern: '{text};{float} {unit};[qPCR|ATP|MPN|other]' slot_uri: MIXS:0000103 oxygen: is_a: environment field aliases: - oxygen description: Oxygen (gas) amount or concentration at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 600 parts per million comments: @@ -2616,7 +1651,7 @@ slots: aliases: - oxygenation status of sample description: Oxygenation status of sample - pattern: '[aerobic|anaerobic|other]' + range: oxy_stat_samp_enum examples: - value: aerobic comments: @@ -2628,7 +1663,7 @@ slots: human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' - range: oxy_stat_samp_enum + pattern: '[aerobic|anaerobic|other]' slot_uri: MIXS:0000753 perturbation: is_a: environment field @@ -2638,7 +1673,7 @@ slots: etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - pattern: '{text};{Rn/start_time/end_time/duration}' + range: string examples: - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M comments: @@ -2650,6 +1685,7 @@ slots: human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' + pattern: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 pollutants: is_a: environment field @@ -2658,7 +1694,7 @@ slots: description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - pattern: '{text};{float} {unit}' + range: string examples: - value: lead;0.15 microgram per cubic meter comments: @@ -2668,6 +1704,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: air' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000107 resp_part_matter: is_a: environment field @@ -2676,7 +1713,7 @@ slots: description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - pattern: '{text};{float} {unit}' + range: string examples: - value: PM2.5;10 microgram per cubic meter comments: @@ -2685,6 +1722,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: air' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000108 samp_salinity: is_a: environment field @@ -2696,7 +1734,7 @@ slots: and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - pattern: '{float} {unit}' + range: quantity value examples: - value: 1 milligram per liter comments: @@ -2713,7 +1751,7 @@ slots: aliases: - sample storage duration description: Duration for which the sample was stored - pattern: '{duration}' + range: string examples: - value: P1Y6M comments: @@ -2725,13 +1763,14 @@ slots: human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' + pattern: '{duration}' slot_uri: MIXS:0000116 samp_store_loc: is_a: environment field aliases: - sample storage location description: Location at which sample was stored, usually name of a specific freezer/room - pattern: '{text}' + range: string examples: - value: Freezer no:5 comments: @@ -2743,13 +1782,14 @@ slots: human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water' + pattern: '{text}' slot_uri: MIXS:0000755 samp_store_temp: is_a: environment field aliases: - sample storage temperature description: Temperature at which sample was stored, e.g. -80 degree Celsius - pattern: '{float} {unit}' + range: quantity value examples: - value: -80 degree Celsius comments: @@ -2768,7 +1808,7 @@ slots: - sample volume or weight for DNA extraction description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - pattern: '{float} {unit}' + range: quantity value examples: - value: 1500 milliliter comments: @@ -2788,7 +1828,7 @@ slots: - solar irradiance description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - pattern: '{float} {unit}' + range: quantity value examples: - value: 1.36 kilowatts per square meter per day comments: @@ -2804,7 +1844,7 @@ slots: aliases: - temperature description: Temperature of the sample at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 25 degree Celsius comments: @@ -2822,7 +1862,7 @@ slots: aliases: - ventilation rate description: Ventilation rate of the system in the sampled premises - pattern: '{float} {unit}' + range: quantity value examples: - value: 750 cubic meter per minute comments: @@ -2837,7 +1877,7 @@ slots: aliases: - ventilation type description: Ventilation system used in the sampled premises - pattern: '{text}' + range: string examples: - value: Operable windows comments: @@ -2846,6 +1886,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used in: 2 packages: air, built environment' + pattern: '{text}' slot_uri: MIXS:0000756 volatile_org_comp: is_a: environment field @@ -2854,7 +1895,7 @@ slots: description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - pattern: '{text};{float} {unit}' + range: string examples: - value: formaldehyde;500 nanogram per liter comments: @@ -2864,13 +1905,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: air' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000115 wind_direction: is_a: environment field aliases: - wind direction description: Wind direction is the direction from which a wind originates - pattern: '{text}' + range: string examples: - value: Northwest comments: @@ -2879,13 +1921,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: air' + pattern: '{text}' slot_uri: MIXS:0000757 wind_speed: is_a: environment field aliases: - wind speed description: Speed of wind measured at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 21 kilometer per hour comments: @@ -2900,8 +1943,7 @@ slots: aliases: - surface material description: Surface materials at the point of sampling - pattern: '[adobe|carpet|cinder blocks|concrete|hay bales|glass|metal|paint|plastic|stainless - steel|stone|stucco|tile|vinyl|wood]' + range: surf_material_enum examples: - value: wood comments: @@ -2910,15 +1952,15 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: built environment' - range: surf_material_enum + pattern: '[adobe|carpet|cinder blocks|concrete|hay bales|glass|metal|paint|plastic|stainless + steel|stone|stucco|tile|vinyl|wood]' slot_uri: MIXS:0000758 surf_air_cont: is_a: environment field aliases: - surface-air contaminant description: Contaminant identified on surface - pattern: '[dust|organic matter|particulate matter|volatile organic compounds|biological - contaminants|radon|nutrients|biocides]' + range: surf_air_cont_enum examples: - value: radon comments: @@ -2927,7 +1969,8 @@ slots: - 'Occurrence: m' - 'Position: 2' - 'This field is used uniquely in: built environment' - range: surf_air_cont_enum + pattern: '[dust|organic matter|particulate matter|volatile organic compounds|biological + contaminants|radon|nutrients|biocides]' slot_uri: MIXS:0000759 rel_air_humidity: is_a: environment field @@ -2935,7 +1978,7 @@ slots: - relative air humidity description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - pattern: '{float} {unit}' + range: quantity value examples: - value: 80% comments: @@ -2951,7 +1994,7 @@ slots: - absolute air humidity description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - pattern: '{float} {unit}' + range: quantity value examples: - value: 9 gram per gram comments: @@ -2966,7 +2009,7 @@ slots: aliases: - surface humidity description: 'Surfaces: water activity as a function of air and material moisture' - pattern: '{float} {unit}' + range: quantity value examples: - value: 10% comments: @@ -2981,7 +2024,7 @@ slots: aliases: - air temperature description: Temperature of the air at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 20 degree Celsius comments: @@ -2996,7 +2039,7 @@ slots: aliases: - surface temperature description: Temperature of the surface at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 15 degree Celsius comments: @@ -3011,7 +2054,7 @@ slots: aliases: - surface moisture pH description: ph measurement of surface - pattern: '{float}' + range: double examples: - value: '7' comments: @@ -3027,8 +2070,7 @@ slots: - building occupancy type description: The primary function for which a building or discrete part of a building is intended to be used - pattern: '[office|market|restaurant|residence|school|residential|commercial|low - rise|high rise|wood framed|office|health care|school|airport|sports complex]' + range: build_occup_type_enum examples: - value: market comments: @@ -3037,14 +2079,15 @@ slots: - 'Occurrence: m' - 'Position: 9' - 'This field is used uniquely in: built environment' - range: build_occup_type_enum + pattern: '[office|market|restaurant|residence|school|residential|commercial|low + rise|high rise|wood framed|office|health care|school|airport|sports complex]' slot_uri: MIXS:0000761 surf_moisture: is_a: environment field aliases: - surface moisture description: Water held on a surface - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.01 gram per square meter comments: @@ -3060,7 +2103,7 @@ slots: - dew point description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - pattern: '{float} {unit}' + range: quantity value examples: - value: 22 degree Celsius comments: @@ -3076,7 +2119,7 @@ slots: - indoor space description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - pattern: '[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]' + range: indoor_space_enum examples: - value: foyer comments: @@ -3085,14 +2128,14 @@ slots: - 'Occurrence: 1' - 'Position: 15' - 'This field is used uniquely in: built environment' - range: indoor_space_enum + pattern: '[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]' slot_uri: MIXS:0000763 indoor_surf: is_a: environment field aliases: - indoor surface description: Type of indoor surface - pattern: '[cabinet|ceiling|counter top|door|shelving|vent cover|window|wall]' + range: indoor_surf_enum examples: - value: wall comments: @@ -3101,15 +2144,14 @@ slots: - 'Occurrence: 1' - 'Position: 16' - 'This field is used uniquely in: built environment' - range: indoor_surf_enum + pattern: '[cabinet|ceiling|counter top|door|shelving|vent cover|window|wall]' slot_uri: MIXS:0000764 filter_type: is_a: environment field aliases: - filter type description: A device which removes solid particulates or airborne molecular contaminants - pattern: '[particulate air filter|chemical air filter|low-MERV pleated media|HEPA|electrostatic|gas-phase - or ultraviolet air treatments]' + range: filter_type_enum examples: - value: HEPA comments: @@ -3118,14 +2160,15 @@ slots: - 'Occurrence: m' - 'Position: 17' - 'This field is used uniquely in: built environment' - range: filter_type_enum + pattern: '[particulate air filter|chemical air filter|low-MERV pleated media|HEPA|electrostatic|gas-phase + or ultraviolet air treatments]' slot_uri: MIXS:0000765 heat_cool_type: is_a: environment field aliases: - heating and cooling system type description: Methods of conditioning or heating a room or building - pattern: '[radiant system|heat pump|forced air system|steam forced heat|wood stove]' + range: heat_cool_type_enum examples: - value: heat pump comments: @@ -3134,7 +2177,7 @@ slots: - 'Occurrence: m' - 'Position: 18' - 'This field is used uniquely in: built environment' - range: heat_cool_type_enum + pattern: '[radiant system|heat pump|forced air system|steam forced heat|wood stove]' slot_uri: MIXS:0000766 substructure_type: is_a: environment field @@ -3142,7 +2185,7 @@ slots: - substructure type description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - pattern: '[crawlspace|slab on grade|basement]' + range: substructure_type_enum examples: - value: basement comments: @@ -3151,14 +2194,14 @@ slots: - 'Occurrence: m' - 'Position: 19' - 'This field is used uniquely in: built environment' - range: substructure_type_enum + pattern: '[crawlspace|slab on grade|basement]' slot_uri: MIXS:0000767 building_setting: is_a: environment field aliases: - building setting description: A location (geography) where a building is set - pattern: '[urban|suburban|exurban|rural]' + range: building_setting_enum examples: - value: rural comments: @@ -3167,7 +2210,7 @@ slots: - 'Occurrence: 1' - 'Position: 20' - 'This field is used uniquely in: built environment' - range: building_setting_enum + pattern: '[urban|suburban|exurban|rural]' slot_uri: MIXS:0000768 light_type: is_a: environment field @@ -3177,7 +2220,7 @@ slots: Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - pattern: '[natural light|electric light|desk lamp|flourescent lights|natural light|none]' + range: light_type_enum examples: - value: desk lamp comments: @@ -3186,7 +2229,7 @@ slots: - 'Occurrence: m' - 'Position: 21' - 'This field is used uniquely in: built environment' - range: light_type_enum + pattern: '[natural light|electric light|desk lamp|flourescent lights|natural light|none]' slot_uri: MIXS:0000769 samp_sort_meth: is_a: environment field @@ -3196,7 +2239,7 @@ slots: suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - pattern: '{text}' + range: string examples: - value: '' comments: @@ -3205,13 +2248,14 @@ slots: - 'Occurrence: m' - 'Position: 22' - 'This field is used uniquely in: built environment' + pattern: '{text}' slot_uri: MIXS:0000216 space_typ_state: is_a: environment field aliases: - space typical state description: Customary or normal state of the space - pattern: '[typically occupied|typically unoccupied]' + range: string examples: - value: typically occupied comments: @@ -3220,13 +2264,14 @@ slots: - 'Occurrence: 1' - 'Position: 23' - 'This field is used uniquely in: built environment' + pattern: '[typically occupied|typically unoccupied]' slot_uri: MIXS:0000770 typ_occup_density: is_a: environment field aliases: - typical occupant density description: Customary or normal density of occupants - pattern: '{float}' + range: double examples: - value: '25' comments: @@ -3241,7 +2286,7 @@ slots: aliases: - occupancy at sampling description: Number of occupants present at time of sample within the given space - pattern: '{integer}' + range: string examples: - value: '10' comments: @@ -3250,13 +2295,14 @@ slots: - 'Occurrence: 1' - 'Position: 25' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000772 occup_density_samp: is_a: environment field aliases: - occupant density at sampling description: Average number of occupants at time of sampling per square footage - pattern: '{float}' + range: double examples: - value: '' comments: @@ -3271,7 +2317,7 @@ slots: aliases: - address description: The street name and building number where the sampling occurred. - pattern: '{integer}{text}' + range: string examples: - value: '' comments: @@ -3280,6 +2326,7 @@ slots: - 'Occurrence: 1' - 'Position: 27' - 'This field is used uniquely in: built environment' + pattern: '{integer}{text}' slot_uri: MIXS:0000218 adj_room: is_a: environment field @@ -3287,7 +2334,7 @@ slots: - adjacent rooms description: List of rooms (room number, room name) immediately adjacent to the sampling room - pattern: '{text};{integer}' + range: string examples: - value: '' comments: @@ -3296,6 +2343,7 @@ slots: - 'Occurrence: 1' - 'Position: 28' - 'This field is used uniquely in: built environment' + pattern: '{text};{integer}' slot_uri: MIXS:0000219 aero_struc: is_a: environment field @@ -3304,7 +2352,7 @@ slots: description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - pattern: '[plane|glider]' + range: string examples: - value: plane comments: @@ -3313,6 +2361,7 @@ slots: - 'Occurrence: 1' - 'Position: 29' - 'This field is used uniquely in: built environment' + pattern: '[plane|glider]' slot_uri: MIXS:0000773 amount_light: is_a: environment field @@ -3320,7 +2369,7 @@ slots: - amount of light description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -3336,7 +2385,7 @@ slots: - architectural structure description: An architectural structure is a human-made, free-standing, immobile outdoor construction - pattern: '[building|shed|home]' + range: arch_struc_enum examples: - value: shed comments: @@ -3345,14 +2394,14 @@ slots: - 'Occurrence: 1' - 'Position: 31' - 'This field is used uniquely in: built environment' - range: arch_struc_enum + pattern: '[building|shed|home]' slot_uri: MIXS:0000774 avg_occup: is_a: environment field aliases: - average daily occupancy description: Daily average occupancy of room - pattern: '{float}' + range: double examples: - value: '2' comments: @@ -3368,7 +2417,7 @@ slots: - average dew point description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - pattern: '{float} {unit}' + range: quantity value examples: - value: 25.5 degree Celsius comments: @@ -3384,7 +2433,7 @@ slots: - average temperature description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - pattern: '{float} {unit}' + range: quantity value examples: - value: 12.5 degree Celsius comments: @@ -3399,7 +2448,7 @@ slots: aliases: - bathroom count description: The number of bathrooms in the building - pattern: '{integer}' + range: string examples: - value: '1' comments: @@ -3408,13 +2457,14 @@ slots: - 'Occurrence: 1' - 'Position: 35' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000776 bedroom_count: is_a: environment field aliases: - bedroom count description: The number of bedrooms in the building - pattern: '{integer}' + range: string examples: - value: '2' comments: @@ -3423,13 +2473,14 @@ slots: - 'Occurrence: 1' - 'Position: 36' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000777 built_struc_age: is_a: environment field aliases: - built structure age description: The age of the built structure since construction - pattern: '{float} {unit}' + range: quantity value examples: - value: '15' comments: @@ -3445,7 +2496,7 @@ slots: - built structure setting description: The characterization of the location of the built structure as high or low human density - pattern: '[urban|rural]' + range: string examples: - value: rural comments: @@ -3454,6 +2505,7 @@ slots: - 'Occurrence: 1' - 'Position: 38' - 'This field is used uniquely in: built environment' + pattern: '[urban|rural]' slot_uri: MIXS:0000778 built_struc_type: is_a: environment field @@ -3461,7 +2513,7 @@ slots: - built structure type description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - pattern: '{text}' + range: string examples: - value: '' comments: @@ -3470,13 +2522,14 @@ slots: - 'Occurrence: 1' - 'Position: 39' - 'This field is used uniquely in: built environment' + pattern: '{text}' slot_uri: MIXS:0000721 ceil_area: is_a: environment field aliases: - ceiling area description: The area of the ceiling space within the room - pattern: '{float} {unit}' + range: quantity value examples: - value: 25 square meter comments: @@ -3492,7 +2545,7 @@ slots: - ceiling condition description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - pattern: '[new|visible wear|needs repair|damaged|rupture]' + range: ceil_cond_enum examples: - value: damaged comments: @@ -3501,15 +2554,14 @@ slots: - 'Occurrence: 1' - 'Position: 41' - 'This field is used uniquely in: built environment' - range: ceil_cond_enum + pattern: '[new|visible wear|needs repair|damaged|rupture]' slot_uri: MIXS:0000779 ceil_finish_mat: is_a: environment field aliases: - ceiling finish material description: The type of material used to finish a ceiling - pattern: '[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral - wool/calcium silicate|wood]' + range: ceil_finish_mat_enum examples: - value: stucco comments: @@ -3518,14 +2570,15 @@ slots: - 'Occurrence: 1' - 'Position: 42' - 'This field is used uniquely in: built environment' - range: ceil_finish_mat_enum + pattern: '[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral + wool/calcium silicate|wood]' slot_uri: MIXS:0000780 ceil_water_mold: is_a: environment field aliases: - ceiling signs of water/mold description: Signs of the presence of mold or mildew on the ceiling - pattern: '[presence of mold visible|no presence of mold visible]' + range: string examples: - value: presence of mold visible comments: @@ -3534,13 +2587,14 @@ slots: - 'Occurrence: 1' - 'Position: 43' - 'This field is used uniquely in: built environment' + pattern: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000781 ceil_struc: is_a: environment field aliases: - ceiling structure description: The construction format of the ceiling - pattern: '[wood frame|concrete]' + range: string examples: - value: concrete comments: @@ -3549,14 +2603,14 @@ slots: - 'Occurrence: 1' - 'Position: 44' - 'This field is used uniquely in: built environment' + pattern: '[wood frame|concrete]' slot_uri: MIXS:0000782 ceil_texture: is_a: environment field aliases: - ceiling texture description: The feel, appearance, or consistency of a ceiling surface - pattern: '[crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange - peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' + range: ceil_texture_enum examples: - value: popcorn comments: @@ -3565,7 +2619,8 @@ slots: - 'Occurrence: 1' - 'Position: 45' - 'This field is used uniquely in: built environment' - range: ceil_texture_enum + pattern: '[crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange + peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' slot_uri: MIXS:0000783 ceil_thermal_mass: is_a: environment field @@ -3575,7 +2630,7 @@ slots: fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -3590,7 +2645,7 @@ slots: aliases: - ceiling type description: The type of ceiling according to the ceiling's appearance or construction - pattern: '[cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched]' + range: ceil_type_enum examples: - value: coffered comments: @@ -3599,14 +2654,14 @@ slots: - 'Occurrence: 1' - 'Position: 47' - 'This field is used uniquely in: built environment' - range: ceil_type_enum + pattern: '[cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched]' slot_uri: MIXS:0000784 cool_syst_id: is_a: environment field aliases: - cooling system identifier description: The cooling system identifier - pattern: '{integer}' + range: string examples: - value: '12345' comments: @@ -3615,13 +2670,14 @@ slots: - 'Occurrence: 1' - 'Position: 48' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000785 date_last_rain: is_a: environment field aliases: - date last rain description: The date of the last time it rained - pattern: '{timestamp}' + range: string examples: - value: 2018-05-11:T14:30Z comments: @@ -3630,15 +2686,14 @@ slots: - 'Occurrence: 1' - 'Position: 49' - 'This field is used uniquely in: built environment' + pattern: '{timestamp}' slot_uri: MIXS:0000786 build_docs: is_a: environment field aliases: - design, construction, and operation documents description: The building design, construction and operation documents - pattern: '[building information model|commissioning report|complaint logs|contract - administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop - drawings|submittals|ventilation system|windows]' + range: build_docs_enum examples: - value: maintenance plans comments: @@ -3647,14 +2702,16 @@ slots: - 'Occurrence: 1' - 'Position: 50' - 'This field is used uniquely in: built environment' - range: build_docs_enum + pattern: '[building information model|commissioning report|complaint logs|contract + administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop + drawings|submittals|ventilation system|windows]' slot_uri: MIXS:0000787 door_size: is_a: environment field aliases: - door area or size description: The size of the door - pattern: '{float} {unit}' + range: quantity value examples: - value: 2.5 square meter comments: @@ -3669,7 +2726,7 @@ slots: aliases: - door condition description: The phsical condition of the door - pattern: '[damaged|needs repair|new|rupture|visible wear]' + range: door_cond_enum examples: - value: new comments: @@ -3678,14 +2735,14 @@ slots: - 'Occurrence: 1' - 'Position: 52' - 'This field is used uniquely in: built environment' - range: door_cond_enum + pattern: '[damaged|needs repair|new|rupture|visible wear]' slot_uri: MIXS:0000788 door_direct: is_a: environment field aliases: - door direction of opening description: The direction the door opens - pattern: '[inward|outward|sideways]' + range: door_direct_enum examples: - value: inward comments: @@ -3694,14 +2751,14 @@ slots: - 'Occurrence: 1' - 'Position: 53' - 'This field is used uniquely in: built environment' - range: door_direct_enum + pattern: '[inward|outward|sideways]' slot_uri: MIXS:0000789 door_loc: is_a: environment field aliases: - door location description: The relative location of the door in the room - pattern: '[north|south|east|west]' + range: door_loc_enum examples: - value: north comments: @@ -3710,15 +2767,14 @@ slots: - 'Occurrence: 1' - 'Position: 54' - 'This field is used uniquely in: built environment' - range: door_loc_enum + pattern: '[north|south|east|west]' slot_uri: MIXS:0000790 door_mat: is_a: environment field aliases: - door material description: The material the door is composed of - pattern: '[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic - alloy|vinyl|wood|wood/plastic composite]' + range: door_mat_enum examples: - value: wood comments: @@ -3727,14 +2783,15 @@ slots: - 'Occurrence: 1' - 'Position: 55' - 'This field is used uniquely in: built environment' - range: door_mat_enum + pattern: '[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic + alloy|vinyl|wood|wood/plastic composite]' slot_uri: MIXS:0000791 door_move: is_a: environment field aliases: - door movement description: The type of movement of the door - pattern: '[collapsible|folding|revolving|rolling shutter|sliding|swinging]' + range: door_move_enum examples: - value: swinging comments: @@ -3743,14 +2800,14 @@ slots: - 'Occurrence: 1' - 'Position: 56' - 'This field is used uniquely in: built environment' - range: door_move_enum + pattern: '[collapsible|folding|revolving|rolling shutter|sliding|swinging]' slot_uri: MIXS:0000792 door_water_mold: is_a: environment field aliases: - door signs of water/mold description: Signs of the presence of mold or mildew on a door - pattern: '[presence of mold visible|no presence of mold visible]' + range: string examples: - value: presence of mold visible comments: @@ -3759,13 +2816,14 @@ slots: - 'Occurrence: 1' - 'Position: 57' - 'This field is used uniquely in: built environment' + pattern: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000793 door_type: is_a: environment field aliases: - door type description: The type of door material - pattern: '[composite|metal|wooden]' + range: door_type_enum examples: - value: wooden comments: @@ -3774,14 +2832,14 @@ slots: - 'Occurrence: 1' - 'Position: 58' - 'This field is used uniquely in: built environment' - range: door_type_enum + pattern: '[composite|metal|wooden]' slot_uri: MIXS:0000794 door_comp_type: is_a: environment field aliases: - door type, composite description: The composite type of the door - pattern: '[metal covered|revolving|sliding|telescopic]' + range: door_comp_type_enum examples: - value: revolving comments: @@ -3790,14 +2848,14 @@ slots: - 'Occurrence: 1' - 'Position: 59' - 'This field is used uniquely in: built environment' - range: door_comp_type_enum + pattern: '[metal covered|revolving|sliding|telescopic]' slot_uri: MIXS:0000795 door_type_metal: is_a: environment field aliases: - door type, metal description: The type of metal door - pattern: '[collapsible|corrugated steel|hollow|rolling shutters|steel plate]' + range: door_type_metal_enum examples: - value: hollow comments: @@ -3806,16 +2864,14 @@ slots: - 'Occurrence: 1' - 'Position: 60' - 'This field is used uniquely in: built environment' - range: door_type_metal_enum + pattern: '[collapsible|corrugated steel|hollow|rolling shutters|steel plate]' slot_uri: MIXS:0000796 door_type_wood: is_a: environment field aliases: - door type, wood description: The type of wood door - pattern: '[bettened and ledged|battened|ledged and braced|battened|ledged and - framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire - gauged]' + range: door_type_wood_enum examples: - value: battened comments: @@ -3824,7 +2880,9 @@ slots: - 'Occurrence: 1' - 'Position: 61' - 'This field is used uniquely in: built environment' - range: door_type_wood_enum + pattern: '[bettened and ledged|battened|ledged and braced|battened|ledged and + framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire + gauged]' slot_uri: MIXS:0000797 drawings: is_a: environment field @@ -3832,7 +2890,7 @@ slots: - drawings description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - pattern: '[operation|as built|construction|bid|design|building navigation map|diagram|sketch]' + range: drawings_enum examples: - value: sketch comments: @@ -3841,14 +2899,14 @@ slots: - 'Occurrence: 1' - 'Position: 62' - 'This field is used uniquely in: built environment' - range: drawings_enum + pattern: '[operation|as built|construction|bid|design|building navigation map|diagram|sketch]' slot_uri: MIXS:0000798 elevator: is_a: environment field aliases: - elevator count description: The number of elevators within the built structure - pattern: '{integer}' + range: string examples: - value: '2' comments: @@ -3857,13 +2915,14 @@ slots: - 'Occurrence: 1' - 'Position: 63' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000799 escalator: is_a: environment field aliases: - escalator count description: The number of escalators within the built structure - pattern: '{integer}' + range: string examples: - value: '4' comments: @@ -3872,13 +2931,14 @@ slots: - 'Occurrence: 1' - 'Position: 64' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000800 exp_duct: is_a: environment field aliases: - exposed ductwork description: The amount of exposed ductwork in the room - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -3893,7 +2953,7 @@ slots: aliases: - exposed pipes description: The number of exposed pipes in the room - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -3902,13 +2962,14 @@ slots: - 'Occurrence: 1' - 'Position: 66' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000220 ext_door: is_a: environment field aliases: - exterior door count description: The number of exterior doors in the built structure - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -3917,13 +2978,14 @@ slots: - 'Occurrence: 1' - 'Position: 67' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000170 fireplace_type: is_a: environment field aliases: - fireplace type description: A firebox with chimney - pattern: '[gas burning|wood burning]' + range: string examples: - value: wood burning comments: @@ -3932,13 +2994,14 @@ slots: - 'Occurrence: 1' - 'Position: 68' - 'This field is used uniquely in: built environment' + pattern: '[gas burning|wood burning]' slot_uri: MIXS:0000802 floor_age: is_a: environment field aliases: - floor age description: The time period since installment of the carpet or flooring - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -3953,7 +3016,7 @@ slots: aliases: - floor area description: The area of the floor space within the room - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -3969,7 +3032,7 @@ slots: - floor condition description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - pattern: '[new|visible wear|needs repair|damaged|rupture]' + range: floor_cond_enum examples: - value: new comments: @@ -3978,7 +3041,7 @@ slots: - 'Occurrence: 1' - 'Position: 71' - 'This field is used uniquely in: built environment' - range: floor_cond_enum + pattern: '[new|visible wear|needs repair|damaged|rupture]' slot_uri: MIXS:0000803 floor_count: is_a: environment field @@ -3986,7 +3049,7 @@ slots: - floor count description: The number of floors in the building, including basements and mechanical penthouse - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -3995,15 +3058,14 @@ slots: - 'Occurrence: 1' - 'Position: 72' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000225 floor_finish_mat: is_a: environment field aliases: - floor finish material description: The floor covering type; the finished surface that is walked on - pattern: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl - composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify - unfinished|sealed|clear finish|paint]' + range: floor_finish_mat_enum examples: - value: carpet comments: @@ -4012,15 +3074,16 @@ slots: - 'Occurrence: 1' - 'Position: 73' - 'This field is used uniquely in: built environment' - range: floor_finish_mat_enum + pattern: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl + composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify + unfinished|sealed|clear finish|paint]' slot_uri: MIXS:0000804 floor_water_mold: is_a: environment field aliases: - floor signs of water/mold description: Signs of the presence of mold or mildew in a room - pattern: '[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling - discoloration|peeling paint or wallpaper|bulging walls|condensation]' + range: floor_water_mold_enum examples: - value: ceiling discoloration comments: @@ -4029,7 +3092,8 @@ slots: - 'Occurrence: 1' - 'Position: 74' - 'This field is used uniquely in: built environment' - range: floor_water_mold_enum + pattern: '[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling + discoloration|peeling paint or wallpaper|bulging walls|condensation]' slot_uri: MIXS:0000805 floor_struc: is_a: environment field @@ -4037,7 +3101,7 @@ slots: - floor structure description: Refers to the structural elements and subfloor upon which the finish flooring is installed - pattern: '[balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete]' + range: floor_struc_enum examples: - value: concrete comments: @@ -4046,14 +3110,14 @@ slots: - 'Occurrence: 1' - 'Position: 75' - 'This field is used uniquely in: built environment' - range: floor_struc_enum + pattern: '[balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete]' slot_uri: MIXS:0000806 floor_thermal_mass: is_a: environment field aliases: - floor thermal mass description: The ability of the floor to provide inertia against temperature fluctuations - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -4068,7 +3132,7 @@ slots: aliases: - frequency of cleaning description: The number of times the building is cleaned per week - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4077,13 +3141,14 @@ slots: - 'Occurrence: 1' - 'Position: 77' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000226 freq_cook: is_a: environment field aliases: - frequency of cooking description: The number of times a meal is cooked per week - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4092,13 +3157,14 @@ slots: - 'Occurrence: 1' - 'Position: 78' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000227 furniture: is_a: environment field aliases: - furniture description: The types of furniture present in the sampled room - pattern: '[cabinet|chair|desks]' + range: furniture_enum examples: - value: chair comments: @@ -4107,14 +3173,14 @@ slots: - 'Occurrence: 1' - 'Position: 79' - 'This field is used uniquely in: built environment' - range: furniture_enum + pattern: '[cabinet|chair|desks]' slot_uri: MIXS:0000807 gender_restroom: is_a: environment field aliases: - gender of restroom description: The gender type of the restroom - pattern: '[male|female]' + range: string examples: - value: male comments: @@ -4123,13 +3189,14 @@ slots: - 'Occurrence: 1' - 'Position: 80' - 'This field is used uniquely in: built environment' + pattern: '[male|female]' slot_uri: MIXS:0000808 hall_count: is_a: environment field aliases: - hallway/corridor count description: The total count of hallways and cooridors in the built structure - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4138,13 +3205,14 @@ slots: - 'Occurrence: 1' - 'Position: 81' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000228 handidness: is_a: environment field aliases: - handidness description: The handidness of the individual sampled - pattern: '[ambidexterity|left handedness|mixed-handedness|right handedness]' + range: handidness_enum examples: - value: right handedness comments: @@ -4153,14 +3221,14 @@ slots: - 'Occurrence: 1' - 'Position: 82' - 'This field is used uniquely in: built environment' - range: handidness_enum + pattern: '[ambidexterity|left handedness|mixed-handedness|right handedness]' slot_uri: MIXS:0000809 heat_deliv_loc: is_a: environment field aliases: - heating delivery locations description: The location of heat delivery within the room - pattern: '[north|south|east|west]' + range: heat_deliv_loc_enum examples: - value: north comments: @@ -4169,14 +3237,14 @@ slots: - 'Occurrence: 1' - 'Position: 83' - 'This field is used uniquely in: built environment' - range: heat_deliv_loc_enum + pattern: '[north|south|east|west]' slot_uri: MIXS:0000810 heat_system_deliv_meth: is_a: environment field aliases: - heating system delivery method description: The method by which the heat is delivered through the system - pattern: '[conductive|radiant]' + range: string examples: - value: radiant comments: @@ -4185,13 +3253,14 @@ slots: - 'Occurrence: 1' - 'Position: 84' - 'This field is used uniquely in: built environment' + pattern: '[conductive|radiant]' slot_uri: MIXS:0000812 heat_system_id: is_a: environment field aliases: - heating system identifier description: The heating system identifier - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4200,13 +3269,14 @@ slots: - 'Occurrence: 1' - 'Position: 85' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000833 height_carper_fiber: is_a: environment field aliases: - height carpet fiber mat description: The average carpet fiber height in the indoor environment - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -4221,7 +3291,7 @@ slots: aliases: - inside lux light description: The recorded value at sampling time (power density) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -4237,7 +3307,7 @@ slots: - interior wall condition description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - pattern: '[new|visible wear|needs repair|damaged|rupture]' + range: int_wall_cond_enum examples: - value: damaged comments: @@ -4246,14 +3316,14 @@ slots: - 'Occurrence: 1' - 'Position: 88' - 'This field is used uniquely in: built environment' - range: int_wall_cond_enum + pattern: '[new|visible wear|needs repair|damaged|rupture]' slot_uri: MIXS:0000813 last_clean: is_a: environment field aliases: - last time swept/mopped/vacuumed description: The last time the floor was cleaned (swept, mopped, vacuumed) - pattern: '{timestamp}' + range: string examples: - value: 2018-05-11:T14:30Z comments: @@ -4262,13 +3332,14 @@ slots: - 'Occurrence: 1' - 'Position: 89' - 'This field is used uniquely in: built environment' + pattern: '{timestamp}' slot_uri: MIXS:0000814 max_occup: is_a: environment field aliases: - maximum occupancy description: The maximum amount of people allowed in the indoor environment - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4277,13 +3348,14 @@ slots: - 'Occurrence: 1' - 'Position: 90' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000229 mech_struc: is_a: environment field aliases: - mechanical structure description: 'mechanical structure: a moving structure' - pattern: '[subway|coach|carriage|elevator|escalator|boat|train|car|bus]' + range: mech_struc_enum examples: - value: elevator comments: @@ -4292,14 +3364,14 @@ slots: - 'Occurrence: 1' - 'Position: 91' - 'This field is used uniquely in: built environment' - range: mech_struc_enum + pattern: '[subway|coach|carriage|elevator|escalator|boat|train|car|bus]' slot_uri: MIXS:0000815 number_plants: is_a: environment field aliases: - number of houseplants description: The number of plant(s) in the sampling space - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4308,13 +3380,14 @@ slots: - 'Occurrence: 1' - 'Position: 92' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000230 number_pets: is_a: environment field aliases: - number of pets description: The number of pets residing in the sampled space - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4323,13 +3396,14 @@ slots: - 'Occurrence: 1' - 'Position: 93' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000231 number_resident: is_a: environment field aliases: - number of residents description: The number of individuals currently occupying in the sampling location - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4338,13 +3412,14 @@ slots: - 'Occurrence: 1' - 'Position: 94' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000232 occup_document: is_a: environment field aliases: - occupancy documentation description: The type of documentation of occupancy - pattern: '[automated count|estimate|manual count|videos]' + range: occup_document_enum examples: - value: estimate comments: @@ -4353,14 +3428,14 @@ slots: - 'Occurrence: 1' - 'Position: 95' - 'This field is used uniquely in: built environment' - range: occup_document_enum + pattern: '[automated count|estimate|manual count|videos]' slot_uri: MIXS:0000816 ext_wall_orient: is_a: environment field aliases: - orientations of exterior wall description: The orientation of the exterior wall - pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' + range: ext_wall_orient_enum examples: - value: northwest comments: @@ -4369,14 +3444,14 @@ slots: - 'Occurrence: 1' - 'Position: 96' - 'This field is used uniquely in: built environment' - range: ext_wall_orient_enum + pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' slot_uri: MIXS:0000817 ext_window_orient: is_a: environment field aliases: - orientations of exterior window description: The compass direction the exterior window of the room is facing - pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' + range: ext_window_orient_enum examples: - value: southwest comments: @@ -4385,14 +3460,14 @@ slots: - 'Occurrence: 1' - 'Position: 97' - 'This field is used uniquely in: built environment' - range: ext_window_orient_enum + pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' slot_uri: MIXS:0000818 rel_humidity_out: is_a: environment field aliases: - outside relative humidity description: The recorded outside relative humidity value at the time of sampling - pattern: '{float} {unit}' + range: quantity value examples: - value: 12 per kilogram of air comments: @@ -4407,7 +3482,7 @@ slots: aliases: - presence of pets, animals, or insects description: The number and type of animals present in the sampling space - pattern: '[cat|dog|rodent|snake|other];{integer}' + range: pres_animal_enum examples: - value: cat;5 comments: @@ -4416,14 +3491,14 @@ slots: - 'Occurrence: 1' - 'Position: 99' - 'This field is used uniquely in: built environment' - range: pres_animal_enum + pattern: '[cat|dog|rodent|snake|other];{integer}' slot_uri: MIXS:0000819 quad_pos: is_a: environment field aliases: - quadrant position description: The quadrant position of the sampling room within the building - pattern: '[North side|West side|South side|East side]' + range: quad_pos_enum examples: - value: West side comments: @@ -4432,14 +3507,14 @@ slots: - 'Occurrence: 1' - 'Position: 100' - 'This field is used uniquely in: built environment' - range: quad_pos_enum + pattern: '[North side|West side|South side|East side]' slot_uri: MIXS:0000820 rel_samp_loc: is_a: environment field aliases: - relative sampling location description: The sampling location within the train car - pattern: '[edge of car|center of car|under a seat]' + range: rel_samp_loc_enum examples: - value: center of car comments: @@ -4448,14 +3523,14 @@ slots: - 'Occurrence: 1' - 'Position: 101' - 'This field is used uniquely in: built environment' - range: rel_samp_loc_enum + pattern: '[edge of car|center of car|under a seat]' slot_uri: MIXS:0000821 room_air_exch_rate: is_a: environment field aliases: - room air exchange rate description: The rate at which outside air replaces indoor air in a given space - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -4471,7 +3546,7 @@ slots: - room architectural elements description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - pattern: '{text}' + range: string examples: - value: '' comments: @@ -4480,13 +3555,14 @@ slots: - 'Occurrence: 1' - 'Position: 103' - 'This field is used uniquely in: built environment' + pattern: '{text}' slot_uri: MIXS:0000233 room_condt: is_a: environment field aliases: - room condition description: The condition of the room at the time of sampling - pattern: '[new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew]' + range: room_condt_enum examples: - value: new comments: @@ -4495,7 +3571,7 @@ slots: - 'Occurrence: 1' - 'Position: 104' - 'This field is used uniquely in: built environment' - range: room_condt_enum + pattern: '[new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew]' slot_uri: MIXS:0000822 room_count: is_a: environment field @@ -4503,7 +3579,7 @@ slots: - room count description: The total count of rooms in the built structure including all room types - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4512,13 +3588,14 @@ slots: - 'Occurrence: 1' - 'Position: 105' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000234 room_dim: is_a: environment field aliases: - room dimensions description: The length, width and height of sampling room - pattern: '{integer} {unit} x {integer} {unit} x {integer} {unit}' + range: string examples: - value: '' comments: @@ -4527,6 +3604,7 @@ slots: - 'Occurrence: 1' - 'Position: 106' - 'This field is used uniquely in: built environment' + pattern: '{integer} {unit} x {integer} {unit} x {integer} {unit}' slot_uri: MIXS:0000192 room_door_dist: is_a: environment field @@ -4534,7 +3612,7 @@ slots: - room door distance description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - pattern: '{integer} {unit}' + range: string examples: - value: '' comments: @@ -4543,13 +3621,14 @@ slots: - 'Occurrence: 1' - 'Position: 107' - 'This field is used uniquely in: built environment' + pattern: '{integer} {unit}' slot_uri: MIXS:0000193 room_loc: is_a: environment field aliases: - room location in building description: The position of the room within the building - pattern: '[corner room|interior room|exterior wall]' + range: room_loc_enum examples: - value: interior room comments: @@ -4558,7 +3637,7 @@ slots: - 'Occurrence: 1' - 'Position: 108' - 'This field is used uniquely in: built environment' - range: room_loc_enum + pattern: '[corner room|interior room|exterior wall]' slot_uri: MIXS:0000823 room_moist_damage_hist: is_a: environment field @@ -4566,7 +3645,7 @@ slots: - room moisture damage or mold history description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4575,13 +3654,14 @@ slots: - 'Occurrence: 1' - 'Position: 109' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000235 room_net_area: is_a: environment field aliases: - room net area description: The net floor area of sampling room. Net area excludes wall thicknesses - pattern: '{integer} {unit}' + range: string examples: - value: '' comments: @@ -4590,13 +3670,14 @@ slots: - 'Occurrence: 1' - 'Position: 110' - 'This field is used uniquely in: built environment' + pattern: '{integer} {unit}' slot_uri: MIXS:0000194 room_occup: is_a: environment field aliases: - room occupancy description: Count of room occupancy at time of sampling - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4605,6 +3686,7 @@ slots: - 'Occurrence: 1' - 'Position: 111' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000236 room_samp_pos: is_a: environment field @@ -4612,8 +3694,7 @@ slots: - room sampling position description: The horizontal sampling position in the room relative to architectural elements - pattern: '[north corner|south corner|west corner|east corner|northeast corner|northwest - corner|southeast corner|southwest corner|center]' + range: room_samp_pos_enum examples: - value: south corner comments: @@ -4622,7 +3703,8 @@ slots: - 'Occurrence: 1' - 'Position: 112' - 'This field is used uniquely in: built environment' - range: room_samp_pos_enum + pattern: '[north corner|south corner|west corner|east corner|northeast corner|northwest + corner|southeast corner|southwest corner|center]' slot_uri: MIXS:0000824 room_type: is_a: environment field @@ -4630,9 +3712,7 @@ slots: - room type description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail - room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical - or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' + range: room_type_enum examples: - value: bathroom comments: @@ -4641,14 +3721,16 @@ slots: - 'Occurrence: 1' - 'Position: 113' - 'This field is used uniquely in: built environment' - range: room_type_enum + pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail + room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical + or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' slot_uri: MIXS:0000825 room_vol: is_a: environment field aliases: - room volume description: Volume of sampling room - pattern: '{integer} {unit}' + range: string examples: - value: '' comments: @@ -4657,13 +3739,14 @@ slots: - 'Occurrence: 1' - 'Position: 114' - 'This field is used uniquely in: built environment' + pattern: '{integer} {unit}' slot_uri: MIXS:0000195 room_window_count: is_a: environment field aliases: - room window count description: Number of windows in the room - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4672,14 +3755,14 @@ slots: - 'Occurrence: 1' - 'Position: 115' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000237 room_connected: is_a: environment field aliases: - rooms connected by a doorway description: List of rooms connected to the sampling room by a doorway - pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail - room|office|stairwell]' + range: room_connected_enum examples: - value: office comments: @@ -4688,7 +3771,8 @@ slots: - 'Occurrence: 1' - 'Position: 116' - 'This field is used uniquely in: built environment' - range: room_connected_enum + pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail + room|office|stairwell]' slot_uri: MIXS:0000826 room_hallway: is_a: environment field @@ -4696,7 +3780,7 @@ slots: - rooms that are on the same hallway description: List of room(s) (room number, room name) located in the same hallway as sampling room - pattern: '{text};{integer}' + range: string examples: - value: '' comments: @@ -4705,6 +3789,7 @@ slots: - 'Occurrence: 1' - 'Position: 117' - 'This field is used uniquely in: built environment' + pattern: '{text};{integer}' slot_uri: MIXS:0000238 room_door_share: is_a: environment field @@ -4712,7 +3797,7 @@ slots: - rooms that share a door with sampling room description: List of room(s) (room number, room name) sharing a door with the sampling room - pattern: '{text};{integer}' + range: string examples: - value: '' comments: @@ -4721,6 +3806,7 @@ slots: - 'Occurrence: 1' - 'Position: 118' - 'This field is used uniquely in: built environment' + pattern: '{text};{integer}' slot_uri: MIXS:0000242 room_wall_share: is_a: environment field @@ -4728,7 +3814,7 @@ slots: - rooms that share a wall with sampling room description: List of room(s) (room number, room name) sharing a wall with the sampling room - pattern: '{text};{integer}' + range: string examples: - value: '' comments: @@ -4737,13 +3823,14 @@ slots: - 'Occurrence: 1' - 'Position: 119' - 'This field is used uniquely in: built environment' + pattern: '{text};{integer}' slot_uri: MIXS:0000243 samp_weather: is_a: environment field aliases: - sampling day weather description: The weather on the sampling day - pattern: '[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]' + range: samp_weather_enum examples: - value: foggy comments: @@ -4752,14 +3839,14 @@ slots: - 'Occurrence: 1' - 'Position: 120' - 'This field is used uniquely in: built environment' - range: samp_weather_enum + pattern: '[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]' slot_uri: MIXS:0000827 samp_floor: is_a: environment field aliases: - sampling floor description: The floor of the building, where the sampling room is located - pattern: '[1st floor|2nd floor|{integer} floor|basement|lobby]' + range: samp_floor_enum examples: - value: 4th floor comments: @@ -4768,7 +3855,7 @@ slots: - 'Occurrence: 1' - 'Position: 121' - 'This field is used uniquely in: built environment' - range: samp_floor_enum + pattern: '[1st floor|2nd floor|{integer} floor|basement|lobby]' slot_uri: MIXS:0000828 samp_room_id: is_a: environment field @@ -4776,7 +3863,7 @@ slots: - sampling room ID or name description: Sampling room number. This ID should be consistent with the designations on the building floor plans - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -4785,13 +3872,14 @@ slots: - 'Occurrence: 1' - 'Position: 122' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000244 samp_time_out: is_a: environment field aliases: - sampling time outside description: The recent and long term history of outside sampling - pattern: '{float}' + range: double examples: - value: '' comments: @@ -4808,7 +3896,7 @@ slots: description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - pattern: '{termLabel} {[termID]}' + range: string examples: - value: autumn [NCIT:C94733] comments: @@ -4817,13 +3905,14 @@ slots: - 'Occurrence: 1' - 'Position: 124' - 'This field is used uniquely in: built environment' + pattern: '{termLabel} {[termID]}' slot_uri: MIXS:0000829 season_use: is_a: environment field aliases: - seasonal use description: The seasons the space is occupied - pattern: '[Spring|Summer|Fall|Winter]' + range: season_use_enum examples: - value: Winter comments: @@ -4832,14 +3921,14 @@ slots: - 'Occurrence: 1' - 'Position: 125' - 'This field is used uniquely in: built environment' - range: season_use_enum + pattern: '[Spring|Summer|Fall|Winter]' slot_uri: MIXS:0000830 shading_device_cond: is_a: environment field aliases: - shading device condition description: The physical condition of the shading device at the time of sampling - pattern: '[damaged|needs repair|new|rupture|visible wear]' + range: shading_device_cond_enum examples: - value: new comments: @@ -4848,14 +3937,14 @@ slots: - 'Occurrence: 1' - 'Position: 126' - 'This field is used uniquely in: built environment' - range: shading_device_cond_enum + pattern: '[damaged|needs repair|new|rupture|visible wear]' slot_uri: MIXS:0000831 shading_device_loc: is_a: environment field aliases: - shading device location description: The location of the shading device in relation to the built structure - pattern: '[exterior|interior]' + range: string examples: - value: exterior comments: @@ -4864,13 +3953,14 @@ slots: - 'Occurrence: 1' - 'Position: 127' - 'This field is used uniquely in: built environment' + pattern: '[exterior|interior]' slot_uri: MIXS:0000832 shading_device_mat: is_a: environment field aliases: - shading device material description: The material the shading device is composed of - pattern: '{text}' + range: string examples: - value: '' comments: @@ -4879,13 +3969,14 @@ slots: - 'Occurrence: 1' - 'Position: 128' - 'This field is used uniquely in: built environment' + pattern: '{text}' slot_uri: MIXS:0000245 shading_device_water_mold: is_a: environment field aliases: - shading device signs of water/mold description: Signs of the presence of mold or mildew on the shading device - pattern: '[presence of mold visible|no presence of mold visible]' + range: string examples: - value: no presence of mold visible comments: @@ -4894,15 +3985,14 @@ slots: - 'Occurrence: 1' - 'Position: 129' - 'This field is used uniquely in: built environment' + pattern: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000834 shading_device_type: is_a: environment field aliases: - shading device type description: The type of shading device - pattern: '[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller - awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian - awning]' + range: shading_device_type_enum examples: - value: slatted aluminum awning comments: @@ -4911,7 +4001,9 @@ slots: - 'Occurrence: 1' - 'Position: 130' - 'This field is used uniquely in: built environment' - range: shading_device_type_enum + pattern: '[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller + awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian + awning]' slot_uri: MIXS:0000835 specific_humidity: is_a: environment field @@ -4920,7 +4012,7 @@ slots: description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - pattern: '{float} {unit}' + range: quantity value examples: - value: 15 per kilogram of air comments: @@ -4936,7 +4028,7 @@ slots: - specifications description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' - pattern: '[operation|as built|construction|bid|design|photos]' + range: specific_enum examples: - value: construction comments: @@ -4945,14 +4037,14 @@ slots: - 'Occurrence: 1' - 'Position: 132' - 'This field is used uniquely in: built environment' - range: specific_enum + pattern: '[operation|as built|construction|bid|design|photos]' slot_uri: MIXS:0000836 temp_out: is_a: environment field aliases: - temperature outside house description: The recorded temperature value at sampling time outside - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 degree Celsius comments: @@ -4967,7 +4059,7 @@ slots: aliases: - train line description: The subway line name - pattern: '[red|green|orange]' + range: train_line_enum examples: - value: red comments: @@ -4976,15 +4068,14 @@ slots: - 'Occurrence: 1' - 'Position: 134' - 'This field is used uniquely in: built environment' - range: train_line_enum + pattern: '[red|green|orange]' slot_uri: MIXS:0000837 train_stat_loc: is_a: environment field aliases: - train station collection location description: The train station collection location - pattern: '[south station above ground|south station underground|south station - amtrak|forest hills|riverside]' + range: train_stat_loc_enum examples: - value: forest hills comments: @@ -4993,14 +4084,15 @@ slots: - 'Occurrence: 1' - 'Position: 135' - 'This field is used uniquely in: built environment' - range: train_stat_loc_enum + pattern: '[south station above ground|south station underground|south station + amtrak|forest hills|riverside]' slot_uri: MIXS:0000838 train_stop_loc: is_a: environment field aliases: - train stop collection location description: The train stop collection location - pattern: '[end|mid|downtown]' + range: train_stop_loc_enum examples: - value: end comments: @@ -5009,15 +4101,14 @@ slots: - 'Occurrence: 1' - 'Position: 136' - 'This field is used uniquely in: built environment' - range: train_stop_loc_enum + pattern: '[end|mid|downtown]' slot_uri: MIXS:0000839 vis_media: is_a: environment field aliases: - visual media description: The building visual media - pattern: '[photos|videos|commonly of the building|site context (adjacent buildings, - vegetation, terrain, streets)|interiors|equipment|3D scans]' + range: vis_media_enum examples: - value: 3D scans comments: @@ -5026,14 +4117,15 @@ slots: - 'Occurrence: 1' - 'Position: 137' - 'This field is used uniquely in: built environment' - range: vis_media_enum + pattern: '[photos|videos|commonly of the building|site context (adjacent buildings, + vegetation, terrain, streets)|interiors|equipment|3D scans]' slot_uri: MIXS:0000840 wall_area: is_a: environment field aliases: - wall area description: The total area of the sampled room's walls - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5049,8 +4141,7 @@ slots: - wall construction type description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - pattern: '[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified - fire resistive|fire resistive]' + range: wall_const_type_enum examples: - value: fire resistive comments: @@ -5059,15 +4150,15 @@ slots: - 'Occurrence: 1' - 'Position: 139' - 'This field is used uniquely in: built environment' - range: wall_const_type_enum + pattern: '[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified + fire resistive|fire resistive]' slot_uri: MIXS:0000841 wall_finish_mat: is_a: environment field aliases: - wall finish material description: The material utilized to finish the outer most layer of the wall - pattern: '[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone - facing|acoustical treatment|wood|metal|masonry]' + range: wall_finish_mat_enum examples: - value: wood comments: @@ -5076,14 +4167,15 @@ slots: - 'Occurrence: 1' - 'Position: 140' - 'This field is used uniquely in: built environment' - range: wall_finish_mat_enum + pattern: '[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone + facing|acoustical treatment|wood|metal|masonry]' slot_uri: MIXS:0000842 wall_height: is_a: environment field aliases: - wall height description: The average height of the walls in the sampled room - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5098,7 +4190,7 @@ slots: aliases: - wall location description: The relative location of the wall within the room - pattern: '[north|south|east|west]' + range: wall_loc_enum examples: - value: north comments: @@ -5107,14 +4199,14 @@ slots: - 'Occurrence: 1' - 'Position: 142' - 'This field is used uniquely in: built environment' - range: wall_loc_enum + pattern: '[north|south|east|west]' slot_uri: MIXS:0000843 wall_water_mold: is_a: environment field aliases: - wall signs of water/mold description: Signs of the presence of mold or mildew on a wall - pattern: '[presence of mold visible|no presence of mold visible]' + range: string examples: - value: no presence of mold visible comments: @@ -5123,13 +4215,14 @@ slots: - 'Occurrence: 1' - 'Position: 143' - 'This field is used uniquely in: built environment' + pattern: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000844 wall_surf_treatment: is_a: environment field aliases: - wall surface treatment description: The surface treatment of interior wall - pattern: '[painted|wall paper|no treatment|paneling|stucco|fabric]' + range: wall_surf_treatment_enum examples: - value: paneling comments: @@ -5138,15 +4231,14 @@ slots: - 'Occurrence: 1' - 'Position: 144' - 'This field is used uniquely in: built environment' - range: wall_surf_treatment_enum + pattern: '[painted|wall paper|no treatment|paneling|stucco|fabric]' slot_uri: MIXS:0000845 wall_texture: is_a: environment field aliases: - wall texture description: The feel, appearance, or consistency of a wall surface - pattern: '[crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange - peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' + range: wall_texture_enum examples: - value: popcorn comments: @@ -5155,7 +4247,8 @@ slots: - 'Occurrence: 1' - 'Position: 145' - 'This field is used uniquely in: built environment' - range: wall_texture_enum + pattern: '[crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange + peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' slot_uri: MIXS:0000846 wall_thermal_mass: is_a: environment field @@ -5164,7 +4257,7 @@ slots: description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5179,7 +4272,7 @@ slots: aliases: - water feature size description: The size of the water feature - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5194,7 +4287,7 @@ slots: aliases: - water feature type description: The type of water feature present within the building being sampled - pattern: '[fountain|pool|standing feature|stream|waterfall]' + range: water_feat_type_enum examples: - value: stream comments: @@ -5203,14 +4296,14 @@ slots: - 'Occurrence: 1' - 'Position: 148' - 'This field is used uniquely in: built environment' - range: water_feat_type_enum + pattern: '[fountain|pool|standing feature|stream|waterfall]' slot_uri: MIXS:0000847 weekday: is_a: environment field aliases: - weekday description: The day of the week when sampling occurred - pattern: '[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]' + range: weekday_enum examples: - value: Sunday comments: @@ -5219,14 +4312,14 @@ slots: - 'Occurrence: 1' - 'Position: 149' - 'This field is used uniquely in: built environment' - range: weekday_enum + pattern: '[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]' slot_uri: MIXS:0000848 window_size: is_a: environment field aliases: - window area/size description: The window's length and width - pattern: '{float} {unit} x {float} {unit}' + range: string examples: - value: '' comments: @@ -5235,13 +4328,14 @@ slots: - 'Occurrence: 1' - 'Position: 150' - 'This field is used uniquely in: built environment' + pattern: '{float} {unit} x {float} {unit}' slot_uri: MIXS:0000224 window_cond: is_a: environment field aliases: - window condition description: The physical condition of the window at the time of sampling - pattern: '[damaged|needs repair|new|rupture|visible wear]' + range: window_cond_enum examples: - value: rupture comments: @@ -5250,14 +4344,14 @@ slots: - 'Occurrence: 1' - 'Position: 151' - 'This field is used uniquely in: built environment' - range: window_cond_enum + pattern: '[damaged|needs repair|new|rupture|visible wear]' slot_uri: MIXS:0000849 window_cover: is_a: environment field aliases: - window covering description: The type of window covering - pattern: '[blinds|curtains|none]' + range: window_cover_enum examples: - value: curtains comments: @@ -5266,14 +4360,14 @@ slots: - 'Occurrence: 1' - 'Position: 152' - 'This field is used uniquely in: built environment' - range: window_cover_enum + pattern: '[blinds|curtains|none]' slot_uri: MIXS:0000850 window_horiz_pos: is_a: environment field aliases: - window horizontal position description: The horizontal position of the window on the wall - pattern: '[left|middle|right]' + range: window_horiz_pos_enum examples: - value: middle comments: @@ -5282,14 +4376,14 @@ slots: - 'Occurrence: 1' - 'Position: 153' - 'This field is used uniquely in: built environment' - range: window_horiz_pos_enum + pattern: '[left|middle|right]' slot_uri: MIXS:0000851 window_loc: is_a: environment field aliases: - window location description: The relative location of the window within the room - pattern: '[north|south|east|west]' + range: window_loc_enum examples: - value: west comments: @@ -5298,14 +4392,14 @@ slots: - 'Occurrence: 1' - 'Position: 154' - 'This field is used uniquely in: built environment' - range: window_loc_enum + pattern: '[north|south|east|west]' slot_uri: MIXS:0000852 window_mat: is_a: environment field aliases: - window material description: The type of material used to finish a window - pattern: '[clad|fiberglass|metal|vinyl|wood]' + range: window_mat_enum examples: - value: wood comments: @@ -5314,14 +4408,14 @@ slots: - 'Occurrence: 1' - 'Position: 155' - 'This field is used uniquely in: built environment' - range: window_mat_enum + pattern: '[clad|fiberglass|metal|vinyl|wood]' slot_uri: MIXS:0000853 window_open_freq: is_a: environment field aliases: - window open frequency description: The number of times windows are opened per week - pattern: '{integer}' + range: string examples: - value: '' comments: @@ -5330,13 +4424,14 @@ slots: - 'Occurrence: 1' - 'Position: 156' - 'This field is used uniquely in: built environment' + pattern: '{integer}' slot_uri: MIXS:0000246 window_water_mold: is_a: environment field aliases: - window signs of water/mold description: Signs of the presence of mold or mildew on the window. - pattern: '[presence of mold visible|no presence of mold visible]' + range: string examples: - value: no presence of mold visible comments: @@ -5345,6 +4440,7 @@ slots: - 'Occurrence: 1' - 'Position: 157' - 'This field is used uniquely in: built environment' + pattern: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000854 window_status: is_a: environment field @@ -5352,7 +4448,7 @@ slots: - window status description: Defines whether the windows were open or closed during environmental testing - pattern: '[closed|open]' + range: string examples: - value: open comments: @@ -5361,13 +4457,14 @@ slots: - 'Occurrence: 1' - 'Position: 158' - 'This field is used uniquely in: built environment' + pattern: '[closed|open]' slot_uri: MIXS:0000855 window_type: is_a: environment field aliases: - window type description: The type of windows - pattern: '[single-hung sash window|horizontal sash window|fixed window]' + range: window_type_enum examples: - value: fixed window comments: @@ -5376,14 +4473,14 @@ slots: - 'Occurrence: 1' - 'Position: 159' - 'This field is used uniquely in: built environment' - range: window_type_enum + pattern: '[single-hung sash window|horizontal sash window|fixed window]' slot_uri: MIXS:0000856 window_vert_pos: is_a: environment field aliases: - window vertical position description: The vertical position of the window on the wall - pattern: '[bottom|middle|top|low|middle|high]' + range: window_vert_pos_enum examples: - value: middle comments: @@ -5392,7 +4489,7 @@ slots: - 'Occurrence: 1' - 'Position: 160' - 'This field is used uniquely in: built environment' - range: window_vert_pos_enum + pattern: '[bottom|middle|top|low|middle|high]' slot_uri: MIXS:0000857 ances_data: is_a: environment field @@ -5401,7 +4498,7 @@ slots: description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - pattern: '{text}' + range: string examples: - value: A/3*B comments: @@ -5410,14 +4507,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000247 biol_stat: is_a: environment field aliases: - biological status description: The level of genome modification - pattern: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal - selection|mutant]' + range: biol_stat_enum examples: - value: natural comments: @@ -5426,7 +4523,8 @@ slots: - 'Occurrence: 1' - 'Position: 2' - 'This field is used in: 2 packages: host-associated, plant-associated' - range: biol_stat_enum + pattern: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal + selection|mutant]' slot_uri: MIXS:0000858 genetic_mod: is_a: environment field @@ -5436,7 +4534,7 @@ slots: naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - pattern: '{PMID}|{DOI}|{URL}|{text}' + range: string examples: - value: aox1A transgenic comments: @@ -5445,13 +4543,14 @@ slots: - 'Occurrence: 1' - 'Position: 3' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000859 host_common_name: is_a: environment field aliases: - host common name description: Common name of the host, e.g. Human - pattern: '{text}' + range: string examples: - value: mussel comments: @@ -5460,14 +4559,14 @@ slots: - 'Occurrence: 1' - 'Position: 4' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000248 samp_capt_status: is_a: environment field aliases: - sample capture status description: Reason for the sample - pattern: '[active surveillance in response to an outbreak|active surveillance - not initiated by an outbreak|farm sample|market sample|other]' + range: samp_capt_status_enum examples: - value: farm sample comments: @@ -5476,7 +4575,8 @@ slots: - 'Occurrence: 1' - 'Position: 5' - 'This field is used in: 2 packages: host-associated, plant-associated' - range: samp_capt_status_enum + pattern: '[active surveillance in response to an outbreak|active surveillance + not initiated by an outbreak|farm sample|market sample|other]' slot_uri: MIXS:0000860 samp_dis_stage: is_a: environment field @@ -5484,7 +4584,7 @@ slots: - sample disease stage description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - pattern: '{text}' + range: string examples: - value: infection comments: @@ -5493,13 +4593,14 @@ slots: - 'Occurrence: 1' - 'Position: 6' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000249 host_taxid: is_a: environment field aliases: - host taxid description: NCBI taxon id of the host, e.g. 9606 - pattern: '{NCBI taxid}' + range: string examples: - value: '7955' comments: @@ -5508,6 +4609,7 @@ slots: - 'Occurrence: 1' - 'Position: 7' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{NCBI taxid}' slot_uri: MIXS:0000250 host_subject_id: is_a: environment field @@ -5515,7 +4617,7 @@ slots: - host subject id description: 'A unique identifier by which each subject can be referred to, de-identified, e.g. #131' - pattern: '{text}' + range: string examples: - value: MPI123 comments: @@ -5525,6 +4627,7 @@ slots: - 'Position: 8' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000861 host_age: is_a: environment field @@ -5532,7 +4635,7 @@ slots: - host age description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - pattern: '{float} {unit}' + range: quantity value examples: - value: 10 days comments: @@ -5548,7 +4651,7 @@ slots: aliases: - host life stage description: Description of life stage of host - pattern: '{text}' + range: string examples: - value: adult comments: @@ -5557,13 +4660,14 @@ slots: - 'Occurrence: 1' - 'Position: 10' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000251 host_sex: is_a: environment field aliases: - host sex description: Physical sex of the host - pattern: '[male|female|neuter|hermaphrodite|not determined]' + range: host_sex_enum examples: - value: female comments: @@ -5573,7 +4677,7 @@ slots: - 'Position: 11' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' - range: host_sex_enum + pattern: '[male|female|neuter|hermaphrodite|not determined]' slot_uri: MIXS:0000811 host_disease_stat: is_a: environment field @@ -5583,7 +4687,7 @@ slots: multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - pattern: '{termLabel} {[termID]}|{text}' + range: string examples: - value: rabies [DOID:11260] comments: @@ -5593,13 +4697,14 @@ slots: - 'Position: 12' - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated' + pattern: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000031 host_body_habitat: is_a: environment field aliases: - host body habitat description: Original body habitat where the sample was obtained from - pattern: '{text}' + range: string examples: - value: nasopharynx comments: @@ -5608,6 +4713,7 @@ slots: - 'Occurrence: 1' - 'Position: 14' - 'This field is used uniquely in: host-associated' + pattern: '{text}' slot_uri: MIXS:0000866 host_body_site: is_a: environment field @@ -5617,7 +4723,7 @@ slots: organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - pattern: '{termLabel} {[termID]}' + range: string examples: - value: gill [UBERON:0002535] comments: @@ -5627,6 +4733,7 @@ slots: - 'Position: 15' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{termLabel} {[termID]}' slot_uri: MIXS:0000867 host_body_product: is_a: environment field @@ -5636,7 +4743,7 @@ slots: was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - pattern: '{termLabel} {[termID]}' + range: string examples: - value: Portion of mucus [fma66938] comments: @@ -5646,13 +4753,14 @@ slots: - 'Position: 16' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{termLabel} {[termID]}' slot_uri: MIXS:0000888 host_tot_mass: is_a: environment field aliases: - host total mass description: Total mass of the host at collection, the unit depends on host - pattern: '{float} {unit}' + range: quantity value examples: - value: 2500 gram comments: @@ -5668,7 +4776,7 @@ slots: aliases: - host height description: The height of subject - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.1 meter comments: @@ -5684,7 +4792,7 @@ slots: aliases: - host length description: The length of subject - pattern: '{float} {unit}' + range: quantity value examples: - value: 1 meter comments: @@ -5700,7 +4808,7 @@ slots: - host diet description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - pattern: '{text}' + range: string examples: - value: herbivore comments: @@ -5710,6 +4818,7 @@ slots: - 'Position: 20' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000869 host_last_meal: is_a: environment field @@ -5717,7 +4826,7 @@ slots: - host last meal description: Content of last meal and time since feeding; can include multiple values - pattern: '{text};{duration}' + range: string examples: - value: corn feed;P2H comments: @@ -5727,13 +4836,14 @@ slots: - 'Position: 21' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{text};{duration}' slot_uri: MIXS:0000870 host_growth_cond: is_a: environment field aliases: - host growth conditions description: Literature reference giving growth conditions of the host - pattern: '{PMID}|{DOI}|{URL}|{text}' + range: string examples: - value: https://academic.oup.com/icesjms/article/68/2/349/617247 comments: @@ -5742,13 +4852,14 @@ slots: - 'Occurrence: 1' - 'Position: 22' - 'This field is used uniquely in: host-associated' + pattern: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000871 host_substrate: is_a: environment field aliases: - host substrate description: The growth substrate of the host - pattern: '{text}' + range: string examples: - value: rock comments: @@ -5757,6 +4868,7 @@ slots: - 'Occurrence: 1' - 'Position: 23' - 'This field is used uniquely in: host-associated' + pattern: '{text}' slot_uri: MIXS:0000252 host_family_relationship: is_a: environment field @@ -5764,7 +4876,7 @@ slots: - host family relationship description: Relationships to other hosts in the same study; can include multiple relationships - pattern: '{text};{text}' + range: string examples: - value: offspring;Mussel25 comments: @@ -5774,13 +4886,14 @@ slots: - 'Position: 24' - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{text};{text}' slot_uri: MIXS:0000872 host_infra_specific_name: is_a: environment field aliases: - host infra-specific name description: Taxonomic information about the host below subspecies level - pattern: '{text}' + range: string examples: - value: borealis comments: @@ -5789,6 +4902,7 @@ slots: - 'Occurrence: 1' - 'Position: 25' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000253 host_infra_specific_rank: is_a: environment field @@ -5796,7 +4910,7 @@ slots: - host infra-specific rank description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - pattern: '{text}' + range: string examples: - value: subspecies comments: @@ -5805,13 +4919,14 @@ slots: - 'Occurrence: 1' - 'Position: 26' - 'This field is used in: 2 packages: host-associated, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000254 host_genotype: is_a: environment field aliases: - host genotype description: Observed genotype - pattern: '{text}' + range: string examples: - value: C57BL/6 comments: @@ -5821,6 +4936,7 @@ slots: - 'Position: 27' - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated' + pattern: '{text}' slot_uri: MIXS:0000365 host_phenotype: is_a: environment field @@ -5829,7 +4945,7 @@ slots: description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - pattern: '{termLabel} {[termID]}' + range: string examples: - value: elongated [PATO:0001154] comments: @@ -5839,13 +4955,14 @@ slots: - 'Position: 28' - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated' + pattern: '{termLabel} {[termID]}' slot_uri: MIXS:0000874 host_body_temp: is_a: environment field aliases: - host body temperature description: Core body temperature of the host when sample was collected - pattern: '{float} {unit}' + range: quantity value examples: - value: 15 degree Celsius comments: @@ -5861,7 +4978,7 @@ slots: aliases: - host dry mass description: Measurement of dry mass - pattern: '{float} {unit}' + range: quantity value examples: - value: 500 gram comments: @@ -5876,7 +4993,7 @@ slots: aliases: - host blood pressure diastolic description: Resting diastolic blood pressure, measured as mm mercury - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5891,7 +5008,7 @@ slots: aliases: - host blood pressure systolic description: Resting systolic blood pressure, measured as mm mercury - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -5906,7 +5023,7 @@ slots: aliases: - host color description: The color of host - pattern: '{text}' + range: string examples: - value: '' comments: @@ -5915,13 +5032,14 @@ slots: - 'Occurrence: 1' - 'Position: 33' - 'This field is used uniquely in: host-associated' + pattern: '{text}' slot_uri: MIXS:0000260 host_shape: is_a: environment field aliases: - host shape description: Morphological shape of host - pattern: '{text}' + range: string examples: - value: round comments: @@ -5930,6 +5048,7 @@ slots: - 'Occurrence: 1' - 'Position: 34' - 'This field is used uniquely in: host-associated' + pattern: '{text}' slot_uri: MIXS:0000261 gravidity: is_a: environment field @@ -5937,7 +5056,7 @@ slots: - gravidity description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - pattern: '{boolean};{timestamp}' + range: string examples: - value: yes;due date:2018-05-11 comments: @@ -5946,13 +5065,14 @@ slots: - 'Occurrence: 1' - 'Position: 35' - 'This field is used uniquely in: host-associated' + pattern: '{boolean};{timestamp}' slot_uri: MIXS:0000875 ihmc_medication_code: is_a: environment field aliases: - IHMC medication code description: Can include multiple medication codes - pattern: '{integer}' + range: string examples: - value: '810' comments: @@ -5962,13 +5082,14 @@ slots: - 'Position: 5' - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{integer}' slot_uri: MIXS:0000884 smoker: is_a: environment field aliases: - smoker description: Specification of smoking status - pattern: '{boolean}' + range: string examples: - value: 'yes' comments: @@ -5977,6 +5098,7 @@ slots: - 'Occurrence: 1' - 'Position: 17' - 'This field is used uniquely in: human-associated' + pattern: '{boolean}' slot_uri: MIXS:0000262 host_hiv_stat: is_a: environment field @@ -5984,7 +5106,7 @@ slots: - host HIV status description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - pattern: '{boolean};{boolean}' + range: string examples: - value: yes;yes comments: @@ -5993,6 +5115,7 @@ slots: - 'Occurrence: 1' - 'Position: 18' - 'This field is used uniquely in: human-associated' + pattern: '{boolean};{boolean}' slot_uri: MIXS:0000265 drug_usage: is_a: environment field @@ -6000,7 +5123,7 @@ slots: - drug usage description: Any drug used by subject and the frequency of usage; can include multiple drugs used - pattern: '{text};{integer}/[year|month|week|day|hour]' + range: drug_usage_enum examples: - value: Lipitor;2/day comments: @@ -6009,14 +5132,14 @@ slots: - 'Occurrence: m' - 'Position: 19' - 'This field is used uniquely in: human-associated' - range: drug_usage_enum + pattern: '{text};{integer}/[year|month|week|day|hour]' slot_uri: MIXS:0000894 host_body_mass_index: is_a: environment field aliases: - host body-mass index description: Body mass index, calculated as weight/(height)squared - pattern: '{float} {unit}' + range: quantity value examples: - value: 22 kilogram per square meter comments: @@ -6033,7 +5156,7 @@ slots: - major diet change in last six months description: Specification of major diet changes in the last six months, if yes the change should be specified - pattern: '{boolean};{text}' + range: string examples: - value: yes;vegetarian diet comments: @@ -6042,6 +5165,7 @@ slots: - 'Occurrence: 1' - 'Position: 21' - 'This field is used uniquely in: human-associated' + pattern: '{boolean};{text}' slot_uri: MIXS:0000266 weight_loss_3_month: is_a: environment field @@ -6049,7 +5173,7 @@ slots: - weight loss in last three months description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - pattern: '{boolean};{float} {unit}' + range: string examples: - value: yes;5 kilogram comments: @@ -6058,13 +5182,14 @@ slots: - 'Occurrence: 1' - 'Position: 22' - 'This field is used uniquely in: human-associated' + pattern: '{boolean};{float} {unit}' slot_uri: MIXS:0000295 ihmc_ethnicity: is_a: environment field aliases: - IHMC ethnicity description: Ethnicity of the subject - pattern: '{integer}|{text}' + range: string examples: - value: caucasian comments: @@ -6074,13 +5199,14 @@ slots: - 'Position: 23' - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{integer}|{text}' slot_uri: MIXS:0000895 host_occupation: is_a: environment field aliases: - host occupation description: Most frequent job performed by subject - pattern: '{integer}' + range: string examples: - value: veterinary comments: @@ -6090,6 +5216,7 @@ slots: - 'Position: 24' - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{integer}' slot_uri: MIXS:0000896 pet_farm_animal: is_a: environment field @@ -6098,7 +5225,7 @@ slots: description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - pattern: '{boolean};{text}' + range: string examples: - value: yes; 5 cats comments: @@ -6107,6 +5234,7 @@ slots: - 'Occurrence: m' - 'Position: 25' - 'This field is used uniquely in: human-associated' + pattern: '{boolean};{text}' slot_uri: MIXS:0000267 travel_out_six_month: is_a: environment field @@ -6114,7 +5242,7 @@ slots: - travel outside the country in last six months description: Specification of the countries travelled in the last six months; can include multiple travels - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6123,13 +5251,14 @@ slots: - 'Occurrence: m' - 'Position: 26' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000268 twin_sibling: is_a: environment field aliases: - twin sibling presence description: Specification of twin sibling presence - pattern: '{boolean}' + range: string examples: - value: 'yes' comments: @@ -6138,13 +5267,14 @@ slots: - 'Occurrence: 1' - 'Position: 27' - 'This field is used uniquely in: human-associated' + pattern: '{boolean}' slot_uri: MIXS:0000326 medic_hist_perform: is_a: environment field aliases: - medical history performed description: Whether full medical history was collected - pattern: '{boolean}' + range: string examples: - value: 'TRUE' comments: @@ -6154,6 +5284,7 @@ slots: - 'Position: 28' - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal' + pattern: '{boolean}' slot_uri: MIXS:0000897 study_complt_stat: is_a: environment field @@ -6161,7 +5292,7 @@ slots: - study completion status description: Specification of study completion status, if no the reason should be specified - pattern: '{boolean};[adverse event|non-compliance|lost to follow up|other-specify]' + range: study_complt_stat_enum examples: - value: no;non-compliance comments: @@ -6171,7 +5302,7 @@ slots: - 'Occurrence: 1' - 'Position: 29' - 'This field is used uniquely in: human-associated' - range: study_complt_stat_enum + pattern: '{boolean};[adverse event|non-compliance|lost to follow up|other-specify]' slot_uri: MIXS:0000898 pulmonary_disord: is_a: environment field @@ -6180,7 +5311,7 @@ slots: description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6189,6 +5320,7 @@ slots: - 'Occurrence: m' - 'Position: 30' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000269 nose_throat_disord: is_a: environment field @@ -6198,7 +5330,7 @@ slots: terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6207,6 +5339,7 @@ slots: - 'Occurrence: m' - 'Position: 31' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000270 blood_blood_disord: is_a: environment field @@ -6215,7 +5348,7 @@ slots: description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6224,13 +5357,14 @@ slots: - 'Occurrence: m' - 'Position: 32' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000271 host_pulse: is_a: environment field aliases: - host pulse description: Resting pulse, measured as beats per minute - pattern: '{float} {unit}' + range: quantity value examples: - value: 65 beats per minute comments: @@ -6246,7 +5380,7 @@ slots: aliases: - amniotic fluid/gestation state description: Specification of the gestation state - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6255,13 +5389,14 @@ slots: - 'Occurrence: 1' - 'Position: 36' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000272 maternal_health_stat: is_a: environment field aliases: - amniotic fluid/maternal health status description: Specification of the maternal health status - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6270,13 +5405,14 @@ slots: - 'Occurrence: 1' - 'Position: 37' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000273 foetal_health_stat: is_a: environment field aliases: - amniotic fluid/foetal health status description: Specification of foetal health status, should also include abortion - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6285,13 +5421,14 @@ slots: - 'Occurrence: 1' - 'Position: 38' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000275 amniotic_fluid_color: is_a: environment field aliases: - amniotic fluid/color description: Specification of the color of the amniotic fluid sample - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6300,6 +5437,7 @@ slots: - 'Occurrence: 1' - 'Position: 39' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000276 urogenit_tract_disor: is_a: environment field @@ -6308,7 +5446,7 @@ slots: description: 'History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). ' - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6317,13 +5455,14 @@ slots: - 'Occurrence: m' - 'Position: 41' - 'This field is used uniquely in: human-associated' + pattern: '{text}' slot_uri: MIXS:0000278 urine_collect_meth: is_a: environment field aliases: - urine/collection method description: Specification of urine collection method - pattern: '[clean catch|catheter]' + range: string examples: - value: catheter comments: @@ -6332,6 +5471,7 @@ slots: - 'Occurrence: 1' - 'Position: 43' - 'This field is used uniquely in: human-associated' + pattern: '[clean catch|catheter]' slot_uri: MIXS:0000899 gastrointest_disord: is_a: environment field @@ -6341,7 +5481,7 @@ slots: disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6350,6 +5490,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: human-gut' + pattern: '{text}' slot_uri: MIXS:0000280 liver_disord: is_a: environment field @@ -6358,7 +5499,7 @@ slots: description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6367,13 +5508,14 @@ slots: - 'Occurrence: m' - 'Position: 2' - 'This field is used uniquely in: human-gut' + pattern: '{text}' slot_uri: MIXS:0000282 special_diet: is_a: environment field aliases: - special diet description: Specification of special diet; can include multiple special diets - pattern: '[low carb|reduced calorie|vegetarian|other(to be specified)]' + range: special_diet_enum examples: - value: other:vegan comments: @@ -6382,7 +5524,7 @@ slots: - 'Occurrence: m' - 'Position: 3' - 'This field is used uniquely in: human-gut' - range: special_diet_enum + pattern: '[low carb|reduced calorie|vegetarian|other(to be specified)]' slot_uri: MIXS:0000905 nose_mouth_teeth_throat_disord: is_a: environment field @@ -6393,7 +5535,7 @@ slots: http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6402,13 +5544,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: human-oral' + pattern: '{text}' slot_uri: MIXS:0000283 time_last_toothbrush: is_a: environment field aliases: - time since last toothbrushing description: Specification of the time since last toothbrushing - pattern: '{duration}' + range: string examples: - value: P2H45M comments: @@ -6417,6 +5560,7 @@ slots: - 'Occurrence: 1' - 'Position: 2' - 'This field is used uniquely in: human-oral' + pattern: '{duration}' slot_uri: MIXS:0000924 dermatology_disord: is_a: environment field @@ -6425,7 +5569,7 @@ slots: description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6434,13 +5578,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: human-skin' + pattern: '{text}' slot_uri: MIXS:0000284 time_since_last_wash: is_a: environment field aliases: - time since last wash description: Specification of the time since last wash - pattern: '{duration}' + range: string examples: - value: P1D comments: @@ -6449,13 +5594,14 @@ slots: - 'Occurrence: 1' - 'Position: 2' - 'This field is used uniquely in: human-skin' + pattern: '{duration}' slot_uri: MIXS:0000943 dominant_hand: is_a: environment field aliases: - dominant hand description: Dominant hand of the subject - pattern: '[left|right|ambidextrous]' + range: dominant_hand_enum examples: - value: right comments: @@ -6464,14 +5610,14 @@ slots: - 'Occurrence: 1' - 'Position: 3' - 'This field is used uniquely in: human-skin' - range: dominant_hand_enum + pattern: '[left|right|ambidextrous]' slot_uri: MIXS:0000944 menarche: is_a: environment field aliases: - menarche description: Date of most recent menstruation - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -6480,13 +5626,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: human-vaginal' + pattern: '{timestamp}' slot_uri: MIXS:0000965 sexual_act: is_a: environment field aliases: - sexual activity description: Current sexual partner and frequency of sex - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6495,13 +5642,14 @@ slots: - 'Occurrence: 1' - 'Position: 2' - 'This field is used uniquely in: human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000285 pregnancy: is_a: environment field aliases: - pregnancy description: Date due of pregnancy - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -6510,13 +5658,14 @@ slots: - 'Occurrence: 1' - 'Position: 3' - 'This field is used uniquely in: human-vaginal' + pattern: '{timestamp}' slot_uri: MIXS:0000966 douche: is_a: environment field aliases: - douche description: Date of most recent douche - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -6525,13 +5674,14 @@ slots: - 'Occurrence: 1' - 'Position: 4' - 'This field is used uniquely in: human-vaginal' + pattern: '{timestamp}' slot_uri: MIXS:0000967 birth_control: is_a: environment field aliases: - birth control description: Specification of birth control medication used - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6540,13 +5690,14 @@ slots: - 'Occurrence: 1' - 'Position: 5' - 'This field is used uniquely in: human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000286 menopause: is_a: environment field aliases: - menopause description: Date of onset of menopause - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -6555,6 +5706,7 @@ slots: - 'Occurrence: 1' - 'Position: 6' - 'This field is used uniquely in: human-vaginal' + pattern: '{timestamp}' slot_uri: MIXS:0000968 hrt: is_a: environment field @@ -6562,7 +5714,7 @@ slots: - HRT description: Whether subject had hormone replacement theraphy, and if yes start date - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -6571,13 +5723,14 @@ slots: - 'Occurrence: 1' - 'Position: 7' - 'This field is used uniquely in: human-vaginal' + pattern: '{timestamp}' slot_uri: MIXS:0000969 hysterectomy: is_a: environment field aliases: - hysterectomy description: Specification of whether hysterectomy was performed - pattern: '{boolean}' + range: string examples: - value: 'no' comments: @@ -6586,6 +5739,7 @@ slots: - 'Occurrence: 1' - 'Position: 8' - 'This field is used uniquely in: human-vaginal' + pattern: '{boolean}' slot_uri: MIXS:0000287 gynecologic_disord: is_a: environment field @@ -6594,7 +5748,7 @@ slots: description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6603,6 +5757,7 @@ slots: - 'Occurrence: m' - 'Position: 9' - 'This field is used uniquely in: human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000288 urogenit_disord: is_a: environment field @@ -6612,7 +5767,7 @@ slots: The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). ' - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6621,6 +5776,7 @@ slots: - 'Occurrence: m' - 'Position: 10' - 'This field is used uniquely in: human-vaginal' + pattern: '{text}' slot_uri: MIXS:0000289 hcr: is_a: environment field @@ -6633,8 +5789,7 @@ slots: includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - pattern: '[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight - Gas Reservoir|other]' + range: hcr_enum examples: - value: Oil Sand comments: @@ -6644,7 +5799,8 @@ slots: - 'Position: 1' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: hcr_enum + pattern: '[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight + Gas Reservoir|other]' slot_uri: MIXS:0000988 hc_produced: is_a: environment field @@ -6652,7 +5808,7 @@ slots: - hydrocarbon type produced description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - pattern: '[Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other]' + range: hc_produced_enum examples: - value: Gas comments: @@ -6662,14 +5818,14 @@ slots: - 'Position: 2' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: hc_produced_enum + pattern: '[Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other]' slot_uri: MIXS:0000989 basin: is_a: environment field aliases: - basin name description: Name of the basin (e.g. Campos) - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6679,13 +5835,14 @@ slots: - 'Position: 3' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000290 field: is_a: environment field aliases: - field name description: Name of the hydrocarbon field (e.g. Albacora) - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6695,13 +5852,14 @@ slots: - 'Position: 4' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000291 reservoir: is_a: environment field aliases: - reservoir name description: Name of the reservoir (e.g. Carapebus) - pattern: '{text}' + range: string examples: - value: '' comments: @@ -6711,13 +5869,14 @@ slots: - 'Position: 5' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000303 hcr_temp: is_a: environment field aliases: - hydrocarbon resource original temperature description: Original temperature of the hydrocarbon resource - pattern: '{float} - {float} {unit}' + range: string examples: - value: 150-295 degree Celsius comments: @@ -6727,6 +5886,7 @@ slots: - 'Position: 6' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{float} - {float} {unit}' slot_uri: MIXS:0000393 tvdss_of_hcr_temp: is_a: environment field @@ -6734,7 +5894,7 @@ slots: - depth (TVDSS) of hydrocarbon resource temperature description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6750,7 +5910,7 @@ slots: aliases: - hydrocarbon resource original pressure description: Original pressure of the hydrocarbon resource - pattern: '{float} - {float} {unit}' + range: string examples: - value: '' comments: @@ -6760,6 +5920,7 @@ slots: - 'Position: 8' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{float} - {float} {unit}' slot_uri: MIXS:0000395 tvdss_of_hcr_pressure: is_a: environment field @@ -6767,7 +5928,7 @@ slots: - depth (TVDSS) of hydrocarbon resource pressure description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6784,7 +5945,7 @@ slots: - permeability description: 'Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' - pattern: '{integer} - {integer} {unit}' + range: string examples: - value: '' comments: @@ -6793,6 +5954,7 @@ slots: - 'Occurrence: 1' - 'Position: 10' - 'This field is used uniquely in: hydrocarbon resources-cores' + pattern: '{integer} - {integer} {unit}' slot_uri: MIXS:0000404 porosity: is_a: environment field @@ -6800,7 +5962,7 @@ slots: - porosity description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - pattern: '{float} - {float} {unit}' + range: string examples: - value: '' comments: @@ -6809,6 +5971,7 @@ slots: - 'Occurrence: 1' - 'Position: 11' - 'This field is used in: 2 packages: hydrocarbon resources-cores, sediment' + pattern: '{float} - {float} {unit}' slot_uri: MIXS:0000211 lithology: is_a: environment field @@ -6816,7 +5979,7 @@ slots: - lithology description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field' - pattern: '[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]' + range: lithology_enum examples: - value: Volcanic comments: @@ -6826,7 +5989,7 @@ slots: - 'Position: 12' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: lithology_enum + pattern: '[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]' slot_uri: MIXS:0000990 depos_env: is_a: environment field @@ -6834,10 +5997,7 @@ slots: - depositional environment description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - pattern: '[Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|Continental - - Lacustrine|Transitional - Deltaic|Transitional - Tidal|Transitional - Lagoonal|Transitional - - Beach|Transitional - Lake|Marine - Shallow|Marine - Deep|Marine - Reef|Other - - Evaporite|Other - Glacial|Other - Volcanic|other]' + range: depos_env_enum examples: - value: Continental - Alluvial comments: @@ -6847,7 +6007,10 @@ slots: - 'Position: 13' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: depos_env_enum + pattern: '[Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|Continental + - Lacustrine|Transitional - Deltaic|Transitional - Tidal|Transitional - Lagoonal|Transitional + - Beach|Transitional - Lake|Marine - Shallow|Marine - Deep|Marine - Reef|Other + - Evaporite|Other - Glacial|Other - Volcanic|other]' slot_uri: MIXS:0000992 hcr_geol_age: is_a: environment field @@ -6855,7 +6018,7 @@ slots: - hydrocarbon resource geological age description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' - pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' + range: hcr_geol_age_enum examples: - value: Silurian comments: @@ -6865,14 +6028,14 @@ slots: - 'Position: 14' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: hcr_geol_age_enum + pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' slot_uri: MIXS:0000993 owc_tvdss: is_a: environment field aliases: - oil water contact depth description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6888,7 +6051,7 @@ slots: - formation water salinity description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6904,7 +6067,7 @@ slots: aliases: - sulfate in formation water description: Original sulfate concentration in the hydrocarbon resource - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6920,7 +6083,7 @@ slots: aliases: - vfa in formation water description: Original volatile fatty acid concentration in the hydrocarbon resource - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -6940,7 +6103,7 @@ slots: fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field' - pattern: '[Type I|Type II|Type III|Type IV|other]' + range: sr_kerog_type_enum examples: - value: Type IV comments: @@ -6949,7 +6112,7 @@ slots: - 'Occurrence: 1' - 'Position: 19' - 'This field is used uniquely in: hydrocarbon resources-cores' - range: sr_kerog_type_enum + pattern: '[Type I|Type II|Type III|Type IV|other]' slot_uri: MIXS:0000994 sr_lithology: is_a: environment field @@ -6957,7 +6120,7 @@ slots: - source rock lithology description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - pattern: '[Clastic|Carbonate|Coal|Biosilicieous|other]' + range: sr_lithology_enum examples: - value: Coal comments: @@ -6966,7 +6129,7 @@ slots: - 'Occurrence: 1' - 'Position: 20' - 'This field is used uniquely in: hydrocarbon resources-cores' - range: sr_lithology_enum + pattern: '[Clastic|Carbonate|Coal|Biosilicieous|other]' slot_uri: MIXS:0000995 sr_dep_env: is_a: environment field @@ -6974,7 +6137,7 @@ slots: - source rock depositional environment description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - pattern: '[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]' + range: sr_dep_env_enum examples: - value: Marine comments: @@ -6983,7 +6146,7 @@ slots: - 'Occurrence: 1' - 'Position: 21' - 'This field is used uniquely in: hydrocarbon resources-cores' - range: sr_dep_env_enum + pattern: '[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]' slot_uri: MIXS:0000996 sr_geol_age: is_a: environment field @@ -6991,7 +6154,7 @@ slots: - source rock geological age description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' - pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' + range: sr_geol_age_enum examples: - value: Silurian comments: @@ -7000,14 +6163,14 @@ slots: - 'Occurrence: 1' - 'Position: 22' - 'This field is used uniquely in: hydrocarbon resources-cores' - range: sr_geol_age_enum + pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' slot_uri: MIXS:0000997 samp_well_name: is_a: environment field aliases: - sample well name description: Name of the well (e.g. BXA1123) where sample was taken - pattern: '{text}' + range: string examples: - value: '' comments: @@ -7017,6 +6180,7 @@ slots: - 'Position: 35' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000296 win: is_a: environment field @@ -7026,7 +6190,7 @@ slots: Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' - pattern: '{text}' + range: string examples: - value: '' comments: @@ -7036,6 +6200,7 @@ slots: - 'Position: 36' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000297 samp_type: is_a: environment field @@ -7045,9 +6210,7 @@ slots: rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - pattern: '[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid - deposit|produced fluid|produced water|injected water|water from treatment plant|fresh - water|sea water|drilling fluid|procedural blank|positive control|negative control|other]' + range: samp_type_enum examples: - value: solid deposit comments: @@ -7057,7 +6220,9 @@ slots: - 'Position: 37' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: samp_type_enum + pattern: '[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid + deposit|produced fluid|produced water|injected water|water from treatment plant|fresh + water|sea water|drilling fluid|procedural blank|positive control|negative control|other]' slot_uri: MIXS:0000998 samp_subtype: is_a: environment field @@ -7066,7 +6231,7 @@ slots: description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - pattern: '[oil phase|water phase|biofilm|not applicable|other]' + range: samp_subtype_enum examples: - value: biofilm comments: @@ -7076,14 +6241,14 @@ slots: - 'Position: 38' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' - range: samp_subtype_enum + pattern: '[oil phase|water phase|biofilm|not applicable|other]' slot_uri: MIXS:0000999 pressure: is_a: environment field aliases: - pressure description: Pressure to which the sample is subject to, in atmospheres - pattern: '{float} {unit}' + range: quantity value examples: - value: 50 atmosphere comments: @@ -7102,7 +6267,7 @@ slots: description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - pattern: '{float}-{float} {unit}' + range: string examples: - value: '' comments: @@ -7111,6 +6276,7 @@ slots: - 'Occurrence: 1' - 'Position: 42' - 'This field is used uniquely in: hydrocarbon resources-cores' + pattern: '{float}-{float} {unit}' slot_uri: MIXS:0000409 samp_md: is_a: environment field @@ -7122,7 +6288,7 @@ slots: same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - pattern: '{float} {unit};[GL|DF|RT|KB|MSL|other]' + range: samp_md_enum examples: - value: 1534 meter;MSL comments: @@ -7131,7 +6297,7 @@ slots: - 'Occurrence: 1' - 'Position: 43' - 'This field is used uniquely in: hydrocarbon resources-cores' - range: samp_md_enum + pattern: '{float} {unit};[GL|DF|RT|KB|MSL|other]' slot_uri: MIXS:0000413 samp_transport_cond: is_a: environment field @@ -7139,7 +6305,7 @@ slots: - sample transport conditions description: "Sample transport duration (in days or hrs) and temperature the sample\ \ was exposed to (e.g. 5.5 days; 20 \xAC\u221EC)" - pattern: '{float} {unit};{float} {unit}' + range: string examples: - value: 5 days;-20 degree Celsius comments: @@ -7149,6 +6315,7 @@ slots: - 'Position: 47' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 organism_count_qpcr_info: is_a: environment field @@ -7159,8 +6326,7 @@ slots: FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)' - pattern: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles' + range: string examples: - value: '' comments: @@ -7172,6 +6338,8 @@ slots: - 'Position: 53' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes; total cycles' slot_uri: MIXS:0000099 ph: is_a: environment field @@ -7179,7 +6347,7 @@ slots: - pH description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - pattern: '{float}' + range: double examples: - value: '7.2' comments: @@ -7197,7 +6365,7 @@ slots: - alkalinity description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - pattern: '{float} {unit}' + range: quantity value examples: - value: 50 milligram per liter comments: @@ -7214,7 +6382,7 @@ slots: aliases: - alkalinity method description: Method used for alkalinity measurement - pattern: '{text}' + range: string examples: - value: titration comments: @@ -7224,13 +6392,14 @@ slots: - 'Position: 57' - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water' + pattern: '{text}' slot_uri: MIXS:0000298 sulfate: is_a: environment field aliases: - sulfate description: Concentration of sulfate in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 micromole per liter comments: @@ -7247,7 +6416,7 @@ slots: aliases: - sulfide description: Concentration of sulfide in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 2 micromole per liter comments: @@ -7264,7 +6433,7 @@ slots: aliases: - total sulfur description: Concentration of total sulfur in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7280,7 +6449,7 @@ slots: aliases: - nitrate description: Concentration of nitrate in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 65 micromole per liter comments: @@ -7297,7 +6466,7 @@ slots: aliases: - nitrite description: Concentration of nitrite in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.5 micromole per liter comments: @@ -7314,7 +6483,7 @@ slots: aliases: - ammonium description: Concentration of ammonium in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 1.5 milligram per liter comments: @@ -7333,7 +6502,7 @@ slots: description: 'Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen' - pattern: '{float} {unit}' + range: quantity value examples: - value: 50 micromole per liter comments: @@ -7349,7 +6518,7 @@ slots: aliases: - dissolved iron description: Concentration of dissolved iron in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7365,7 +6534,7 @@ slots: aliases: - sodium description: Sodium concentration in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 10.5 milligram per liter comments: @@ -7382,7 +6551,7 @@ slots: aliases: - chloride description: Concentration of chloride in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 5000 milligram per liter comments: @@ -7399,7 +6568,7 @@ slots: aliases: - potassium description: Concentration of potassium in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 463 milligram per liter comments: @@ -7416,7 +6585,7 @@ slots: aliases: - magnesium description: Concentration of magnesium in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 52.8 micromole per kilogram comments: @@ -7433,7 +6602,7 @@ slots: aliases: - calcium description: Concentration of calcium in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.2 micromole per liter comments: @@ -7450,7 +6619,7 @@ slots: aliases: - total iron description: Concentration of total iron in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7467,7 +6636,7 @@ slots: - dissolved organic carbon description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - pattern: '{float} {unit}' + range: quantity value examples: - value: 197 micromole per liter comments: @@ -7484,7 +6653,7 @@ slots: - dissolved inorganic carbon description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - pattern: '{float} {unit}' + range: quantity value examples: - value: 2059 micromole per kilogram comments: @@ -7501,7 +6670,7 @@ slots: aliases: - dissolved inorganic phosphorus description: Concentration of dissolved inorganic phosphorus in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 56.5 micromole per liter comments: @@ -7518,7 +6687,7 @@ slots: - total phosphorus description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.03 milligram per liter comments: @@ -7535,7 +6704,7 @@ slots: - suspended solids description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -7546,6 +6715,7 @@ slots: - 'Position: 76' - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000150 density: is_a: environment field @@ -7553,7 +6723,7 @@ slots: - density description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - pattern: '{float} {unit}' + range: quantity value examples: - value: 1000 kilogram per cubic meter comments: @@ -7571,7 +6741,7 @@ slots: - dissolved carbon dioxide description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 milligram per liter comments: @@ -7589,7 +6759,7 @@ slots: - dissolved oxygen in fluids description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7605,7 +6775,7 @@ slots: aliases: - volatile fatty acids description: Concentration of Volatile Fatty Acids in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7621,7 +6791,7 @@ slots: aliases: - benzene description: Concentration of benzene in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7637,7 +6807,7 @@ slots: aliases: - toluene description: Concentration of toluene in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7653,7 +6823,7 @@ slots: aliases: - ethylbenzene description: Concentration of ethylbenzene in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7669,7 +6839,7 @@ slots: aliases: - xylene description: Concentration of xylene in the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7687,7 +6857,7 @@ slots: description: "API gravity is a measure of how heavy or light a petroleum liquid\ \ is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\ \ 31.1\xAC\u221E API)" - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7706,7 +6876,7 @@ slots: \ is determined by the amount of\xAC\u2020potassium hydroxide\xAC\u2020in milligrams\ \ that is needed to neutralize the acids in one gram of oil.\xAC\u2020It is\ \ an important quality measurement of\xAC\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7724,7 +6894,7 @@ slots: description: "A measure of oil's resistance\xAC\u2020to gradual deformation by\xAC\ \u2020shear stress\xAC\u2020or\xAC\u2020tensile stress (e.g. 3.5 cp; 100 \xAC\ \u221EC)" - pattern: '{float} {unit};{float} {unit}' + range: string examples: - value: '' comments: @@ -7734,6 +6904,7 @@ slots: - 'Position: 87' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 pour_point: is_a: environment field @@ -7743,7 +6914,7 @@ slots: \ characteristics. In crude oil a high\xAC\u2020pour point\xAC\u2020is generally\ \ associated with a high paraffin content, typically found in crude deriving\ \ from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7763,7 +6934,7 @@ slots: \ polarizability and polarity. There are three main methods to obtain SARA results.\ \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -7773,6 +6944,7 @@ slots: - 'Position: 89' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000131 aromatics_pc: is_a: environment field @@ -7783,7 +6955,7 @@ slots: \ polarizability and polarity. There are three main methods to obtain SARA results.\ \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -7793,6 +6965,7 @@ slots: - 'Position: 90' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000133 resins_pc: is_a: environment field @@ -7803,7 +6976,7 @@ slots: \ polarizability and polarity. There are three main methods to obtain SARA results.\ \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -7813,6 +6986,7 @@ slots: - 'Position: 91' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000134 asphaltenes_pc: is_a: environment field @@ -7823,7 +6997,7 @@ slots: \ polarizability and polarity. There are three main methods to obtain SARA results.\ \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -7833,6 +7007,7 @@ slots: - 'Position: 92' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000135 additional_info: is_a: environment field @@ -7840,7 +7015,7 @@ slots: - additional info description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - pattern: '{text}' + range: string examples: - value: '' comments: @@ -7850,13 +7025,14 @@ slots: - 'Position: 94' - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs' + pattern: '{text}' slot_uri: MIXS:0000300 prod_start_date: is_a: environment field aliases: - production start date description: Date of field's first production - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -7865,13 +7041,14 @@ slots: - 'Occurrence: 1' - 'Position: 23' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{timestamp}' slot_uri: MIXS:0001008 prod_rate: is_a: environment field aliases: - production rate description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7886,7 +7063,7 @@ slots: aliases: - water production rate description: Water production rates per well (e.g. 987 m3 / day) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7902,7 +7079,7 @@ slots: - water cut description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7918,7 +7095,7 @@ slots: - injection water fraction description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -7936,8 +7113,7 @@ slots: for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - pattern: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer - Addition|Surfactant Addition|Not Applicable|other];{timestamp}' + range: add_recov_method_enum examples: - value: Polymer Addition;2018-06-21T14:30Z comments: @@ -7946,7 +7122,8 @@ slots: - 'Occurrence: 1' - 'Position: 28' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - range: add_recov_method_enum + pattern: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer + Addition|Surfactant Addition|Not Applicable|other];{timestamp}' slot_uri: MIXS:0001009 iw_bt_date_well: is_a: environment field @@ -7954,7 +7131,7 @@ slots: - injection water breakthrough date of specific well description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - pattern: '{timestamp}' + range: string examples: - value: '2018-05-11' comments: @@ -7963,6 +7140,7 @@ slots: - 'Occurrence: 1' - 'Position: 29' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{timestamp}' slot_uri: MIXS:0001010 biocide: is_a: environment field @@ -7970,7 +7148,7 @@ slots: - biocide administration description: List of biocides (commercial name of product and supplier) and date of administration - pattern: '{text};{text};{timestamp}' + range: string examples: - value: ALPHA 1427;Baker Hughes;2008-01-23 comments: @@ -7979,6 +7157,7 @@ slots: - 'Occurrence: 1' - 'Position: 30' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{text};{text};{timestamp}' slot_uri: MIXS:0001011 biocide_admin_method: is_a: environment field @@ -7987,7 +7166,7 @@ slots: description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' + range: string examples: - value: '' comments: @@ -7996,6 +7175,7 @@ slots: - 'Occurrence: 1' - 'Position: 31' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' slot_uri: MIXS:0000456 chem_treatment: is_a: environment field @@ -8006,7 +7186,7 @@ slots: demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - pattern: '{text};{text};{timestamp}' + range: string examples: - value: ACCENT 1125;DOW;2010-11-17 comments: @@ -8015,6 +7195,7 @@ slots: - 'Occurrence: 1' - 'Position: 32' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{text};{text};{timestamp}' slot_uri: MIXS:0001012 chem_treatment_method: is_a: environment field @@ -8023,7 +7204,7 @@ slots: description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' + range: string examples: - value: '' comments: @@ -8032,6 +7213,7 @@ slots: - 'Occurrence: 1' - 'Position: 33' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' slot_uri: MIXS:0000457 samp_loc_corr_rate: is_a: environment field @@ -8044,7 +7226,7 @@ slots: of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - pattern: '{float} - {float} {unit}' + range: string examples: - value: '' comments: @@ -8053,6 +7235,7 @@ slots: - 'Occurrence: 1' - 'Position: 34' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{float} - {float} {unit}' slot_uri: MIXS:0000136 samp_collection_point: is_a: environment field @@ -8061,7 +7244,7 @@ slots: description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - pattern: '[well|test well|drilling rig|wellhead|separator|storage tank|other]' + range: samp_collection_point_enum examples: - value: well comments: @@ -8070,7 +7253,7 @@ slots: - 'Occurrence: 1' - 'Position: 39' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - range: samp_collection_point_enum + pattern: '[well|test well|drilling rig|wellhead|separator|storage tank|other]' slot_uri: MIXS:0001015 samp_preserv: is_a: environment field @@ -8078,7 +7261,7 @@ slots: - preservative added to sample description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -8087,13 +7270,14 @@ slots: - 'Occurrence: 1' - 'Position: 46' - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000463 alkyl_diethers: is_a: environment field aliases: - alkyl diethers description: Concentration of alkyl diethers - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.005 mole per liter comments: @@ -8108,7 +7292,7 @@ slots: aliases: - aminopeptidase activity description: Measurement of aminopeptidase activity - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.269 mole per liter per hour comments: @@ -8123,7 +7307,7 @@ slots: aliases: - bacterial carbon production description: Measurement of bacterial carbon production - pattern: '{float} {unit}' + range: quantity value examples: - value: 2.53 microgram per liter per hour comments: @@ -8139,7 +7323,7 @@ slots: - biomass description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - pattern: '{text};{float} {unit}' + range: string examples: - value: total;20 gram comments: @@ -8149,13 +7333,14 @@ slots: - 'Position: 1' - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000174 bishomohopanol: is_a: environment field aliases: - bishomohopanol description: Concentration of bishomohopanol - pattern: '{float} {unit}' + range: quantity value examples: - value: 14 microgram per liter comments: @@ -8170,7 +7355,7 @@ slots: aliases: - bromide description: Concentration of bromide - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.05 parts per million comments: @@ -8186,7 +7371,7 @@ slots: aliases: - carbon/nitrogen ratio description: Ratio of amount or concentrations of carbon to nitrogen - pattern: '{float} {unit}' + range: quantity value examples: - value: '0.417361111' comments: @@ -8201,7 +7386,7 @@ slots: aliases: - chlorophyll description: Concentration of chlorophyll - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 milligram per cubic meter comments: @@ -8218,7 +7403,7 @@ slots: - diether lipids description: Concentration of diether lipids; can include multiple types of diether lipids - pattern: '{text};{float} {unit}' + range: string examples: - value: 0.2 nanogram per liter comments: @@ -8228,13 +7413,14 @@ slots: - 'Position: 1' - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000178 diss_hydrogen: is_a: environment field aliases: - dissolved hydrogen description: Concentration of dissolved hydrogen - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.3 micromole per liter comments: @@ -8251,7 +7437,7 @@ slots: - dissolved organic nitrogen description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.05 micromole per liter comments: @@ -8267,7 +7453,7 @@ slots: aliases: - dissolved oxygen description: Concentration of dissolved oxygen - pattern: '{float} {unit}' + range: quantity value examples: - value: 175 micromole per kilogram comments: @@ -8283,7 +7469,7 @@ slots: aliases: - glucosidase activity description: Measurement of glucosidase activity - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 mol per liter per hour comments: @@ -8298,7 +7484,7 @@ slots: aliases: - mean friction velocity description: Measurement of mean friction velocity - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.5 meter per second comments: @@ -8313,7 +7499,7 @@ slots: aliases: - mean peak friction velocity description: Measurement of mean peak friction velocity - pattern: '{float} {unit}' + range: quantity value examples: - value: 1 meter per second comments: @@ -8328,7 +7514,7 @@ slots: aliases: - n-alkanes description: Concentration of n-alkanes; can include multiple n-alkanes - pattern: '{text};{float} {unit}' + range: string examples: - value: n-hexadecane;100 milligram per liter comments: @@ -8337,13 +7523,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000503 nitro: is_a: environment field aliases: - nitrogen description: Concentration of nitrogen (total) - pattern: '{float} {unit}' + range: quantity value examples: - value: 4.2 micromole per liter comments: @@ -8359,7 +7546,7 @@ slots: aliases: - organic carbon description: Concentration of organic carbon - pattern: '{float} {unit}' + range: quantity value examples: - value: 1.5 microgram per liter comments: @@ -8375,7 +7562,7 @@ slots: aliases: - organic matter description: Concentration of organic matter - pattern: '{float} {unit}' + range: quantity value examples: - value: 1.75 milligram per cubic meter comments: @@ -8391,7 +7578,7 @@ slots: aliases: - organic nitrogen description: Concentration of organic nitrogen - pattern: '{float} {unit}' + range: quantity value examples: - value: 4 micromole per liter comments: @@ -8407,7 +7594,7 @@ slots: aliases: - particulate organic carbon description: Concentration of particulate organic carbon - pattern: '{float} {unit}' + range: quantity value examples: - value: 1.92 micromole per liter comments: @@ -8422,7 +7609,7 @@ slots: aliases: - petroleum hydrocarbon description: Concentration of petroleum hydrocarbon - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.05 micromole per liter comments: @@ -8437,7 +7624,7 @@ slots: aliases: - phaeopigments description: Concentration of phaeopigments; can include multiple phaeopigments - pattern: '{text};{float} {unit}' + range: string examples: - value: 2.5 milligram per cubic meter comments: @@ -8446,13 +7633,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000180 phosphate: is_a: environment field aliases: - phosphate description: Concentration of phosphate - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.7 micromole per liter comments: @@ -8468,7 +7656,7 @@ slots: aliases: - phospholipid fatty acid description: Concentration of phospholipid fatty acids; can include multiple values - pattern: '{text};{float} {unit}' + range: string examples: - value: 2.98 milligram per liter comments: @@ -8478,6 +7666,7 @@ slots: - 'Position: 1' - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000181 redox_potential: is_a: environment field @@ -8485,7 +7674,7 @@ slots: - redox potential description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - pattern: '{float} {unit}' + range: quantity value examples: - value: 300 millivolt comments: @@ -8505,7 +7694,7 @@ slots: the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - pattern: '{float} {unit}' + range: quantity value examples: - value: 25 practical salinity unit comments: @@ -8521,7 +7710,7 @@ slots: aliases: - silicate description: Concentration of silicate - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.05 micromole per liter comments: @@ -8537,7 +7726,7 @@ slots: aliases: - total carbon description: Total carbon content - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -8552,7 +7741,7 @@ slots: aliases: - total nitrogen content description: Total nitrogen content of the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -8568,7 +7757,7 @@ slots: - total organic carbon description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -8584,7 +7773,7 @@ slots: - turbidity description: Measure of the amount of cloudiness or haziness in water caused by individual particles - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.3 nephelometric turbidity units comments: @@ -8599,7 +7788,7 @@ slots: aliases: - water content description: Water content measurement - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -8614,7 +7803,7 @@ slots: aliases: - water current description: Measurement of magnitude and direction of flow within a fluid - pattern: '{float} {unit}' + range: quantity value examples: - value: 10 cubic meter per second comments: @@ -8633,7 +7822,7 @@ slots: should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8642,6 +7831,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 antibiotic_regm: is_a: environment field @@ -8652,7 +7842,7 @@ slots: including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8661,6 +7851,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000553 biotic_regm: is_a: environment field @@ -8668,7 +7859,7 @@ slots: - biotic regimen description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - pattern: '{text}' + range: string examples: - value: sample inoculated with Rhizobium spp. Culture comments: @@ -8677,6 +7868,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text}' slot_uri: MIXS:0001038 chem_mutagen: is_a: environment field @@ -8686,7 +7878,7 @@ slots: amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8695,6 +7887,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000555 climate_environment: is_a: environment field @@ -8704,7 +7897,7 @@ slots: regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - pattern: '{text};{Rn/start_time/end_time/duration}' + range: string examples: - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8713,6 +7906,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 cult_root_med: is_a: environment field @@ -8722,7 +7916,7 @@ slots: medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - pattern: '{text}|{PMID}|{DOI}|{URL}' + range: string examples: - value: http://himedialabs.com/TD/PT158.pdf comments: @@ -8731,6 +7925,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text}|{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001041 fertilizer_regm: is_a: environment field @@ -8741,7 +7936,7 @@ slots: how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M comments: @@ -8750,6 +7945,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000556 fungicide_regm: is_a: environment field @@ -8759,7 +7955,7 @@ slots: the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8768,6 +7964,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000557 gaseous_environment: is_a: environment field @@ -8776,7 +7973,7 @@ slots: description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8786,6 +7983,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 gravity: is_a: environment field @@ -8796,7 +7994,7 @@ slots: treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8805,6 +8003,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000559 growth_facil: is_a: environment field @@ -8813,7 +8012,7 @@ slots: description: 'Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' - pattern: '{text}|{termLabel} {[termID]}' + range: string examples: - value: Growth chamber [CO_715:0000189] comments: @@ -8822,13 +8021,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text}|{termLabel} {[termID]}' slot_uri: MIXS:0001043 growth_habit: is_a: environment field aliases: - growth habit description: Characteristic shape, appearance or growth form of a plant species - pattern: '[erect|semi-erect|spreading|prostrate]' + range: growth_habit_enum examples: - value: spreading comments: @@ -8837,7 +8037,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' - range: growth_habit_enum + pattern: '[erect|semi-erect|spreading|prostrate]' slot_uri: MIXS:0001044 growth_hormone_regm: is_a: environment field @@ -8848,7 +8048,7 @@ slots: how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8858,6 +8058,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000560 herbicide_regm: is_a: environment field @@ -8868,7 +8069,7 @@ slots: herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8877,13 +8078,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000561 host_wet_mass: is_a: environment field aliases: - host wet mass description: Measurement of wet mass - pattern: '{float} {unit}' + range: quantity value examples: - value: 1500 gram comments: @@ -8902,7 +8104,7 @@ slots: include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8911,6 +8113,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 light_regm: is_a: environment field @@ -8918,7 +8121,7 @@ slots: - light regimen description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - pattern: '{text};{float} {unit};{float} {unit}' + range: string examples: - value: incandescant light;10 lux;450 nanometer comments: @@ -8927,6 +8130,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 mechanical_damage: is_a: environment field @@ -8934,7 +8138,7 @@ slots: - mechanical damage description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - pattern: '{text};{text}' + range: string examples: - value: pruning;bark comments: @@ -8943,6 +8147,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{text}' slot_uri: MIXS:0001052 mineral_nutr_regm: is_a: environment field @@ -8953,7 +8158,7 @@ slots: regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8963,6 +8168,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000570 non_mineral_nutr_regm: is_a: environment field @@ -8973,7 +8179,7 @@ slots: nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -8983,6 +8189,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000571 ph_regm: is_a: environment field @@ -8992,7 +8199,7 @@ slots: levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - pattern: '{float};{Rn/start_time/end_time/duration}' + range: string examples: - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M comments: @@ -9001,6 +8208,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001056 pesticide_regm: is_a: environment field @@ -9011,7 +8219,7 @@ slots: how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9020,6 +8228,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000573 plant_growth_med: is_a: environment field @@ -9030,8 +8239,7 @@ slots: vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - pattern: '{termLabel} {[termID]} or [husk|other artificial liquid medium|other - artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' + range: plant_growth_med_enum examples: - value: hydroponic plant culture media [EO:0007067] comments: @@ -9040,14 +8248,15 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' - range: plant_growth_med_enum + pattern: '{termLabel} {[termID]} or [husk|other artificial liquid medium|other + artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' slot_uri: MIXS:0001057 plant_product: is_a: environment field aliases: - plant product description: Substance produced by the plant, where the sample was obtained from - pattern: '{text}' + range: string examples: - value: xylem sap [PO:0025539] comments: @@ -9056,6 +8265,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text}' slot_uri: MIXS:0001058 plant_sex: is_a: environment field @@ -9063,7 +8273,7 @@ slots: - plant sex description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - pattern: '[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]' + range: plant_sex_enum examples: - value: Hermaphroditic comments: @@ -9072,7 +8282,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' - range: plant_sex_enum + pattern: '[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]' slot_uri: MIXS:0001059 plant_struc: is_a: environment field @@ -9082,7 +8292,7 @@ slots: (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - pattern: '{termLabel} {[termID]}' + range: string examples: - value: epidermis [PO:0005679] comments: @@ -9091,6 +8301,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{termLabel} {[termID]}' slot_uri: MIXS:0001060 radiation_regm: is_a: environment field @@ -9101,7 +8312,7 @@ slots: or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9111,6 +8322,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000575 rainfall_regm: is_a: environment field @@ -9120,7 +8332,7 @@ slots: of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9129,6 +8341,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000576 root_cond: is_a: environment field @@ -9136,7 +8349,7 @@ slots: - rooting conditions description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - pattern: '{PMID}|{DOI}|{URL}|{text}' + range: string examples: - value: http://himedialabs.com/TD/PT158.pdf comments: @@ -9145,13 +8358,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001061 root_med_carbon: is_a: environment field aliases: - rooting medium carbon description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - pattern: '{text};{float} {unit}' + range: string examples: - value: sucrose comments: @@ -9160,6 +8374,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000577 root_med_macronutr: is_a: environment field @@ -9167,7 +8382,7 @@ slots: - rooting medium macronutrients description: "Measurement of the culture rooting medium macronutrients (N,P, K,\ \ Ca, Mg, S); e.g. KH2PO4 (170\xAC\u2020mg/L)." - pattern: '{text};{float} {unit}' + range: string examples: - value: "KH2PO4;170\xAC\u2020milligram per liter" comments: @@ -9176,6 +8391,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000578 root_med_micronutr: is_a: environment field @@ -9183,7 +8399,7 @@ slots: - rooting medium micronutrients description: "Measurement of the culture rooting medium micronutrients (Fe, Mn,\ \ Zn, B, Cu, Mo); e.g. H3BO3 (6.2\xAC\u2020mg/L)." - pattern: '{text};{float} {unit}' + range: string examples: - value: "H3BO3;6.2\xAC\u2020milligram per liter" comments: @@ -9192,6 +8408,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000579 root_med_suppl: is_a: environment field @@ -9200,7 +8417,7 @@ slots: description: "Organic supplements of the culture rooting medium, such as vitamins,\ \ amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic\ \ acid (0.5\xAC\u2020mg/L)." - pattern: '{text};{float} {unit}' + range: string examples: - value: nicotinic acid;0.5 milligram per liter comments: @@ -9209,13 +8426,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000580 root_med_ph: is_a: environment field aliases: - rooting medium pH description: pH measurement of the culture rooting medium; e.g. 5.5. - pattern: '{float}' + range: double examples: - value: '7.5' comments: @@ -9231,7 +8449,7 @@ slots: - rooting medium regulators description: "Growth regulators in the culture rooting medium such as cytokinins,\ \ auxins, gybberellins, abscisic acid; e.g. 0.5\xAC\u2020mg/L NAA." - pattern: '{text};{float} {unit}' + range: string examples: - value: abscisic acid;0.75 milligram per liter comments: @@ -9240,6 +8458,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000581 root_med_solid: is_a: environment field @@ -9247,7 +8466,7 @@ slots: - rooting medium solidifier description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - pattern: '{text}' + range: string examples: - value: agar comments: @@ -9256,6 +8475,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text}' slot_uri: MIXS:0001063 salt_regm: is_a: environment field @@ -9266,7 +8486,7 @@ slots: treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9275,6 +8495,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000582 season_environment: is_a: environment field @@ -9284,7 +8505,7 @@ slots: summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - pattern: '{text};{Rn/start_time/end_time/duration}' + range: string examples: - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9293,6 +8514,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001068 standing_water_regm: is_a: environment field @@ -9302,7 +8524,7 @@ slots: life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{text};{Rn/start_time/end_time/duration}' + range: string examples: - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9311,13 +8533,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001069 tiss_cult_growth_med: is_a: environment field aliases: - tissue culture growth media description: Description of plant tissue culture growth media used - pattern: '{PMID}|{DOI}|{URL}|{text}' + range: string examples: - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf comments: @@ -9326,6 +8549,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001070 water_temp_regm: is_a: environment field @@ -9335,7 +8559,7 @@ slots: degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9344,6 +8568,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000590 watering_regm: is_a: environment field @@ -9353,7 +8578,7 @@ slots: treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' + range: string examples: - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M comments: @@ -9362,6 +8587,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: plant-associated' + pattern: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 particle_class: is_a: environment field @@ -9370,7 +8596,7 @@ slots: description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -9379,13 +8605,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: sediment' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000206 sediment_type: is_a: environment field aliases: - sediment type description: Information about the sediment type based on major constituents - pattern: '[biogenous|cosmogenous|hydrogenous|lithogenous]' + range: sediment_type_enum examples: - value: biogenous comments: @@ -9394,14 +8621,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: sediment' - range: sediment_type_enum + pattern: '[biogenous|cosmogenous|hydrogenous|lithogenous]' slot_uri: MIXS:0001078 tidal_stage: is_a: environment field aliases: - tidal stage description: Stage of tide - pattern: '[low tide|ebb tide|flood tide|high tide]' + range: tidal_stage_enum examples: - value: high tide comments: @@ -9410,14 +8637,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used in: 2 packages: sediment, water' - range: tidal_stage_enum + pattern: '[low tide|ebb tide|flood tide|high tide]' slot_uri: MIXS:0000750 tot_depth_water_col: is_a: environment field aliases: - total depth of water column description: Measurement of total depth of water column - pattern: '{float} {unit}' + range: quantity value examples: - value: 500 meter comments: @@ -9432,6 +8659,15 @@ slots: aliases: - current land use description: Present state of sample site + range: cur_land_use_enum + examples: + - value: conifers + comments: + - 'Expected value: enumeration' + - 'Preferred unit: ' + - 'Occurrence: 1' + - 'Position: 1' + - 'This field is used uniquely in: soil' pattern: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands @@ -9445,15 +8681,6 @@ slots: receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]' - examples: - - value: conifers - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: soil' - range: cur_land_use_enum slot_uri: MIXS:0001080 cur_vegetation: is_a: environment field @@ -9461,7 +8688,7 @@ slots: - current vegetation description: Vegetation classification from one or more standard classification systems, or agricultural crop - pattern: '{text}' + range: string examples: - value: '' comments: @@ -9470,13 +8697,14 @@ slots: - 'Occurrence: 1' - 'Position: 2' - 'This field is used uniquely in: soil' + pattern: '{text}' slot_uri: MIXS:0000312 cur_vegetation_meth: is_a: environment field aliases: - current vegetation method description: Reference or method used in vegetation classification - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9485,13 +8713,14 @@ slots: - 'Occurrence: 1' - 'Position: 3' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000314 previous_land_use: is_a: environment field aliases: - history/previous land use description: Previous land use and dates - pattern: '{text};{timestamp}' + range: string examples: - value: '' comments: @@ -9500,13 +8729,14 @@ slots: - 'Occurrence: 1' - 'Position: 4' - 'This field is used uniquely in: soil' + pattern: '{text};{timestamp}' slot_uri: MIXS:0000315 previous_land_use_meth: is_a: environment field aliases: - history/previous land use method description: Reference or method used in determining previous land use and dates - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9515,13 +8745,14 @@ slots: - 'Occurrence: 1' - 'Position: 5' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000316 crop_rotation: is_a: environment field aliases: - history/crop rotation description: Whether or not crop is rotated, and if yes, rotation schedule - pattern: '{boolean};{Rn/start_time/end_time/duration}' + range: string examples: - value: yes;R2/2017-01-01/2018-12-31/P6M comments: @@ -9530,13 +8761,14 @@ slots: - 'Occurrence: 1' - 'Position: 6' - 'This field is used uniquely in: soil' + pattern: '{boolean};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000318 agrochem_addition: is_a: environment field aliases: - history/agrochemical additions description: Addition of fertilizers, pesticides, etc. - amount and time of applications - pattern: '{text};{float} {unit};{timestamp}' + range: string examples: - value: roundup;5 milligram per liter;2018-06-21 comments: @@ -9545,14 +8777,14 @@ slots: - 'Occurrence: m' - 'Position: 7' - 'This field is used uniquely in: soil' + pattern: '{text};{float} {unit};{timestamp}' slot_uri: MIXS:0000639 tillage: is_a: environment field aliases: - history/tillage description: Note method(s) used for tilling - pattern: '[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc - plough]' + range: tillage_enum examples: - value: chisel comments: @@ -9561,14 +8793,15 @@ slots: - 'Occurrence: m' - 'Position: 8' - 'This field is used uniquely in: soil' - range: tillage_enum + pattern: '[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc + plough]' slot_uri: MIXS:0001081 fire: is_a: environment field aliases: - history/fire description: Historical and/or physical evidence of fire - pattern: '{timestamp}' + range: string examples: - value: '' comments: @@ -9577,13 +8810,14 @@ slots: - 'Occurrence: 1' - 'Position: 9' - 'This field is used uniquely in: soil' + pattern: '{timestamp}' slot_uri: MIXS:0001086 flooding: is_a: environment field aliases: - history/flooding description: Historical and/or physical evidence of flooding - pattern: '{timestamp}' + range: string examples: - value: '' comments: @@ -9592,13 +8826,14 @@ slots: - 'Occurrence: 1' - 'Position: 10' - 'This field is used uniquely in: soil' + pattern: '{timestamp}' slot_uri: MIXS:0000319 extreme_event: is_a: environment field aliases: - history/extreme events description: Unusual physical events that may have affected microbial populations - pattern: '{timestamp}' + range: string examples: - value: '' comments: @@ -9607,6 +8842,7 @@ slots: - 'Occurrence: 1' - 'Position: 11' - 'This field is used uniquely in: soil' + pattern: '{timestamp}' slot_uri: MIXS:0000320 horizon: is_a: environment field @@ -9615,7 +8851,7 @@ slots: description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - pattern: '[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]' + range: horizon_enum examples: - value: A horizon comments: @@ -9624,14 +8860,14 @@ slots: - 'Occurrence: 1' - 'Position: 12' - 'This field is used uniquely in: soil' - range: horizon_enum + pattern: '[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]' slot_uri: MIXS:0001082 horizon_meth: is_a: environment field aliases: - horizon method description: Reference or method used in determining the horizon - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9640,6 +8876,7 @@ slots: - 'Occurrence: 1' - 'Position: 13' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000321 sieving: is_a: environment field @@ -9647,7 +8884,7 @@ slots: - composite design/sieving (if any) description: Collection design of pooled samples and/or sieve size and amount of sample sieved - pattern: '{{text}|{float} {unit}};{float} {unit}' + range: string examples: - value: '' comments: @@ -9656,13 +8893,14 @@ slots: - 'Occurrence: 1' - 'Position: 14' - 'This field is used uniquely in: soil' + pattern: '{{text}|{float} {unit}};{float} {unit}' slot_uri: MIXS:0000322 water_content_soil_meth: is_a: environment field aliases: - water content method description: Reference or method used in determining the water content of soil - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9671,6 +8909,7 @@ slots: - 'Occurrence: 1' - 'Position: 16' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000323 pool_dna_extracts: is_a: environment field @@ -9678,7 +8917,7 @@ slots: - pooling of DNA extracts (if done) description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - pattern: '{boolean};{integer}' + range: string examples: - value: yes;5 comments: @@ -9687,6 +8926,7 @@ slots: - 'Occurrence: 1' - 'Position: 18' - 'This field is used uniquely in: soil' + pattern: '{boolean};{integer}' slot_uri: MIXS:0000325 store_cond: is_a: environment field @@ -9694,7 +8934,7 @@ slots: - storage conditions (fresh/frozen/other) description: Explain how and for how long the soil sample was stored before DNA extraction - pattern: '{text};{duration}' + range: string examples: - value: -20 degree Celsius freezer;P2Y10D comments: @@ -9703,13 +8943,14 @@ slots: - 'Occurrence: 1' - 'Position: 19' - 'This field is used uniquely in: soil' + pattern: '{text};{duration}' slot_uri: MIXS:0000327 link_climate_info: is_a: environment field aliases: - link to climate information description: Link to climate resource - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9718,13 +8959,14 @@ slots: - 'Occurrence: 1' - 'Position: 20' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000328 annual_temp: is_a: environment field aliases: - mean annual temperature description: Mean annual temperature - pattern: '{float} {unit}' + range: quantity value examples: - value: 12.5 degree Celsius comments: @@ -9739,7 +8981,7 @@ slots: aliases: - mean seasonal temperature description: Mean seasonal temperature - pattern: '{float} {unit}' + range: quantity value examples: - value: 18 degree Celsius comments: @@ -9755,7 +8997,7 @@ slots: - mean annual precipitation description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -9771,7 +9013,7 @@ slots: - mean seasonal precipitation description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -9786,7 +9028,7 @@ slots: aliases: - link to classification information description: Link to digitized soil maps or other soil classification information - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9795,6 +9037,7 @@ slots: - 'Occurrence: 1' - 'Position: 25' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000329 fao_class: is_a: environment field @@ -9802,7 +9045,7 @@ slots: - soil_taxonomic/FAO classification description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - pattern: '[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]' + range: fao_class_enum examples: - value: Luvisols comments: @@ -9811,14 +9054,14 @@ slots: - 'Occurrence: 1' - 'Position: 26' - 'This field is used uniquely in: soil' - range: fao_class_enum + pattern: '[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]' slot_uri: MIXS:0001083 local_class: is_a: environment field aliases: - soil_taxonomic/local classification description: Soil classification based on local soil classification system - pattern: '{text}' + range: string examples: - value: '' comments: @@ -9827,13 +9070,14 @@ slots: - 'Occurrence: 1' - 'Position: 27' - 'This field is used uniquely in: soil' + pattern: '{text}' slot_uri: MIXS:0000330 local_class_meth: is_a: environment field aliases: - soil_taxonomic/local classification method description: Reference or method used in determining the local soil classification - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9842,13 +9086,14 @@ slots: - 'Occurrence: 1' - 'Position: 28' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000331 soil_type: is_a: environment field aliases: - soil type description: Soil series name or other lower-level classification - pattern: '{text}' + range: string examples: - value: '' comments: @@ -9857,6 +9102,7 @@ slots: - 'Occurrence: 1' - 'Position: 29' - 'This field is used uniquely in: soil' + pattern: '{text}' slot_uri: MIXS:0000332 soil_type_meth: is_a: environment field @@ -9864,7 +9110,7 @@ slots: - soil type method description: Reference or method used in determining soil series name or other lower-level classification - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9873,6 +9119,7 @@ slots: - 'Occurrence: 1' - 'Position: 30' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000334 slope_gradient: is_a: environment field @@ -9881,7 +9128,7 @@ slots: description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -9899,7 +9146,7 @@ slots: to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -9915,7 +9162,7 @@ slots: - profile position description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - pattern: '[summit|shoulder|backslope|footslope|toeslope]' + range: profile_position_enum examples: - value: summit comments: @@ -9924,15 +9171,14 @@ slots: - 'Occurrence: 1' - 'Position: 33' - 'This field is used uniquely in: soil' - range: profile_position_enum + pattern: '[summit|shoulder|backslope|footslope|toeslope]' slot_uri: MIXS:0001084 drainage_class: is_a: environment field aliases: - drainage classification description: Drainage classification from a standard system such as the USDA system - pattern: '[very poorly|poorly|somewhat poorly|moderately well|well|excessively - drained]' + range: drainage_class_enum examples: - value: well comments: @@ -9941,7 +9187,8 @@ slots: - 'Occurrence: 1' - 'Position: 34' - 'This field is used uniquely in: soil' - range: drainage_class_enum + pattern: '[very poorly|poorly|somewhat poorly|moderately well|well|excessively + drained]' slot_uri: MIXS:0001085 texture: is_a: environment field @@ -9951,7 +9198,7 @@ slots: in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -9966,7 +9213,7 @@ slots: aliases: - texture method description: Reference or method used in determining soil texture - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9975,13 +9222,14 @@ slots: - 'Occurrence: 1' - 'Position: 36' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000336 ph_meth: is_a: environment field aliases: - pH method description: Reference or method used in determining ph - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -9990,13 +9238,14 @@ slots: - 'Occurrence: 1' - 'Position: 38' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 tot_org_c_meth: is_a: environment field aliases: - total organic carbon method description: Reference or method used in determining total organic carbon - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10005,13 +9254,14 @@ slots: - 'Occurrence: 1' - 'Position: 40' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000337 tot_nitro_content_meth: is_a: environment field aliases: - total nitrogen content method description: Reference or method used in determining the total nitrogen - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10020,6 +9270,7 @@ slots: - 'Occurrence: 1' - 'Position: 42' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000338 microbial_biomass: is_a: environment field @@ -10028,7 +9279,7 @@ slots: description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10043,7 +9294,7 @@ slots: aliases: - microbial biomass method description: Reference or method used in determining microbial biomass - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10052,13 +9303,14 @@ slots: - 'Occurrence: 1' - 'Position: 44' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000339 link_addit_analys: is_a: environment field aliases: - links to additional analysis description: Link to additional analysis results performed on the sample - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10067,13 +9319,14 @@ slots: - 'Occurrence: 1' - 'Position: 45' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000340 extreme_salinity: is_a: environment field aliases: - extreme_unusual_properties/salinity description: Measured salinity - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10088,7 +9341,7 @@ slots: aliases: - extreme_unusual_properties/salinity method description: Reference or method used in determining salinity - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10097,6 +9350,7 @@ slots: - 'Occurrence: 1' - 'Position: 47' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 heavy_metals: is_a: environment field @@ -10104,7 +9358,7 @@ slots: - extreme_unusual_properties/heavy metals description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10113,13 +9367,14 @@ slots: - 'Occurrence: m' - 'Position: 48' - 'This field is used uniquely in: soil' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000652 heavy_metals_meth: is_a: environment field aliases: - extreme_unusual_properties/heavy metals method description: Reference or method used in determining heavy metals - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10128,13 +9383,14 @@ slots: - 'Occurrence: 1' - 'Position: 49' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000343 al_sat: is_a: environment field aliases: - extreme_unusual_properties/Al saturation description: Aluminum saturation (esp. For tropical soils) - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10149,7 +9405,7 @@ slots: aliases: - extreme_unusual_properties/Al saturation method description: Reference or method used in determining Al saturation - pattern: '{PMID}|{DOI}|{URL}' + range: string examples: - value: '' comments: @@ -10158,6 +9414,7 @@ slots: - 'Occurrence: 1' - 'Position: 51' - 'This field is used uniquely in: soil' + pattern: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000324 biochem_oxygen_dem: is_a: environment field @@ -10166,7 +9423,7 @@ slots: description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10183,7 +9440,7 @@ slots: description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10198,7 +9455,7 @@ slots: aliases: - efficiency percent description: Percentage of volatile solids removed from the anaerobic digestor - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10215,7 +9472,7 @@ slots: description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10224,6 +9481,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000660 gaseous_substances: is_a: environment field @@ -10231,7 +9489,7 @@ slots: - gaseous substances description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10240,6 +9498,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000661 indust_eff_percent: is_a: environment field @@ -10247,7 +9506,7 @@ slots: - industrial effluent percent description: Percentage of industrial effluents received by wastewater treatment plant - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10263,7 +9522,7 @@ slots: - inorganic particles description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10272,6 +9531,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000664 org_particles: is_a: environment field @@ -10279,7 +9539,7 @@ slots: - organic particles description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10288,6 +9548,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000665 pre_treatment: is_a: environment field @@ -10295,7 +9556,7 @@ slots: - pre-treatment description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10304,6 +9565,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000348 primary_treatment: is_a: environment field @@ -10312,7 +9574,7 @@ slots: description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10321,6 +9583,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000349 reactor_type: is_a: environment field @@ -10329,7 +9592,7 @@ slots: description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10338,6 +9601,7 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000350 secondary_treatment: is_a: environment field @@ -10345,7 +9609,7 @@ slots: - secondary treatment description: The process for substantially degrading the biological content of the sewage - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10354,13 +9618,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000351 sewage_type: is_a: environment field aliases: - sewage type description: Type of wastewater treatment plant as municipial or industrial - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10369,13 +9634,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000215 sludge_retent_time: is_a: environment field aliases: - sludge retention time description: The time activated sludge remains in reactor - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10391,7 +9657,7 @@ slots: - soluble inorganic material description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10401,6 +9667,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000672 soluble_org_mat: is_a: environment field @@ -10408,7 +9675,7 @@ slots: - soluble organic material description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - pattern: '{text};{float} {unit}' + range: string examples: - value: '' comments: @@ -10418,6 +9685,7 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0000673 tertiary_treatment: is_a: environment field @@ -10425,7 +9693,7 @@ slots: - tertiary treatment description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10434,13 +9702,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000352 tot_phosphate: is_a: environment field aliases: - total phosphate description: Total amount or concentration of phosphate - pattern: '{float} {unit}' + range: quantity value examples: - value: '' comments: @@ -10456,7 +9725,7 @@ slots: - wastewater type description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - pattern: '{text}' + range: string examples: - value: '' comments: @@ -10465,13 +9734,14 @@ slots: - 'Occurrence: 1' - 'Position: 1' - 'This field is used uniquely in: wastewater_sludge' + pattern: '{text}' slot_uri: MIXS:0000353 atmospheric_data: is_a: environment field aliases: - atmospheric data description: Measurement of atmospheric data; can include multiple data - pattern: '{text};{float} {unit}' + range: string examples: - value: wind speed;9 knots comments: @@ -10480,13 +9750,14 @@ slots: - 'Occurrence: m' - 'Position: 1' - 'This field is used uniquely in: water' + pattern: '{text};{float} {unit}' slot_uri: MIXS:0001097 bac_prod: is_a: environment field aliases: - bacterial production description: Bacterial production in the water column measured by isotope uptake - pattern: '{float} {unit}' + range: quantity value examples: - value: 5 milligram per cubic meter per day comments: @@ -10501,7 +9772,7 @@ slots: aliases: - bacterial respiration description: Measurement of bacterial respiration in the water column - pattern: '{float} {unit}' + range: quantity value examples: - value: 300 micromole oxygen per liter per hour comments: @@ -10517,7 +9788,7 @@ slots: aliases: - conductivity description: Electrical conductivity of water - pattern: '{float} {unit}' + range: quantity value examples: - value: 10 milliSiemens per centimeter comments: @@ -10532,7 +9803,7 @@ slots: aliases: - dissolved inorganic nitrogen description: Concentration of dissolved inorganic nitrogen - pattern: '{float} {unit}' + range: quantity value examples: - value: 761 micromole per liter comments: @@ -10548,7 +9819,7 @@ slots: - downward PAR description: Visible waveband radiance and irradiance measurements in the water column - pattern: '{float} {unit}' + range: quantity value examples: - value: 28.71 microEinstein per square meter per second comments: @@ -10564,7 +9835,7 @@ slots: aliases: - fluorescence description: Raw or converted fluorescence of water - pattern: '{float} {unit}' + range: quantity value examples: - value: 2.5 volts comments: @@ -10579,7 +9850,7 @@ slots: aliases: - light intensity description: Measurement of light intensity - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.3 lux comments: @@ -10594,7 +9865,7 @@ slots: aliases: - particulate organic nitrogen description: Concentration of particulate organic nitrogen - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.3 micromole per liter comments: @@ -10609,7 +9880,7 @@ slots: aliases: - photon flux description: Measurement of photon flux - pattern: '{float} {unit}' + range: quantity value examples: - value: 3.926 micromole photons per second per square meter comments: @@ -10625,7 +9896,7 @@ slots: - primary production description: Measurement of primary production, generally measured as isotope uptake - pattern: '{float} {unit}' + range: quantity value examples: - value: 100 milligram per cubic meter per day comments: @@ -10642,7 +9913,7 @@ slots: - size-fraction lower threshold description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.2 micrometer comments: @@ -10658,7 +9929,7 @@ slots: - size-fraction upper threshold description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - pattern: '{float} {unit}' + range: quantity value examples: - value: 20 micrometer comments: @@ -10673,7 +9944,7 @@ slots: aliases: - soluble reactive phosphorus description: Concentration of soluble reactive phosphorus - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.1 milligram per liter comments: @@ -10688,7 +9959,7 @@ slots: aliases: - suspended particulate matter description: Concentration of suspended particulate matter - pattern: '{float} {unit}' + range: quantity value examples: - value: 0.5 milligram per liter comments: @@ -10704,7 +9975,7 @@ slots: - total dissolved nitrogen description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' - pattern: '{float} {unit}' + range: quantity value examples: - value: 40 microgram per liter comments: @@ -10719,7 +9990,7 @@ slots: aliases: - total inorganic nitrogen description: Total inorganic nitrogen content - pattern: '{float} {unit}' + range: quantity value examples: - value: 40 microgram per liter comments: @@ -10734,7 +10005,7 @@ slots: aliases: - total particulate carbon description: Total particulate carbon content - pattern: '{float} {unit}' + range: quantity value examples: - value: 35 micromole per liter comments: @@ -10745,8 +10016,20 @@ slots: - 'This field is used uniquely in: water' slot_uri: MIXS:0000747 classes: - core: - description: core package + quantity value: + description: used to record a measurement + attributes: + has unit: + description: Example "m" + has numeric value: + range: double + has raw value: + string_serialization: '{has numeric value} {has unit}' + migs_eu: + mixin: true + description: migs_eu Checklist + todos: + - add details here slots: - submitted_to_insdc - investigation_type @@ -10754,9 +10037,6 @@ classes: - project_name - experimental_factor - lat_lon - - depth - - alt - - elev - geo_loc_name - collection_date - env_broad_scale @@ -10777,15 +10057,10 @@ classes: - health_disease_stat - trophic_level - propagation - - encoded_traits - - rel_to_oxygen - isol_growth_condt - samp_collect_device - samp_mat_process - - size_frac - samp_size - - source_uvig - - virus_enrich_appr - nucl_acid_ext - nucl_acid_amp - lib_size @@ -10793,15 +10068,8 @@ classes: - lib_layout - lib_vector - lib_screen - - target_gene - - target_subfragment - - pcr_primers - - mid - adapters - - pcr_cond - seq_meth - - seq_quality_check - - chimera_check - tax_ident - assembly_qual - assembly_name @@ -10812,23 +10080,1938 @@ classes: - ref_db - sim_search_meth - tax_class - - x_16s_recover - - x_16s_recover_software - - trnas - - trna_ext_software - compl_score - compl_software - - compl_appr - - contam_score - - contam_screen_input - - contam_screen_param - - decontam_software - - sort_tech - - single_cell_lysis_appr - - single_cell_lysis_prot - - wga_amp_appr - - wga_amp_kit - - bin_param + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + ploidy: + required: 'False' + num_replicons: + required: 'False' + extrachrom_elements: + required: 'False' + estimated_size: + required: 'False' + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + pathogenicity: + comments: + - conditional mandatory + biotic_relationship: + required: 'False' + specific_host: + required: 'False' + host_spec_range: + required: 'False' + health_disease_stat: + required: 'False' + trophic_level: + comments: + - conditional mandatory + propagation: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + required: 'False' + samp_size: + required: 'False' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + required: 'False' + lib_reads_seqd: + required: 'False' + lib_layout: + required: 'False' + lib_vector: + required: 'False' + lib_screen: + required: 'False' + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + comments: + - conditional mandatory + assembly_qual: + required: 'True' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + comments: + - conditional mandatory + number_contig: + required: 'True' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + compl_score: + required: 'False' + compl_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + migs_ba: + mixin: true + description: migs_ba Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - num_replicons + - extrachrom_elements + - estimated_size + - ref_biomaterial + - source_mat_id + - pathogenicity + - biotic_relationship + - specific_host + - host_spec_range + - health_disease_stat + - trophic_level + - encoded_traits + - rel_to_oxygen + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - compl_score + - compl_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + num_replicons: + required: 'True' + extrachrom_elements: + comments: + - conditional mandatory + estimated_size: + required: 'False' + ref_biomaterial: + required: 'True' + source_mat_id: + comments: + - conditional mandatory + pathogenicity: + comments: + - conditional mandatory + biotic_relationship: + comments: + - conditional mandatory + specific_host: + comments: + - conditional mandatory + host_spec_range: + required: 'False' + health_disease_stat: + comments: + - conditional mandatory + trophic_level: + comments: + - conditional mandatory + encoded_traits: + required: 'False' + rel_to_oxygen: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + required: 'False' + samp_size: + required: 'False' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + required: 'False' + lib_reads_seqd: + required: 'False' + lib_layout: + required: 'False' + lib_vector: + required: 'False' + lib_screen: + required: 'False' + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + comments: + - conditional mandatory + assembly_qual: + required: 'True' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + comments: + - conditional mandatory + number_contig: + required: 'True' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + compl_score: + required: 'False' + compl_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + migs_pl: + mixin: true + description: migs_pl Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - estimated_size + - ref_biomaterial + - source_mat_id + - specific_host + - host_spec_range + - propagation + - encoded_traits + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - compl_score + - compl_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + estimated_size: + required: 'False' + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + specific_host: + comments: + - conditional mandatory + host_spec_range: + required: 'False' + propagation: + required: 'True' + encoded_traits: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + required: 'False' + samp_size: + required: 'False' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + required: 'False' + lib_reads_seqd: + required: 'False' + lib_layout: + required: 'False' + lib_vector: + required: 'False' + lib_screen: + required: 'False' + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + comments: + - conditional mandatory + assembly_qual: + required: 'False' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + comments: + - conditional mandatory + number_contig: + required: 'False' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + compl_score: + required: 'False' + compl_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + migs_vi: + mixin: true + description: migs_vi Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - num_replicons + - estimated_size + - ref_biomaterial + - source_mat_id + - pathogenicity + - biotic_relationship + - specific_host + - host_spec_range + - health_disease_stat + - propagation + - encoded_traits + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - samp_size + - virus_enrich_appr + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - compl_score + - compl_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + num_replicons: + comments: + - conditional mandatory + estimated_size: + required: 'False' + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + pathogenicity: + comments: + - conditional mandatory + biotic_relationship: + required: 'False' + specific_host: + comments: + - conditional mandatory + host_spec_range: + comments: + - conditional mandatory + health_disease_stat: + comments: + - conditional mandatory + propagation: + required: 'True' + encoded_traits: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + required: 'False' + samp_size: + required: 'False' + virus_enrich_appr: + comments: + - conditional mandatory + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + required: 'False' + lib_reads_seqd: + required: 'False' + lib_layout: + required: 'False' + lib_vector: + required: 'False' + lib_screen: + required: 'False' + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + comments: + - conditional mandatory + assembly_qual: + required: 'False' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + comments: + - conditional mandatory + number_contig: + required: 'False' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + compl_score: + required: 'False' + compl_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + migs_org: + mixin: true + description: migs_org Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - extrachrom_elements + - estimated_size + - ref_biomaterial + - source_mat_id + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - compl_score + - compl_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + extrachrom_elements: + comments: + - conditional mandatory + estimated_size: + required: 'False' + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + required: 'False' + samp_size: + required: 'False' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + required: 'False' + lib_reads_seqd: + required: 'False' + lib_layout: + required: 'False' + lib_vector: + required: 'False' + lib_screen: + required: 'False' + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + comments: + - conditional mandatory + assembly_qual: + required: 'False' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + comments: + - conditional mandatory + number_contig: + required: 'False' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + compl_score: + required: 'False' + compl_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + me: + mixin: true + description: me Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - ref_biomaterial + - source_mat_id + - rel_to_oxygen + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - mid + - adapters + - seq_meth + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + comments: + - conditional mandatory + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + rel_to_oxygen: + required: 'False' + samp_collect_device: + comments: + - conditional mandatory + samp_mat_process: + comments: + - conditional mandatory + size_frac: + required: 'False' + samp_size: + comments: + - conditional mandatory + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + comments: + - conditional mandatory + lib_reads_seqd: + comments: + - conditional mandatory + lib_layout: + comments: + - conditional mandatory + lib_vector: + comments: + - conditional mandatory + lib_screen: + comments: + - conditional mandatory + mid: + comments: + - conditional mandatory + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + assembly_qual: + comments: + - conditional mandatory + assembly_name: + comments: + - conditional mandatory + assembly_software: + comments: + - conditional mandatory + annot: + comments: + - conditional mandatory + number_contig: + comments: + - conditional mandatory + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + mimarks_s: + mixin: true + description: mimarks_s Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - source_mat_id + - rel_to_oxygen + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - target_gene + - target_subfragment + - pcr_primers + - mid + - adapters + - pcr_cond + - seq_meth + - seq_quality_check + - chimera_check + - assembly_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + comments: + - conditional mandatory + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + source_mat_id: + comments: + - conditional mandatory + rel_to_oxygen: + required: 'False' + samp_collect_device: + comments: + - conditional mandatory + samp_mat_process: + comments: + - conditional mandatory + size_frac: + required: 'False' + samp_size: + comments: + - conditional mandatory + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + comments: + - conditional mandatory + lib_reads_seqd: + comments: + - conditional mandatory + lib_layout: + comments: + - conditional mandatory + lib_vector: + comments: + - conditional mandatory + lib_screen: + comments: + - conditional mandatory + target_gene: + required: 'True' + target_subfragment: + comments: + - conditional mandatory + pcr_primers: + comments: + - conditional mandatory + mid: + comments: + - conditional mandatory + adapters: + comments: + - conditional mandatory + pcr_cond: + comments: + - conditional mandatory + seq_meth: + required: 'True' + seq_quality_check: + comments: + - conditional mandatory + chimera_check: + comments: + - conditional mandatory + assembly_software: + comments: + - conditional mandatory + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + mimarks_c: + mixin: true + description: mimarks_c Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - extrachrom_elements + - source_mat_id + - biotic_relationship + - trophic_level + - rel_to_oxygen + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - target_gene + - target_subfragment + - pcr_primers + - pcr_cond + - seq_meth + - seq_quality_check + - chimera_check + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + required: 'False' + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + subspecf_gen_lin: + comments: + - conditional mandatory + extrachrom_elements: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + biotic_relationship: + comments: + - conditional mandatory + trophic_level: + comments: + - conditional mandatory + rel_to_oxygen: + comments: + - conditional mandatory + isol_growth_condt: + required: 'True' + samp_collect_device: + required: 'False' + samp_mat_process: + comments: + - conditional mandatory + samp_size: + required: 'False' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + target_gene: + required: 'True' + target_subfragment: + comments: + - conditional mandatory + pcr_primers: + comments: + - conditional mandatory + pcr_cond: + comments: + - conditional mandatory + seq_meth: + required: 'True' + seq_quality_check: + comments: + - conditional mandatory + chimera_check: + comments: + - conditional mandatory + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + misag: + mixin: true + description: misag Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - ref_biomaterial + - source_mat_id + - rel_to_oxygen + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - mid + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - x_16s_recover + - x_16s_recover_software + - trnas + - trna_ext_software + - compl_score + - compl_software + - compl_appr + - contam_score + - contam_screen_input + - contam_screen_param + - decontam_software + - sort_tech + - single_cell_lysis_appr + - single_cell_lysis_prot + - wga_amp_appr + - wga_amp_kit + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + comments: + - conditional mandatory + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + rel_to_oxygen: + required: 'False' + samp_collect_device: + comments: + - conditional mandatory + samp_mat_process: + comments: + - conditional mandatory + size_frac: + required: 'False' + samp_size: + comments: + - conditional mandatory + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + comments: + - conditional mandatory + lib_reads_seqd: + comments: + - conditional mandatory + lib_layout: + comments: + - conditional mandatory + lib_vector: + comments: + - conditional mandatory + lib_screen: + comments: + - conditional mandatory + mid: + comments: + - conditional mandatory + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + required: 'True' + assembly_qual: + required: 'True' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + required: 'False' + number_contig: + required: 'False' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + x_16s_recover: + required: 'False' + x_16s_recover_software: + required: 'False' + trnas: + required: 'False' + trna_ext_software: + required: 'False' + compl_score: + required: 'True' + compl_software: + required: 'True' + compl_appr: + required: 'False' + contam_score: + required: 'True' + contam_screen_input: + required: 'False' + contam_screen_param: + required: 'False' + decontam_software: + required: 'False' + sort_tech: + required: 'True' + single_cell_lysis_appr: + required: 'True' + single_cell_lysis_prot: + required: 'False' + wga_amp_appr: + required: 'True' + wga_amp_kit: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + mimag: + mixin: true + description: mimag Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - ref_biomaterial + - source_mat_id + - rel_to_oxygen + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - mid + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - x_16s_recover + - x_16s_recover_software + - trnas + - trna_ext_software + - compl_score + - compl_software + - compl_appr + - contam_score + - contam_screen_input + - contam_screen_param + - decontam_software + - bin_param + - bin_software + - reassembly_bin + - mag_cov_software + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + comments: + - conditional mandatory + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + rel_to_oxygen: + required: 'False' + samp_collect_device: + comments: + - conditional mandatory + samp_mat_process: + comments: + - conditional mandatory + size_frac: + required: 'False' + samp_size: + comments: + - conditional mandatory + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + comments: + - conditional mandatory + lib_reads_seqd: + comments: + - conditional mandatory + lib_layout: + comments: + - conditional mandatory + lib_vector: + comments: + - conditional mandatory + lib_screen: + comments: + - conditional mandatory + mid: + comments: + - conditional mandatory + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + required: 'True' + assembly_qual: + required: 'True' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + required: 'False' + number_contig: + required: 'False' + feat_pred: + required: 'False' + ref_db: + required: 'False' + sim_search_meth: + required: 'False' + tax_class: + required: 'False' + x_16s_recover: + required: 'False' + x_16s_recover_software: + required: 'False' + trnas: + required: 'False' + trna_ext_software: + required: 'False' + compl_score: + required: 'True' + compl_software: + required: 'True' + compl_appr: + required: 'False' + contam_score: + required: 'True' + contam_screen_input: + required: 'False' + contam_screen_param: + required: 'False' + decontam_software: + required: 'False' + bin_param: + required: 'True' + bin_software: + required: 'True' + reassembly_bin: + required: 'False' + mag_cov_software: + required: 'False' + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + miuvig: + mixin: true + description: miuvig Checklist + todos: + - add details here + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - estimated_size + - ref_biomaterial + - source_mat_id + - pathogenicity + - biotic_relationship + - specific_host + - host_spec_range + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - source_uvig + - virus_enrich_appr + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - mid + - adapters + - seq_meth + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - trnas + - trna_ext_software + - compl_score + - compl_software + - compl_appr + - sort_tech + - single_cell_lysis_appr + - single_cell_lysis_prot + - wga_amp_appr + - wga_amp_kit + - bin_param + - bin_software + - reassembly_bin + - mag_cov_software + - vir_ident_software + - pred_genome_type + - pred_genome_struc + - detec_type + - votu_class_appr + - votu_seq_comp_appr + - votu_db + - host_pred_appr + - host_pred_est_acc + - url + - sop + slot_usage: + submitted_to_insdc: + required: 'True' + investigation_type: + required: 'True' + sample_name: {} + project_name: + required: 'True' + experimental_factor: + comments: + - conditional mandatory + lat_lon: + required: 'True' + geo_loc_name: + required: 'True' + collection_date: + required: 'True' + env_broad_scale: + required: 'True' + env_local_scale: + required: 'True' + env_medium: + required: 'True' + env_package: + comments: + - conditional mandatory + estimated_size: + required: 'False' + ref_biomaterial: + required: 'False' + source_mat_id: + comments: + - conditional mandatory + pathogenicity: + required: 'False' + biotic_relationship: + required: 'False' + specific_host: + required: 'False' + host_spec_range: + required: 'False' + samp_collect_device: + comments: + - conditional mandatory + samp_mat_process: + comments: + - conditional mandatory + size_frac: + comments: + - conditional mandatory + samp_size: + comments: + - conditional mandatory + source_uvig: + required: 'True' + virus_enrich_appr: + required: 'True' + nucl_acid_ext: + comments: + - conditional mandatory + nucl_acid_amp: + comments: + - conditional mandatory + lib_size: + comments: + - conditional mandatory + lib_reads_seqd: + comments: + - conditional mandatory + lib_layout: + comments: + - conditional mandatory + lib_vector: + comments: + - conditional mandatory + lib_screen: + comments: + - conditional mandatory + mid: + comments: + - conditional mandatory + adapters: + comments: + - conditional mandatory + seq_meth: + required: 'True' + tax_ident: + required: 'False' + assembly_qual: + required: 'True' + assembly_name: + comments: + - conditional mandatory + assembly_software: + required: 'True' + annot: + required: 'False' + number_contig: + required: 'True' + feat_pred: + comments: + - conditional mandatory + ref_db: + comments: + - conditional mandatory + sim_search_meth: + comments: + - conditional mandatory + tax_class: + comments: + - conditional mandatory + trnas: + required: 'False' + trna_ext_software: + required: 'False' + compl_score: + comments: + - conditional mandatory + compl_software: + required: 'False' + compl_appr: + comments: + - conditional mandatory + sort_tech: + comments: + - conditional mandatory + single_cell_lysis_appr: + comments: + - conditional mandatory + single_cell_lysis_prot: + comments: + - conditional mandatory + wga_amp_appr: + comments: + - conditional mandatory + wga_amp_kit: + comments: + - conditional mandatory + bin_param: + comments: + - conditional mandatory + bin_software: + comments: + - conditional mandatory + reassembly_bin: + comments: + - conditional mandatory + mag_cov_software: + required: 'False' + vir_ident_software: + required: 'True' + pred_genome_type: + required: 'True' + pred_genome_struc: + required: 'True' + detec_type: + required: 'True' + votu_class_appr: + comments: + - conditional mandatory + votu_seq_comp_appr: + comments: + - conditional mandatory + votu_db: + comments: + - conditional mandatory + host_pred_appr: + comments: + - conditional mandatory + host_pred_est_acc: + comments: + - conditional mandatory + url: + comments: + - conditional mandatory + sop: + comments: + - conditional mandatory + core: + description: Core package. Do not use this directly, this is used to build other + packages + slots: + - submitted_to_insdc + - investigation_type + - sample_name + - project_name + - experimental_factor + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium + - env_package + - subspecf_gen_lin + - ploidy + - num_replicons + - extrachrom_elements + - estimated_size + - ref_biomaterial + - source_mat_id + - pathogenicity + - biotic_relationship + - specific_host + - host_spec_range + - health_disease_stat + - trophic_level + - propagation + - encoded_traits + - rel_to_oxygen + - isol_growth_condt + - samp_collect_device + - samp_mat_process + - size_frac + - samp_size + - source_uvig + - virus_enrich_appr + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - target_gene + - target_subfragment + - pcr_primers + - mid + - adapters + - pcr_cond + - seq_meth + - seq_quality_check + - chimera_check + - tax_ident + - assembly_qual + - assembly_name + - assembly_software + - annot + - number_contig + - feat_pred + - ref_db + - sim_search_meth + - tax_class + - x_16s_recover + - x_16s_recover_software + - trnas + - trna_ext_software + - compl_score + - compl_software + - compl_appr + - contam_score + - contam_screen_input + - contam_screen_param + - decontam_software + - sort_tech + - single_cell_lysis_appr + - single_cell_lysis_prot + - wga_amp_appr + - wga_amp_kit + - bin_param - bin_software - reassembly_bin - mag_cov_software @@ -10847,6 +12030,15 @@ classes: description: air mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - barometric_press - carb_dioxide - carb_monoxide @@ -10877,6 +12069,15 @@ classes: description: built environment mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - surf_material - surf_air_cont - rel_air_humidity @@ -11042,6 +12243,15 @@ classes: description: host-associated mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - ances_data - biol_stat - genetic_mod @@ -11092,6 +12302,15 @@ classes: description: human-associated mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - host_subject_id - host_age - host_sex @@ -11146,6 +12365,15 @@ classes: description: human-gut mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - gastrointest_disord - liver_disord - special_diet @@ -11185,6 +12413,15 @@ classes: description: human-oral mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - nose_mouth_teeth_throat_disord - time_last_toothbrush - host_subject_id @@ -11223,6 +12460,15 @@ classes: description: human-skin mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - dermatology_disord - time_since_last_wash - dominant_hand @@ -11262,6 +12508,15 @@ classes: description: human-vaginal mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - menarche - sexual_act - pregnancy @@ -11308,6 +12563,15 @@ classes: description: hydrocarbon resources-cores mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - hcr - hc_produced - basin @@ -11392,6 +12656,15 @@ classes: description: hydrocarbon resources-fluids/swabs mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - hcr - hc_produced - basin @@ -11481,6 +12754,15 @@ classes: description: microbial mat/biofilm mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - alkalinity - alkyl_diethers - aminopept_act @@ -11546,6 +12828,15 @@ classes: description: miscellaneous natural or artificial environment mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - alkalinity - ammonium - biomass @@ -11592,6 +12883,15 @@ classes: description: plant-associated mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - air_temp_regm - ances_data - antibiotic_regm @@ -11668,6 +12968,15 @@ classes: description: sediment mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - alkalinity - alkyl_diethers - aminopept_act @@ -11739,6 +13048,15 @@ classes: description: soil mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - cur_land_use - cur_vegetation - cur_vegetation_meth @@ -11796,6 +13114,15 @@ classes: description: wastewater/sludge mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - alkalinity - biochem_oxygen_dem - chem_administration @@ -11838,6 +13165,15 @@ classes: description: water mappings: [] slots: + - lat_lon + - depth + - alt + - elev + - geo_loc_name + - collection_date + - env_broad_scale + - env_local_scale + - env_medium - alkalinity - alkalinity_method - alkyl_diethers @@ -11920,116 +13256,6 @@ classes: - turbidity - water_current slot_usage: {} - migs_eu: - mixin: true - description: migs_eu Checklist - todos: - - add details here - migs_ba: - mixin: true - description: migs_ba Checklist - todos: - - add details here - migs_pl: - mixin: true - description: migs_pl Checklist - todos: - - add details here - migs_vi: - mixin: true - description: migs_vi Checklist - todos: - - add details here - migs_org: - mixin: true - description: migs_org Checklist - todos: - - add details here - me: - mixin: true - description: me Checklist - todos: - - add details here - mimarks_s: - mixin: true - description: mimarks_s Checklist - todos: - - add details here - mimarks_c: - mixin: true - description: mimarks_c Checklist - todos: - - add details here - misag: - mixin: true - description: misag Checklist - todos: - - add details here - mimag: - mixin: true - description: mimag Checklist - todos: - - add details here - miuvig: - mixin: true - description: miuvig Checklist - todos: - - add details here - core migs_eu: - is_a: core - mixins: - - migs_eu - description: Combinatorial checklist for core with migs_eu - core migs_ba: - is_a: core - mixins: - - migs_ba - description: Combinatorial checklist for core with migs_ba - core migs_pl: - is_a: core - mixins: - - migs_pl - description: Combinatorial checklist for core with migs_pl - core migs_vi: - is_a: core - mixins: - - migs_vi - description: Combinatorial checklist for core with migs_vi - core migs_org: - is_a: core - mixins: - - migs_org - description: Combinatorial checklist for core with migs_org - core me: - is_a: core - mixins: - - me - description: Combinatorial checklist for core with me - core mimarks_s: - is_a: core - mixins: - - mimarks_s - description: Combinatorial checklist for core with mimarks_s - core mimarks_c: - is_a: core - mixins: - - mimarks_c - description: Combinatorial checklist for core with mimarks_c - core misag: - is_a: core - mixins: - - misag - description: Combinatorial checklist for core with misag - core mimag: - is_a: core - mixins: - - mimag - description: Combinatorial checklist for core with mimag - core miuvig: - is_a: core - mixins: - - miuvig - description: Combinatorial checklist for core with miuvig air migs_eu: is_a: air mixins: From 6e361dcc12f5da16a0a3c6b78b1dddb19f746cb3 Mon Sep 17 00:00:00 2001 From: cmungall Date: Mon, 19 Apr 2021 16:33:35 -0700 Subject: [PATCH 6/7] regen --- Makefile | 59 +- mixs6/Air.md | 24 +- mixs6/AirMIGSBacteria.md | 395 +++++ mixs6/AirMIGSEukaryote.md | 395 +++++ mixs6/AirMIGSPlant.md | 365 ++++ mixs6/AirMIGSVirus.md | 390 +++++ mixs6/AirMIMARKSSpecimen.md | 315 ++++ mixs6/AirMIMARKSSurvey.md | 295 ++++ mixs6/AirMe.md | 146 +- mixs6/AirMigsOrg.md | 162 +- mixs6/AirMimag.md | 210 +-- mixs6/AirMisag.md | 214 +-- mixs6/AirMiuvig.md | 266 +-- mixs6/BuiltEnvironment.md | 24 +- mixs6/BuiltEnvironmentMIGSBacteria.md | 935 +++++++++++ mixs6/BuiltEnvironmentMIGSEukaryote.md | 935 +++++++++++ mixs6/BuiltEnvironmentMIGSPlant.md | 905 ++++++++++ mixs6/BuiltEnvironmentMIGSVirus.md | 930 +++++++++++ mixs6/BuiltEnvironmentMIMARKSSpecimen.md | 855 ++++++++++ mixs6/BuiltEnvironmentMIMARKSSurvey.md | 835 ++++++++++ mixs6/BuiltEnvironmentMe.md | 146 +- mixs6/BuiltEnvironmentMigsOrg.md | 162 +- mixs6/BuiltEnvironmentMimag.md | 210 +-- mixs6/BuiltEnvironmentMisag.md | 214 +-- mixs6/BuiltEnvironmentMiuvig.md | 266 +-- mixs6/Host-associated.md | 24 +- mixs6/Host-associatedMIGSBacteria.md | 475 ++++++ mixs6/Host-associatedMIGSEukaryote.md | 475 ++++++ mixs6/Host-associatedMIGSPlant.md | 445 +++++ mixs6/Host-associatedMIGSVirus.md | 470 ++++++ mixs6/Host-associatedMIMARKSSpecimen.md | 395 +++++ mixs6/Host-associatedMIMARKSSurvey.md | 375 +++++ mixs6/Host-associatedMe.md | 146 +- mixs6/Host-associatedMigsOrg.md | 162 +- mixs6/Host-associatedMimag.md | 210 +-- mixs6/Host-associatedMisag.md | 214 +-- mixs6/Host-associatedMiuvig.md | 266 +-- mixs6/Human-associated.md | 24 +- mixs6/Human-associatedMIGSBacteria.md | 491 ++++++ mixs6/Human-associatedMIGSEukaryote.md | 491 ++++++ mixs6/Human-associatedMIGSPlant.md | 461 +++++ mixs6/Human-associatedMIGSVirus.md | 486 ++++++ mixs6/Human-associatedMIMARKSSpecimen.md | 411 +++++ mixs6/Human-associatedMIMARKSSurvey.md | 391 +++++ mixs6/Human-associatedMe.md | 146 +- mixs6/Human-associatedMigsOrg.md | 162 +- mixs6/Human-associatedMimag.md | 210 +-- mixs6/Human-associatedMisag.md | 214 +-- mixs6/Human-associatedMiuvig.md | 266 +-- mixs6/Human-gut.md | 24 +- mixs6/Human-gutMIGSBacteria.md | 431 +++++ mixs6/Human-gutMIGSEukaryote.md | 431 +++++ mixs6/Human-gutMIGSPlant.md | 401 +++++ mixs6/Human-gutMIGSVirus.md | 426 +++++ mixs6/Human-gutMIMARKSSpecimen.md | 351 ++++ mixs6/Human-gutMIMARKSSurvey.md | 331 ++++ mixs6/Human-gutMe.md | 146 +- mixs6/Human-gutMigsOrg.md | 162 +- mixs6/Human-gutMimag.md | 210 +-- mixs6/Human-gutMisag.md | 214 +-- mixs6/Human-gutMiuvig.md | 266 +-- mixs6/Human-oral.md | 24 +- mixs6/Human-oralMIGSBacteria.md | 427 +++++ mixs6/Human-oralMIGSEukaryote.md | 427 +++++ mixs6/Human-oralMIGSPlant.md | 397 +++++ mixs6/Human-oralMIGSVirus.md | 422 +++++ mixs6/Human-oralMIMARKSSpecimen.md | 347 ++++ mixs6/Human-oralMIMARKSSurvey.md | 327 ++++ mixs6/Human-oralMe.md | 146 +- mixs6/Human-oralMigsOrg.md | 162 +- mixs6/Human-oralMimag.md | 210 +-- mixs6/Human-oralMisag.md | 214 +-- mixs6/Human-oralMiuvig.md | 266 +-- mixs6/Human-skin.md | 24 +- mixs6/Human-skinMIGSBacteria.md | 431 +++++ mixs6/Human-skinMIGSEukaryote.md | 431 +++++ mixs6/Human-skinMIGSPlant.md | 401 +++++ mixs6/Human-skinMIGSVirus.md | 426 +++++ mixs6/Human-skinMIMARKSSpecimen.md | 351 ++++ mixs6/Human-skinMIMARKSSurvey.md | 331 ++++ mixs6/Human-skinMe.md | 146 +- mixs6/Human-skinMigsOrg.md | 162 +- mixs6/Human-skinMimag.md | 210 +-- mixs6/Human-skinMisag.md | 214 +-- mixs6/Human-skinMiuvig.md | 266 +-- mixs6/Human-vaginal.md | 24 +- mixs6/Human-vaginalMIGSBacteria.md | 459 +++++ mixs6/Human-vaginalMIGSEukaryote.md | 459 +++++ mixs6/Human-vaginalMIGSPlant.md | 429 +++++ mixs6/Human-vaginalMIGSVirus.md | 454 +++++ mixs6/Human-vaginalMIMARKSSpecimen.md | 379 +++++ mixs6/Human-vaginalMIMARKSSurvey.md | 359 ++++ mixs6/Human-vaginalMe.md | 146 +- mixs6/Human-vaginalMigsOrg.md | 162 +- mixs6/Human-vaginalMimag.md | 210 +-- mixs6/Human-vaginalMisag.md | 214 +-- mixs6/Human-vaginalMiuvig.md | 266 +-- mixs6/HydrocarbonResources-cores.md | 24 +- .../HydrocarbonResources-coresMIGSBacteria.md | 611 +++++++ ...HydrocarbonResources-coresMIGSEukaryote.md | 611 +++++++ mixs6/HydrocarbonResources-coresMIGSPlant.md | 581 +++++++ mixs6/HydrocarbonResources-coresMIGSVirus.md | 606 +++++++ ...drocarbonResources-coresMIMARKSSpecimen.md | 531 ++++++ ...HydrocarbonResources-coresMIMARKSSurvey.md | 511 ++++++ mixs6/HydrocarbonResources-coresMe.md | 146 +- mixs6/HydrocarbonResources-coresMigsOrg.md | 162 +- mixs6/HydrocarbonResources-coresMimag.md | 210 +-- mixs6/HydrocarbonResources-coresMisag.md | 214 +-- mixs6/HydrocarbonResources-coresMiuvig.md | 266 +-- mixs6/HydrocarbonResources-fluidsSwabs.md | 24 +- ...carbonResources-fluidsSwabsMIGSBacteria.md | 631 +++++++ ...arbonResources-fluidsSwabsMIGSEukaryote.md | 631 +++++++ ...drocarbonResources-fluidsSwabsMIGSPlant.md | 601 +++++++ ...drocarbonResources-fluidsSwabsMIGSVirus.md | 626 +++++++ ...bonResources-fluidsSwabsMIMARKSSpecimen.md | 551 ++++++ ...arbonResources-fluidsSwabsMIMARKSSurvey.md | 531 ++++++ mixs6/HydrocarbonResources-fluidsSwabsMe.md | 146 +- ...HydrocarbonResources-fluidsSwabsMigsOrg.md | 162 +- .../HydrocarbonResources-fluidsSwabsMimag.md | 210 +-- .../HydrocarbonResources-fluidsSwabsMisag.md | 214 +-- .../HydrocarbonResources-fluidsSwabsMiuvig.md | 266 +-- mixs6/MIGSBacteria.md | 152 ++ mixs6/MIGSEukaryote.md | 152 ++ mixs6/MIGSPlant.md | 140 ++ mixs6/MIGSVirus.md | 150 ++ mixs6/MIGS_bacteria_adapters.md | 47 + mixs6/MIGS_bacteria_annot.md | 47 + mixs6/MIGS_bacteria_assembly_name.md | 47 + mixs6/MIGS_bacteria_assembly_qual.md | 40 + mixs6/MIGS_bacteria_assembly_software.md | 40 + mixs6/MIGS_bacteria_biotic_relationship.md | 47 + mixs6/MIGS_bacteria_collection_date.md | 23 + mixs6/MIGS_bacteria_compl_score.md | 40 + mixs6/MIGS_bacteria_compl_software.md | 40 + mixs6/MIGS_bacteria_encoded_traits.md | 40 + mixs6/MIGS_bacteria_env_broad_scale.md | 23 + mixs6/MIGS_bacteria_env_local_scale.md | 23 + mixs6/MIGS_bacteria_env_medium.md | 23 + mixs6/MIGS_bacteria_env_package.md | 47 + mixs6/MIGS_bacteria_estimated_size.md | 40 + mixs6/MIGS_bacteria_experimental_factor.md | 40 + mixs6/MIGS_bacteria_extrachrom_elements.md | 47 + mixs6/MIGS_bacteria_feat_pred.md | 40 + mixs6/MIGS_bacteria_geo_loc_name.md | 23 + mixs6/MIGS_bacteria_health_disease_stat.md | 47 + mixs6/MIGS_bacteria_host_spec_range.md | 40 + mixs6/MIGS_bacteria_investigation_type.md | 40 + mixs6/MIGS_bacteria_isol_growth_condt.md | 40 + mixs6/MIGS_bacteria_lat_lon.md | 23 + mixs6/MIGS_bacteria_lib_layout.md | 40 + mixs6/MIGS_bacteria_lib_reads_seqd.md | 40 + mixs6/MIGS_bacteria_lib_screen.md | 40 + mixs6/MIGS_bacteria_lib_size.md | 40 + mixs6/MIGS_bacteria_lib_vector.md | 40 + mixs6/MIGS_bacteria_nucl_acid_amp.md | 47 + mixs6/MIGS_bacteria_nucl_acid_ext.md | 47 + mixs6/MIGS_bacteria_num_replicons.md | 40 + mixs6/MIGS_bacteria_number_contig.md | 40 + mixs6/MIGS_bacteria_pathogenicity.md | 47 + mixs6/MIGS_bacteria_project_name.md | 40 + mixs6/MIGS_bacteria_ref_biomaterial.md | 40 + mixs6/MIGS_bacteria_ref_db.md | 40 + mixs6/MIGS_bacteria_rel_to_oxygen.md | 47 + mixs6/MIGS_bacteria_samp_collect_device.md | 40 + mixs6/MIGS_bacteria_samp_mat_process.md | 40 + mixs6/MIGS_bacteria_samp_size.md | 40 + mixs6/MIGS_bacteria_sample_name.md | 40 + mixs6/MIGS_bacteria_seq_meth.md | 40 + mixs6/MIGS_bacteria_sim_search_meth.md | 40 + mixs6/MIGS_bacteria_sop.md | 47 + mixs6/MIGS_bacteria_source_mat_id.md | 47 + mixs6/MIGS_bacteria_specific_host.md | 47 + mixs6/MIGS_bacteria_submitted_to_insdc.md | 40 + mixs6/MIGS_bacteria_subspecf_gen_lin.md | 47 + mixs6/MIGS_bacteria_tax_class.md | 40 + mixs6/MIGS_bacteria_tax_ident.md | 47 + mixs6/MIGS_bacteria_trophic_level.md | 47 + mixs6/MIGS_bacteria_url.md | 47 + mixs6/MIGS_eukaryote_adapters.md | 47 + mixs6/MIGS_eukaryote_annot.md | 47 + mixs6/MIGS_eukaryote_assembly_name.md | 47 + mixs6/MIGS_eukaryote_assembly_qual.md | 40 + mixs6/MIGS_eukaryote_assembly_software.md | 40 + mixs6/MIGS_eukaryote_biotic_relationship.md | 40 + mixs6/MIGS_eukaryote_collection_date.md | 23 + mixs6/MIGS_eukaryote_compl_score.md | 40 + mixs6/MIGS_eukaryote_compl_software.md | 40 + mixs6/MIGS_eukaryote_env_broad_scale.md | 23 + mixs6/MIGS_eukaryote_env_local_scale.md | 23 + mixs6/MIGS_eukaryote_env_medium.md | 23 + mixs6/MIGS_eukaryote_env_package.md | 47 + mixs6/MIGS_eukaryote_estimated_size.md | 40 + mixs6/MIGS_eukaryote_experimental_factor.md | 40 + mixs6/MIGS_eukaryote_extrachrom_elements.md | 40 + mixs6/MIGS_eukaryote_feat_pred.md | 40 + mixs6/MIGS_eukaryote_geo_loc_name.md | 23 + mixs6/MIGS_eukaryote_health_disease_stat.md | 40 + mixs6/MIGS_eukaryote_host_spec_range.md | 40 + mixs6/MIGS_eukaryote_investigation_type.md | 40 + mixs6/MIGS_eukaryote_isol_growth_condt.md | 40 + mixs6/MIGS_eukaryote_lat_lon.md | 23 + mixs6/MIGS_eukaryote_lib_layout.md | 40 + mixs6/MIGS_eukaryote_lib_reads_seqd.md | 40 + mixs6/MIGS_eukaryote_lib_screen.md | 40 + mixs6/MIGS_eukaryote_lib_size.md | 40 + mixs6/MIGS_eukaryote_lib_vector.md | 40 + mixs6/MIGS_eukaryote_nucl_acid_amp.md | 47 + mixs6/MIGS_eukaryote_nucl_acid_ext.md | 47 + mixs6/MIGS_eukaryote_num_replicons.md | 40 + mixs6/MIGS_eukaryote_number_contig.md | 40 + mixs6/MIGS_eukaryote_pathogenicity.md | 47 + mixs6/MIGS_eukaryote_ploidy.md | 40 + mixs6/MIGS_eukaryote_project_name.md | 40 + mixs6/MIGS_eukaryote_propagation.md | 47 + mixs6/MIGS_eukaryote_ref_biomaterial.md | 40 + mixs6/MIGS_eukaryote_ref_db.md | 40 + mixs6/MIGS_eukaryote_samp_collect_device.md | 40 + mixs6/MIGS_eukaryote_samp_mat_process.md | 40 + mixs6/MIGS_eukaryote_samp_size.md | 40 + mixs6/MIGS_eukaryote_sample_name.md | 40 + mixs6/MIGS_eukaryote_seq_meth.md | 40 + mixs6/MIGS_eukaryote_sim_search_meth.md | 40 + mixs6/MIGS_eukaryote_sop.md | 47 + mixs6/MIGS_eukaryote_source_mat_id.md | 47 + mixs6/MIGS_eukaryote_specific_host.md | 40 + mixs6/MIGS_eukaryote_submitted_to_insdc.md | 40 + mixs6/MIGS_eukaryote_subspecf_gen_lin.md | 47 + mixs6/MIGS_eukaryote_tax_class.md | 40 + mixs6/MIGS_eukaryote_tax_ident.md | 47 + mixs6/MIGS_eukaryote_trophic_level.md | 47 + mixs6/MIGS_eukaryote_url.md | 47 + mixs6/MIGS_plant_adapters.md | 47 + mixs6/MIGS_plant_annot.md | 47 + mixs6/MIGS_plant_assembly_name.md | 47 + mixs6/MIGS_plant_assembly_qual.md | 40 + mixs6/MIGS_plant_assembly_software.md | 40 + mixs6/MIGS_plant_collection_date.md | 23 + mixs6/MIGS_plant_compl_score.md | 40 + mixs6/MIGS_plant_compl_software.md | 40 + mixs6/MIGS_plant_encoded_traits.md | 47 + mixs6/MIGS_plant_env_broad_scale.md | 23 + mixs6/MIGS_plant_env_local_scale.md | 23 + mixs6/MIGS_plant_env_medium.md | 23 + mixs6/MIGS_plant_env_package.md | 47 + mixs6/MIGS_plant_estimated_size.md | 40 + mixs6/MIGS_plant_experimental_factor.md | 40 + mixs6/MIGS_plant_feat_pred.md | 40 + mixs6/MIGS_plant_geo_loc_name.md | 23 + mixs6/MIGS_plant_host_spec_range.md | 40 + mixs6/MIGS_plant_investigation_type.md | 40 + mixs6/MIGS_plant_isol_growth_condt.md | 40 + mixs6/MIGS_plant_lat_lon.md | 23 + mixs6/MIGS_plant_lib_layout.md | 40 + mixs6/MIGS_plant_lib_reads_seqd.md | 40 + mixs6/MIGS_plant_lib_screen.md | 40 + mixs6/MIGS_plant_lib_size.md | 40 + mixs6/MIGS_plant_lib_vector.md | 40 + mixs6/MIGS_plant_nucl_acid_amp.md | 47 + mixs6/MIGS_plant_nucl_acid_ext.md | 47 + mixs6/MIGS_plant_number_contig.md | 40 + mixs6/MIGS_plant_project_name.md | 40 + mixs6/MIGS_plant_propagation.md | 40 + mixs6/MIGS_plant_ref_biomaterial.md | 40 + mixs6/MIGS_plant_ref_db.md | 40 + mixs6/MIGS_plant_samp_collect_device.md | 40 + mixs6/MIGS_plant_samp_mat_process.md | 40 + mixs6/MIGS_plant_samp_size.md | 40 + mixs6/MIGS_plant_sample_name.md | 40 + mixs6/MIGS_plant_seq_meth.md | 40 + mixs6/MIGS_plant_sim_search_meth.md | 40 + mixs6/MIGS_plant_sop.md | 47 + mixs6/MIGS_plant_source_mat_id.md | 47 + mixs6/MIGS_plant_specific_host.md | 47 + mixs6/MIGS_plant_submitted_to_insdc.md | 40 + mixs6/MIGS_plant_subspecf_gen_lin.md | 47 + mixs6/MIGS_plant_tax_class.md | 40 + mixs6/MIGS_plant_tax_ident.md | 47 + mixs6/MIGS_plant_url.md | 47 + mixs6/MIGS_virus_adapters.md | 47 + mixs6/MIGS_virus_annot.md | 47 + mixs6/MIGS_virus_assembly_name.md | 47 + mixs6/MIGS_virus_assembly_qual.md | 40 + mixs6/MIGS_virus_assembly_software.md | 40 + mixs6/MIGS_virus_biotic_relationship.md | 40 + mixs6/MIGS_virus_collection_date.md | 23 + mixs6/MIGS_virus_compl_score.md | 40 + mixs6/MIGS_virus_compl_software.md | 40 + mixs6/MIGS_virus_encoded_traits.md | 47 + mixs6/MIGS_virus_env_broad_scale.md | 23 + mixs6/MIGS_virus_env_local_scale.md | 23 + mixs6/MIGS_virus_env_medium.md | 23 + mixs6/MIGS_virus_env_package.md | 47 + mixs6/MIGS_virus_estimated_size.md | 40 + mixs6/MIGS_virus_experimental_factor.md | 40 + mixs6/MIGS_virus_feat_pred.md | 40 + mixs6/MIGS_virus_geo_loc_name.md | 23 + mixs6/MIGS_virus_health_disease_stat.md | 47 + mixs6/MIGS_virus_host_spec_range.md | 47 + mixs6/MIGS_virus_investigation_type.md | 40 + mixs6/MIGS_virus_isol_growth_condt.md | 40 + mixs6/MIGS_virus_lat_lon.md | 23 + mixs6/MIGS_virus_lib_layout.md | 40 + mixs6/MIGS_virus_lib_reads_seqd.md | 40 + mixs6/MIGS_virus_lib_screen.md | 40 + mixs6/MIGS_virus_lib_size.md | 40 + mixs6/MIGS_virus_lib_vector.md | 40 + mixs6/MIGS_virus_nucl_acid_amp.md | 47 + mixs6/MIGS_virus_nucl_acid_ext.md | 47 + mixs6/MIGS_virus_num_replicons.md | 47 + mixs6/MIGS_virus_number_contig.md | 40 + mixs6/MIGS_virus_pathogenicity.md | 47 + mixs6/MIGS_virus_project_name.md | 40 + mixs6/MIGS_virus_propagation.md | 40 + mixs6/MIGS_virus_ref_biomaterial.md | 40 + mixs6/MIGS_virus_ref_db.md | 40 + mixs6/MIGS_virus_samp_collect_device.md | 40 + mixs6/MIGS_virus_samp_mat_process.md | 40 + mixs6/MIGS_virus_samp_size.md | 40 + mixs6/MIGS_virus_sample_name.md | 40 + mixs6/MIGS_virus_seq_meth.md | 40 + mixs6/MIGS_virus_sim_search_meth.md | 40 + mixs6/MIGS_virus_sop.md | 47 + mixs6/MIGS_virus_source_mat_id.md | 47 + mixs6/MIGS_virus_specific_host.md | 47 + mixs6/MIGS_virus_submitted_to_insdc.md | 40 + mixs6/MIGS_virus_subspecf_gen_lin.md | 47 + mixs6/MIGS_virus_tax_class.md | 40 + mixs6/MIGS_virus_tax_ident.md | 47 + mixs6/MIGS_virus_url.md | 47 + mixs6/MIGS_virus_virus_enrich_appr.md | 47 + mixs6/MIMARKSSpecimen.md | 120 ++ mixs6/MIMARKSSurvey.md | 112 ++ mixs6/MIMARKS_specimen_adapters.md | 47 + mixs6/MIMARKS_specimen_assembly_software.md | 47 + mixs6/MIMARKS_specimen_chimera_check.md | 47 + mixs6/MIMARKS_specimen_collection_date.md | 23 + mixs6/MIMARKS_specimen_env_broad_scale.md | 23 + mixs6/MIMARKS_specimen_env_local_scale.md | 23 + mixs6/MIMARKS_specimen_env_medium.md | 23 + mixs6/MIMARKS_specimen_env_package.md | 47 + mixs6/MIMARKS_specimen_experimental_factor.md | 47 + mixs6/MIMARKS_specimen_geo_loc_name.md | 23 + mixs6/MIMARKS_specimen_investigation_type.md | 40 + mixs6/MIMARKS_specimen_lat_lon.md | 23 + mixs6/MIMARKS_specimen_lib_layout.md | 47 + mixs6/MIMARKS_specimen_lib_reads_seqd.md | 47 + mixs6/MIMARKS_specimen_lib_screen.md | 47 + mixs6/MIMARKS_specimen_lib_size.md | 47 + mixs6/MIMARKS_specimen_lib_vector.md | 47 + mixs6/MIMARKS_specimen_mid.md | 47 + mixs6/MIMARKS_specimen_nucl_acid_amp.md | 47 + mixs6/MIMARKS_specimen_nucl_acid_ext.md | 47 + mixs6/MIMARKS_specimen_pcr_cond.md | 47 + mixs6/MIMARKS_specimen_pcr_primers.md | 47 + mixs6/MIMARKS_specimen_project_name.md | 40 + mixs6/MIMARKS_specimen_rel_to_oxygen.md | 40 + mixs6/MIMARKS_specimen_samp_collect_device.md | 47 + mixs6/MIMARKS_specimen_samp_mat_process.md | 47 + mixs6/MIMARKS_specimen_samp_size.md | 47 + mixs6/MIMARKS_specimen_sample_name.md | 40 + mixs6/MIMARKS_specimen_seq_meth.md | 40 + mixs6/MIMARKS_specimen_seq_quality_check.md | 47 + mixs6/MIMARKS_specimen_size_frac.md | 40 + mixs6/MIMARKS_specimen_sop.md | 47 + mixs6/MIMARKS_specimen_source_mat_id.md | 47 + mixs6/MIMARKS_specimen_submitted_to_insdc.md | 40 + mixs6/MIMARKS_specimen_target_gene.md | 40 + mixs6/MIMARKS_specimen_target_subfragment.md | 47 + mixs6/MIMARKS_specimen_url.md | 47 + mixs6/MIMARKS_survey_biotic_relationship.md | 47 + mixs6/MIMARKS_survey_chimera_check.md | 47 + mixs6/MIMARKS_survey_collection_date.md | 23 + mixs6/MIMARKS_survey_env_broad_scale.md | 23 + mixs6/MIMARKS_survey_env_local_scale.md | 23 + mixs6/MIMARKS_survey_env_medium.md | 23 + mixs6/MIMARKS_survey_env_package.md | 47 + mixs6/MIMARKS_survey_experimental_factor.md | 40 + mixs6/MIMARKS_survey_extrachrom_elements.md | 40 + mixs6/MIMARKS_survey_geo_loc_name.md | 23 + mixs6/MIMARKS_survey_investigation_type.md | 40 + mixs6/MIMARKS_survey_isol_growth_condt.md | 40 + mixs6/MIMARKS_survey_lat_lon.md | 23 + mixs6/MIMARKS_survey_nucl_acid_amp.md | 47 + mixs6/MIMARKS_survey_nucl_acid_ext.md | 47 + mixs6/MIMARKS_survey_pcr_cond.md | 47 + mixs6/MIMARKS_survey_pcr_primers.md | 47 + mixs6/MIMARKS_survey_project_name.md | 40 + mixs6/MIMARKS_survey_rel_to_oxygen.md | 47 + mixs6/MIMARKS_survey_samp_collect_device.md | 40 + mixs6/MIMARKS_survey_samp_mat_process.md | 47 + mixs6/MIMARKS_survey_samp_size.md | 40 + mixs6/MIMARKS_survey_sample_name.md | 40 + mixs6/MIMARKS_survey_seq_meth.md | 40 + mixs6/MIMARKS_survey_seq_quality_check.md | 47 + mixs6/MIMARKS_survey_sop.md | 47 + mixs6/MIMARKS_survey_source_mat_id.md | 47 + mixs6/MIMARKS_survey_submitted_to_insdc.md | 40 + mixs6/MIMARKS_survey_subspecf_gen_lin.md | 47 + mixs6/MIMARKS_survey_target_gene.md | 40 + mixs6/MIMARKS_survey_target_subfragment.md | 47 + mixs6/MIMARKS_survey_trophic_level.md | 47 + mixs6/MIMARKS_survey_url.md | 47 + mixs6/Me.md | 129 +- mixs6/MicrobialMatBiofilm.md | 24 +- mixs6/MicrobialMatBiofilmMIGSBacteria.md | 535 ++++++ mixs6/MicrobialMatBiofilmMIGSEukaryote.md | 535 ++++++ mixs6/MicrobialMatBiofilmMIGSPlant.md | 505 ++++++ mixs6/MicrobialMatBiofilmMIGSVirus.md | 530 ++++++ mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md | 455 +++++ mixs6/MicrobialMatBiofilmMIMARKSSurvey.md | 435 +++++ mixs6/MicrobialMatBiofilmMe.md | 146 +- mixs6/MicrobialMatBiofilmMigsOrg.md | 162 +- mixs6/MicrobialMatBiofilmMimag.md | 210 +-- mixs6/MicrobialMatBiofilmMisag.md | 214 +-- mixs6/MicrobialMatBiofilmMiuvig.md | 266 +-- mixs6/MigsOrg.md | 137 +- mixs6/Mimag.md | 161 +- mixs6/Misag.md | 163 +- ...ellaneousNaturalOrArtificialEnvironment.md | 24 +- ...uralOrArtificialEnvironmentMIGSBacteria.md | 459 +++++ ...ralOrArtificialEnvironmentMIGSEukaryote.md | 459 +++++ ...NaturalOrArtificialEnvironmentMIGSPlant.md | 429 +++++ ...NaturalOrArtificialEnvironmentMIGSVirus.md | 454 +++++ ...lOrArtificialEnvironmentMIMARKSSpecimen.md | 379 +++++ ...ralOrArtificialEnvironmentMIMARKSSurvey.md | 359 ++++ ...laneousNaturalOrArtificialEnvironmentMe.md | 146 +- ...usNaturalOrArtificialEnvironmentMigsOrg.md | 162 +- ...eousNaturalOrArtificialEnvironmentMimag.md | 210 +-- ...eousNaturalOrArtificialEnvironmentMisag.md | 214 +-- ...ousNaturalOrArtificialEnvironmentMiuvig.md | 266 +-- mixs6/Miuvig.md | 189 ++- mixs6/Plant-associated.md | 24 +- mixs6/Plant-associatedMIGSBacteria.md | 579 +++++++ mixs6/Plant-associatedMIGSEukaryote.md | 579 +++++++ mixs6/Plant-associatedMIGSPlant.md | 549 ++++++ mixs6/Plant-associatedMIGSVirus.md | 574 +++++++ mixs6/Plant-associatedMIMARKSSpecimen.md | 499 ++++++ mixs6/Plant-associatedMIMARKSSurvey.md | 479 ++++++ mixs6/Plant-associatedMe.md | 146 +- mixs6/Plant-associatedMigsOrg.md | 162 +- mixs6/Plant-associatedMimag.md | 210 +-- mixs6/Plant-associatedMisag.md | 214 +-- mixs6/Plant-associatedMiuvig.md | 266 +-- mixs6/QuantityValue.md | 196 +++ mixs6/Sediment.md | 24 +- mixs6/SedimentMIGSBacteria.md | 559 +++++++ mixs6/SedimentMIGSEukaryote.md | 559 +++++++ mixs6/SedimentMIGSPlant.md | 529 ++++++ mixs6/SedimentMIGSVirus.md | 554 ++++++ mixs6/SedimentMIMARKSSpecimen.md | 479 ++++++ mixs6/SedimentMIMARKSSurvey.md | 459 +++++ mixs6/SedimentMe.md | 146 +- mixs6/SedimentMigsOrg.md | 162 +- mixs6/SedimentMimag.md | 210 +-- mixs6/SedimentMisag.md | 214 +-- mixs6/SedimentMiuvig.md | 266 +-- mixs6/Soil.md | 24 +- mixs6/SoilMIGSBacteria.md | 503 ++++++ mixs6/SoilMIGSEukaryote.md | 503 ++++++ mixs6/SoilMIGSPlant.md | 473 ++++++ mixs6/SoilMIGSVirus.md | 498 ++++++ mixs6/SoilMIMARKSSpecimen.md | 423 +++++ mixs6/SoilMIMARKSSurvey.md | 403 +++++ mixs6/SoilMe.md | 146 +- mixs6/SoilMigsOrg.md | 162 +- mixs6/SoilMimag.md | 210 +-- mixs6/SoilMisag.md | 214 +-- mixs6/SoilMiuvig.md | 266 +-- mixs6/WastewaterSludge.md | 24 +- mixs6/WastewaterSludgeMIGSBacteria.md | 443 +++++ mixs6/WastewaterSludgeMIGSEukaryote.md | 443 +++++ mixs6/WastewaterSludgeMIGSPlant.md | 413 +++++ mixs6/WastewaterSludgeMIGSVirus.md | 438 +++++ mixs6/WastewaterSludgeMIMARKSSpecimen.md | 363 ++++ mixs6/WastewaterSludgeMIMARKSSurvey.md | 343 ++++ mixs6/WastewaterSludgeMe.md | 146 +- mixs6/WastewaterSludgeMigsOrg.md | 162 +- mixs6/WastewaterSludgeMimag.md | 210 +-- mixs6/WastewaterSludgeMisag.md | 214 +-- mixs6/WastewaterSludgeMiuvig.md | 266 +-- mixs6/Water.md | 24 +- mixs6/WaterMIGSBacteria.md | 619 +++++++ mixs6/WaterMIGSEukaryote.md | 619 +++++++ mixs6/WaterMIGSPlant.md | 589 +++++++ mixs6/WaterMIGSVirus.md | 614 +++++++ mixs6/WaterMIMARKSSpecimen.md | 539 ++++++ mixs6/WaterMIMARKSSurvey.md | 519 ++++++ mixs6/WaterMe.md | 146 +- mixs6/WaterMigsOrg.md | 162 +- mixs6/WaterMimag.md | 210 +-- mixs6/WaterMisag.md | 214 +-- mixs6/WaterMiuvig.md | 266 +-- mixs6/abs_air_humidity.md | 22 +- mixs6/adapters.md | 20 +- mixs6/add_recov_method.md | 22 +- mixs6/additional_info.md | 44 +- mixs6/address.md | 22 +- mixs6/adj_room.md | 22 +- mixs6/aero_struc.md | 22 +- mixs6/agrochem_addition.md | 22 +- mixs6/air_temp.md | 22 +- mixs6/air_temp_regm.md | 22 +- mixs6/al_sat.md | 22 +- mixs6/al_sat_meth.md | 22 +- mixs6/alkalinity.md | 154 +- mixs6/alkalinity_method.md | 66 +- mixs6/alkyl_diethers.md | 66 +- mixs6/alt.md | 374 ++--- mixs6/aminopept_act.md | 66 +- mixs6/ammonium.md | 132 +- mixs6/amniotic_fluid_color.md | 22 +- mixs6/amount_light.md | 22 +- mixs6/ances_data.md | 44 +- mixs6/annot.md | 18 +- mixs6/annual_precpt.md | 22 +- mixs6/annual_temp.md | 22 +- mixs6/antibiotic_regm.md | 22 +- mixs6/api.md | 44 +- mixs6/arch_struc.md | 22 +- mixs6/aromatics_pc.md | 44 +- mixs6/asphaltenes_pc.md | 44 +- mixs6/assembly_name.md | 18 +- mixs6/assembly_qual.md | 18 +- mixs6/assembly_software.md | 20 +- mixs6/atmospheric_data.md | 22 +- mixs6/avg_dew_point.md | 22 +- mixs6/avg_occup.md | 22 +- mixs6/avg_temp.md | 22 +- mixs6/bac_prod.md | 22 +- mixs6/bac_resp.md | 22 +- mixs6/bacteria_carb_prod.md | 66 +- mixs6/barometric_press.md | 22 +- mixs6/basin.md | 44 +- mixs6/bathroom_count.md | 22 +- mixs6/bedroom_count.md | 22 +- mixs6/benzene.md | 44 +- mixs6/bin_param.md | 4 +- mixs6/bin_software.md | 4 +- mixs6/biochem_oxygen_dem.md | 22 +- mixs6/biocide.md | 22 +- mixs6/biocide_admin_method.md | 22 +- mixs6/biol_stat.md | 44 +- mixs6/biomass.md | 88 +- mixs6/biotic_regm.md | 22 +- mixs6/biotic_relationship.md | 10 +- mixs6/birth_control.md | 22 +- mixs6/bishomohopanol.md | 66 +- mixs6/blood_blood_disord.md | 22 +- mixs6/bromide.md | 88 +- mixs6/build_docs.md | 22 +- mixs6/build_occup_type.md | 22 +- mixs6/building_setting.md | 22 +- mixs6/built_struc_age.md | 22 +- mixs6/built_struc_set.md | 22 +- mixs6/built_struc_type.md | 22 +- mixs6/calcium.md | 132 +- mixs6/carb_dioxide.md | 44 +- mixs6/carb_monoxide.md | 22 +- mixs6/carb_nitro_ratio.md | 66 +- mixs6/ceil_area.md | 22 +- mixs6/ceil_cond.md | 22 +- mixs6/ceil_finish_mat.md | 22 +- mixs6/ceil_struc.md | 22 +- mixs6/ceil_texture.md | 22 +- mixs6/ceil_thermal_mass.md | 22 +- mixs6/ceil_type.md | 22 +- mixs6/ceil_water_mold.md | 22 +- mixs6/chem_administration.md | 286 ++-- mixs6/chem_mutagen.md | 22 +- mixs6/chem_oxygen_dem.md | 22 +- mixs6/chem_treatment.md | 22 +- mixs6/chem_treatment_method.md | 22 +- mixs6/chimera_check.md | 4 +- mixs6/chloride.md | 132 +- mixs6/chlorophyll.md | 88 +- mixs6/climate_environment.md | 22 +- mixs6/collection_date.md | 396 ++--- mixs6/compl_appr.md | 6 +- mixs6/compl_score.md | 16 +- mixs6/compl_software.md | 16 +- mixs6/conduc.md | 22 +- mixs6/contam_score.md | 4 +- mixs6/contam_screen_input.md | 4 +- mixs6/contam_screen_param.md | 4 +- mixs6/cool_syst_id.md | 22 +- mixs6/crop_rotation.md | 22 +- mixs6/cult_root_med.md | 22 +- mixs6/cur_land_use.md | 22 +- mixs6/cur_vegetation.md | 22 +- mixs6/cur_vegetation_meth.md | 22 +- mixs6/date_last_rain.md | 22 +- mixs6/decontam_software.md | 4 +- mixs6/density.md | 110 +- mixs6/depos_env.md | 44 +- mixs6/depth.md | 374 ++--- mixs6/dermatology_disord.md | 22 +- mixs6/detec_type.md | 2 +- mixs6/dew_point.md | 22 +- mixs6/diet_last_six_month.md | 22 +- mixs6/diether_lipids.md | 88 +- mixs6/diss_carb_dioxide.md | 132 +- mixs6/diss_hydrogen.md | 88 +- mixs6/diss_inorg_carb.md | 132 +- mixs6/diss_inorg_nitro.md | 22 +- mixs6/diss_inorg_phosp.md | 66 +- mixs6/diss_iron.md | 44 +- mixs6/diss_org_carb.md | 110 +- mixs6/diss_org_nitro.md | 88 +- mixs6/diss_oxygen.md | 88 +- mixs6/diss_oxygen_fluid.md | 44 +- mixs6/dominant_hand.md | 22 +- mixs6/door_comp_type.md | 22 +- mixs6/door_cond.md | 22 +- mixs6/door_direct.md | 22 +- mixs6/door_loc.md | 22 +- mixs6/door_mat.md | 22 +- mixs6/door_move.md | 22 +- mixs6/door_size.md | 22 +- mixs6/door_type.md | 22 +- mixs6/door_type_metal.md | 22 +- mixs6/door_type_wood.md | 22 +- mixs6/door_water_mold.md | 22 +- mixs6/douche.md | 22 +- mixs6/down_par.md | 22 +- mixs6/drainage_class.md | 22 +- mixs6/drawings.md | 22 +- mixs6/drug_usage.md | 22 +- mixs6/efficiency_percent.md | 22 +- mixs6/elev.md | 374 ++--- mixs6/elevator.md | 22 +- mixs6/emulsions.md | 22 +- mixs6/encoded_traits.md | 6 +- mixs6/env_broad_scale.md | 396 ++--- mixs6/env_local_scale.md | 396 ++--- mixs6/env_medium.md | 396 ++--- mixs6/env_package.md | 22 +- mixs6/escalator.md | 22 +- mixs6/estimated_size.md | 12 +- mixs6/ethylbenzene.md | 44 +- mixs6/exp_duct.md | 22 +- mixs6/exp_pipe.md | 22 +- mixs6/experimental_factor.md | 22 +- mixs6/ext_door.md | 22 +- mixs6/ext_wall_orient.md | 22 +- mixs6/ext_window_orient.md | 22 +- mixs6/extrachrom_elements.md | 8 +- mixs6/extreme_event.md | 22 +- mixs6/extreme_salinity.md | 22 +- mixs6/fao_class.md | 22 +- mixs6/feat_pred.md | 18 +- mixs6/fertilizer_regm.md | 22 +- mixs6/field.md | 44 +- mixs6/filter_type.md | 22 +- mixs6/fire.md | 22 +- mixs6/fireplace_type.md | 22 +- mixs6/flooding.md | 22 +- mixs6/floor_age.md | 22 +- mixs6/floor_area.md | 22 +- mixs6/floor_cond.md | 22 +- mixs6/floor_count.md | 22 +- mixs6/floor_finish_mat.md | 22 +- mixs6/floor_struc.md | 22 +- mixs6/floor_thermal_mass.md | 22 +- mixs6/floor_water_mold.md | 22 +- mixs6/fluor.md | 22 +- mixs6/foetal_health_stat.md | 22 +- mixs6/freq_clean.md | 22 +- mixs6/freq_cook.md | 22 +- mixs6/fungicide_regm.md | 22 +- mixs6/furniture.md | 22 +- mixs6/gaseous_environment.md | 22 +- mixs6/gaseous_substances.md | 22 +- mixs6/gastrointest_disord.md | 22 +- mixs6/gender_restroom.md | 22 +- mixs6/genetic_mod.md | 44 +- mixs6/geo_loc_name.md | 396 ++--- mixs6/gestation_state.md | 22 +- mixs6/glucosidase_act.md | 66 +- mixs6/gravidity.md | 22 +- mixs6/gravity.md | 22 +- mixs6/growth_facil.md | 22 +- mixs6/growth_habit.md | 22 +- mixs6/growth_hormone_regm.md | 22 +- mixs6/gynecologic_disord.md | 22 +- mixs6/hall_count.md | 22 +- mixs6/handidness.md | 22 +- mixs6/hc_produced.md | 44 +- mixs6/hcr.md | 44 +- mixs6/hcr_fw_salinity.md | 44 +- mixs6/hcr_geol_age.md | 44 +- mixs6/hcr_pressure.md | 44 +- mixs6/hcr_temp.md | 44 +- mixs6/health_disease_stat.md | 6 +- mixs6/heat_cool_type.md | 22 +- mixs6/heat_deliv_loc.md | 22 +- mixs6/heat_system_deliv_meth.md | 22 +- mixs6/heat_system_id.md | 22 +- mixs6/heavy_metals.md | 22 +- mixs6/heavy_metals_meth.md | 22 +- mixs6/height_carper_fiber.md | 22 +- mixs6/herbicide_regm.md | 22 +- mixs6/horizon.md | 22 +- mixs6/horizon_meth.md | 22 +- mixs6/host_age.md | 154 +- mixs6/host_blood_press_diast.md | 22 +- mixs6/host_blood_press_syst.md | 22 +- mixs6/host_body_habitat.md | 22 +- mixs6/host_body_mass_index.md | 110 +- mixs6/host_body_product.md | 132 +- mixs6/host_body_site.md | 132 +- mixs6/host_body_temp.md | 132 +- mixs6/host_color.md | 22 +- mixs6/host_common_name.md | 44 +- mixs6/host_diet.md | 132 +- mixs6/host_disease_stat.md | 154 +- mixs6/host_dry_mass.md | 44 +- mixs6/host_family_relationship.md | 132 +- mixs6/host_genotype.md | 154 +- mixs6/host_growth_cond.md | 22 +- mixs6/host_height.md | 154 +- mixs6/host_hiv_stat.md | 22 +- mixs6/host_infra_specific_name.md | 44 +- mixs6/host_infra_specific_rank.md | 44 +- mixs6/host_last_meal.md | 132 +- mixs6/host_length.md | 44 +- mixs6/host_life_stage.md | 44 +- mixs6/host_occupation.md | 110 +- mixs6/host_phenotype.md | 154 +- mixs6/host_pred_appr.md | 2 +- mixs6/host_pred_est_acc.md | 2 +- mixs6/host_pulse.md | 110 +- mixs6/host_sex.md | 132 +- mixs6/host_shape.md | 22 +- mixs6/host_spec_range.md | 10 +- mixs6/host_subject_id.md | 132 +- mixs6/host_substrate.md | 22 +- mixs6/host_taxid.md | 44 +- mixs6/host_tot_mass.md | 154 +- mixs6/host_wet_mass.md | 22 +- mixs6/hrt.md | 22 +- mixs6/humidity.md | 22 +- mixs6/humidity_regm.md | 22 +- mixs6/hysterectomy.md | 22 +- mixs6/ihmc_ethnicity.md | 110 +- mixs6/ihmc_medication_code.md | 110 +- mixs6/index.md | 1480 ++++++++--------- mixs6/indoor_space.md | 22 +- mixs6/indoor_surf.md | 22 +- mixs6/indust_eff_percent.md | 22 +- mixs6/inorg_particles.md | 22 +- mixs6/inside_lux.md | 22 +- mixs6/int_wall_cond.md | 22 +- mixs6/investigation_type.md | 22 +- mixs6/isol_growth_condt.md | 12 +- mixs6/iw_bt_date_well.md | 22 +- mixs6/iwf.md | 22 +- mixs6/last_clean.md | 22 +- mixs6/lat_lon.md | 396 ++--- mixs6/lib_layout.md | 20 +- mixs6/lib_reads_seqd.md | 20 +- mixs6/lib_screen.md | 20 +- mixs6/lib_size.md | 20 +- mixs6/lib_vector.md | 20 +- mixs6/light_intensity.md | 22 +- mixs6/light_regm.md | 22 +- mixs6/light_type.md | 22 +- mixs6/link_addit_analys.md | 22 +- mixs6/link_class_info.md | 22 +- mixs6/link_climate_info.md | 22 +- mixs6/lithology.md | 44 +- mixs6/liver_disord.md | 22 +- mixs6/local_class.md | 22 +- mixs6/local_class_meth.md | 22 +- mixs6/mag_cov_software.md | 4 +- mixs6/magnesium.md | 110 +- mixs6/maternal_health_stat.md | 22 +- mixs6/max_occup.md | 22 +- mixs6/me_adapters.md | 47 + mixs6/me_annot.md | 47 + mixs6/me_assembly_name.md | 47 + mixs6/me_assembly_qual.md | 47 + mixs6/me_assembly_software.md | 47 + mixs6/me_collection_date.md | 23 + mixs6/me_env_broad_scale.md | 23 + mixs6/me_env_local_scale.md | 23 + mixs6/me_env_medium.md | 23 + mixs6/me_env_package.md | 47 + mixs6/me_experimental_factor.md | 47 + mixs6/me_feat_pred.md | 40 + mixs6/me_geo_loc_name.md | 23 + mixs6/me_investigation_type.md | 40 + mixs6/me_lat_lon.md | 23 + mixs6/me_lib_layout.md | 47 + mixs6/me_lib_reads_seqd.md | 47 + mixs6/me_lib_screen.md | 47 + mixs6/me_lib_size.md | 47 + mixs6/me_lib_vector.md | 47 + mixs6/me_mid.md | 47 + mixs6/me_nucl_acid_amp.md | 47 + mixs6/me_nucl_acid_ext.md | 47 + mixs6/me_number_contig.md | 47 + mixs6/me_project_name.md | 40 + mixs6/me_ref_biomaterial.md | 40 + mixs6/me_ref_db.md | 40 + mixs6/me_rel_to_oxygen.md | 40 + mixs6/me_samp_collect_device.md | 47 + mixs6/me_samp_mat_process.md | 47 + mixs6/me_samp_size.md | 47 + mixs6/me_sample_name.md | 40 + mixs6/me_seq_meth.md | 40 + mixs6/me_sim_search_meth.md | 40 + mixs6/me_size_frac.md | 40 + mixs6/me_sop.md | 47 + mixs6/me_source_mat_id.md | 47 + mixs6/me_submitted_to_insdc.md | 40 + mixs6/me_tax_class.md | 40 + mixs6/me_url.md | 47 + mixs6/mean_frict_vel.md | 66 +- mixs6/mean_peak_frict_vel.md | 66 +- mixs6/mech_struc.md | 22 +- mixs6/mechanical_damage.md | 22 +- mixs6/medic_hist_perform.md | 110 +- mixs6/menarche.md | 22 +- mixs6/menopause.md | 22 +- mixs6/methane.md | 66 +- mixs6/microbial_biomass.md | 22 +- mixs6/microbial_biomass_meth.md | 22 +- mixs6/mid.md | 10 +- mixs6/migs_ba_adapters.md | 47 + mixs6/migs_ba_annot.md | 47 + mixs6/migs_ba_assembly_name.md | 47 + mixs6/migs_ba_assembly_qual.md | 40 + mixs6/migs_ba_assembly_software.md | 40 + mixs6/migs_ba_biotic_relationship.md | 47 + mixs6/migs_ba_collection_date.md | 23 + mixs6/migs_ba_compl_score.md | 40 + mixs6/migs_ba_compl_software.md | 40 + mixs6/migs_ba_encoded_traits.md | 40 + mixs6/migs_ba_env_broad_scale.md | 23 + mixs6/migs_ba_env_local_scale.md | 23 + mixs6/migs_ba_env_medium.md | 23 + mixs6/migs_ba_env_package.md | 47 + mixs6/migs_ba_estimated_size.md | 40 + mixs6/migs_ba_experimental_factor.md | 40 + mixs6/migs_ba_extrachrom_elements.md | 47 + mixs6/migs_ba_feat_pred.md | 40 + mixs6/migs_ba_geo_loc_name.md | 23 + mixs6/migs_ba_health_disease_stat.md | 47 + mixs6/migs_ba_host_spec_range.md | 40 + mixs6/migs_ba_investigation_type.md | 40 + mixs6/migs_ba_isol_growth_condt.md | 40 + mixs6/migs_ba_lat_lon.md | 23 + mixs6/migs_ba_lib_layout.md | 40 + mixs6/migs_ba_lib_reads_seqd.md | 40 + mixs6/migs_ba_lib_screen.md | 40 + mixs6/migs_ba_lib_size.md | 40 + mixs6/migs_ba_lib_vector.md | 40 + mixs6/migs_ba_nucl_acid_amp.md | 47 + mixs6/migs_ba_nucl_acid_ext.md | 47 + mixs6/migs_ba_num_replicons.md | 40 + mixs6/migs_ba_number_contig.md | 40 + mixs6/migs_ba_pathogenicity.md | 47 + mixs6/migs_ba_project_name.md | 40 + mixs6/migs_ba_ref_biomaterial.md | 40 + mixs6/migs_ba_ref_db.md | 40 + mixs6/migs_ba_rel_to_oxygen.md | 47 + mixs6/migs_ba_samp_collect_device.md | 40 + mixs6/migs_ba_samp_mat_process.md | 40 + mixs6/migs_ba_samp_size.md | 40 + mixs6/migs_ba_sample_name.md | 40 + mixs6/migs_ba_seq_meth.md | 40 + mixs6/migs_ba_sim_search_meth.md | 40 + mixs6/migs_ba_sop.md | 47 + mixs6/migs_ba_source_mat_id.md | 47 + mixs6/migs_ba_specific_host.md | 47 + mixs6/migs_ba_submitted_to_insdc.md | 40 + mixs6/migs_ba_subspecf_gen_lin.md | 47 + mixs6/migs_ba_tax_class.md | 40 + mixs6/migs_ba_tax_ident.md | 47 + mixs6/migs_ba_trophic_level.md | 47 + mixs6/migs_ba_url.md | 47 + mixs6/migs_eu_adapters.md | 47 + mixs6/migs_eu_annot.md | 47 + mixs6/migs_eu_assembly_name.md | 47 + mixs6/migs_eu_assembly_qual.md | 40 + mixs6/migs_eu_assembly_software.md | 40 + mixs6/migs_eu_biotic_relationship.md | 40 + mixs6/migs_eu_collection_date.md | 23 + mixs6/migs_eu_compl_score.md | 40 + mixs6/migs_eu_compl_software.md | 40 + mixs6/migs_eu_env_broad_scale.md | 23 + mixs6/migs_eu_env_local_scale.md | 23 + mixs6/migs_eu_env_medium.md | 23 + mixs6/migs_eu_env_package.md | 47 + mixs6/migs_eu_estimated_size.md | 40 + mixs6/migs_eu_experimental_factor.md | 40 + mixs6/migs_eu_extrachrom_elements.md | 40 + mixs6/migs_eu_feat_pred.md | 40 + mixs6/migs_eu_geo_loc_name.md | 23 + mixs6/migs_eu_health_disease_stat.md | 40 + mixs6/migs_eu_host_spec_range.md | 40 + mixs6/migs_eu_investigation_type.md | 40 + mixs6/migs_eu_isol_growth_condt.md | 40 + mixs6/migs_eu_lat_lon.md | 23 + mixs6/migs_eu_lib_layout.md | 40 + mixs6/migs_eu_lib_reads_seqd.md | 40 + mixs6/migs_eu_lib_screen.md | 40 + mixs6/migs_eu_lib_size.md | 40 + mixs6/migs_eu_lib_vector.md | 40 + mixs6/migs_eu_nucl_acid_amp.md | 47 + mixs6/migs_eu_nucl_acid_ext.md | 47 + mixs6/migs_eu_num_replicons.md | 40 + mixs6/migs_eu_number_contig.md | 40 + mixs6/migs_eu_pathogenicity.md | 47 + mixs6/migs_eu_ploidy.md | 40 + mixs6/migs_eu_project_name.md | 40 + mixs6/migs_eu_propagation.md | 47 + mixs6/migs_eu_ref_biomaterial.md | 40 + mixs6/migs_eu_ref_db.md | 40 + mixs6/migs_eu_samp_collect_device.md | 40 + mixs6/migs_eu_samp_mat_process.md | 40 + mixs6/migs_eu_samp_size.md | 40 + mixs6/migs_eu_sample_name.md | 40 + mixs6/migs_eu_seq_meth.md | 40 + mixs6/migs_eu_sim_search_meth.md | 40 + mixs6/migs_eu_sop.md | 47 + mixs6/migs_eu_source_mat_id.md | 47 + mixs6/migs_eu_specific_host.md | 40 + mixs6/migs_eu_submitted_to_insdc.md | 40 + mixs6/migs_eu_subspecf_gen_lin.md | 47 + mixs6/migs_eu_tax_class.md | 40 + mixs6/migs_eu_tax_ident.md | 47 + mixs6/migs_eu_trophic_level.md | 47 + mixs6/migs_eu_url.md | 47 + mixs6/migs_org_adapters.md | 47 + mixs6/migs_org_annot.md | 47 + mixs6/migs_org_assembly_name.md | 47 + mixs6/migs_org_assembly_qual.md | 40 + mixs6/migs_org_assembly_software.md | 40 + mixs6/migs_org_collection_date.md | 23 + mixs6/migs_org_compl_score.md | 40 + mixs6/migs_org_compl_software.md | 40 + mixs6/migs_org_env_broad_scale.md | 23 + mixs6/migs_org_env_local_scale.md | 23 + mixs6/migs_org_env_medium.md | 23 + mixs6/migs_org_env_package.md | 47 + mixs6/migs_org_estimated_size.md | 40 + mixs6/migs_org_experimental_factor.md | 40 + mixs6/migs_org_extrachrom_elements.md | 47 + mixs6/migs_org_feat_pred.md | 40 + mixs6/migs_org_geo_loc_name.md | 23 + mixs6/migs_org_investigation_type.md | 40 + mixs6/migs_org_isol_growth_condt.md | 40 + mixs6/migs_org_lat_lon.md | 23 + mixs6/migs_org_lib_layout.md | 40 + mixs6/migs_org_lib_reads_seqd.md | 40 + mixs6/migs_org_lib_screen.md | 40 + mixs6/migs_org_lib_size.md | 40 + mixs6/migs_org_lib_vector.md | 40 + mixs6/migs_org_nucl_acid_amp.md | 47 + mixs6/migs_org_nucl_acid_ext.md | 47 + mixs6/migs_org_number_contig.md | 40 + mixs6/migs_org_project_name.md | 40 + mixs6/migs_org_ref_biomaterial.md | 40 + mixs6/migs_org_ref_db.md | 40 + mixs6/migs_org_samp_collect_device.md | 40 + mixs6/migs_org_samp_mat_process.md | 40 + mixs6/migs_org_samp_size.md | 40 + mixs6/migs_org_sample_name.md | 40 + mixs6/migs_org_seq_meth.md | 40 + mixs6/migs_org_sim_search_meth.md | 40 + mixs6/migs_org_sop.md | 47 + mixs6/migs_org_source_mat_id.md | 47 + mixs6/migs_org_submitted_to_insdc.md | 40 + mixs6/migs_org_subspecf_gen_lin.md | 47 + mixs6/migs_org_tax_class.md | 40 + mixs6/migs_org_tax_ident.md | 47 + mixs6/migs_org_url.md | 47 + mixs6/migs_pl_adapters.md | 47 + mixs6/migs_pl_annot.md | 47 + mixs6/migs_pl_assembly_name.md | 47 + mixs6/migs_pl_assembly_qual.md | 40 + mixs6/migs_pl_assembly_software.md | 40 + mixs6/migs_pl_collection_date.md | 23 + mixs6/migs_pl_compl_score.md | 40 + mixs6/migs_pl_compl_software.md | 40 + mixs6/migs_pl_encoded_traits.md | 47 + mixs6/migs_pl_env_broad_scale.md | 23 + mixs6/migs_pl_env_local_scale.md | 23 + mixs6/migs_pl_env_medium.md | 23 + mixs6/migs_pl_env_package.md | 47 + mixs6/migs_pl_estimated_size.md | 40 + mixs6/migs_pl_experimental_factor.md | 40 + mixs6/migs_pl_feat_pred.md | 40 + mixs6/migs_pl_geo_loc_name.md | 23 + mixs6/migs_pl_host_spec_range.md | 40 + mixs6/migs_pl_investigation_type.md | 40 + mixs6/migs_pl_isol_growth_condt.md | 40 + mixs6/migs_pl_lat_lon.md | 23 + mixs6/migs_pl_lib_layout.md | 40 + mixs6/migs_pl_lib_reads_seqd.md | 40 + mixs6/migs_pl_lib_screen.md | 40 + mixs6/migs_pl_lib_size.md | 40 + mixs6/migs_pl_lib_vector.md | 40 + mixs6/migs_pl_nucl_acid_amp.md | 47 + mixs6/migs_pl_nucl_acid_ext.md | 47 + mixs6/migs_pl_number_contig.md | 40 + mixs6/migs_pl_project_name.md | 40 + mixs6/migs_pl_propagation.md | 40 + mixs6/migs_pl_ref_biomaterial.md | 40 + mixs6/migs_pl_ref_db.md | 40 + mixs6/migs_pl_samp_collect_device.md | 40 + mixs6/migs_pl_samp_mat_process.md | 40 + mixs6/migs_pl_samp_size.md | 40 + mixs6/migs_pl_sample_name.md | 40 + mixs6/migs_pl_seq_meth.md | 40 + mixs6/migs_pl_sim_search_meth.md | 40 + mixs6/migs_pl_sop.md | 47 + mixs6/migs_pl_source_mat_id.md | 47 + mixs6/migs_pl_specific_host.md | 47 + mixs6/migs_pl_submitted_to_insdc.md | 40 + mixs6/migs_pl_subspecf_gen_lin.md | 47 + mixs6/migs_pl_tax_class.md | 40 + mixs6/migs_pl_tax_ident.md | 47 + mixs6/migs_pl_url.md | 47 + mixs6/migs_vi_adapters.md | 47 + mixs6/migs_vi_annot.md | 47 + mixs6/migs_vi_assembly_name.md | 47 + mixs6/migs_vi_assembly_qual.md | 40 + mixs6/migs_vi_assembly_software.md | 40 + mixs6/migs_vi_biotic_relationship.md | 40 + mixs6/migs_vi_collection_date.md | 23 + mixs6/migs_vi_compl_score.md | 40 + mixs6/migs_vi_compl_software.md | 40 + mixs6/migs_vi_encoded_traits.md | 47 + mixs6/migs_vi_env_broad_scale.md | 23 + mixs6/migs_vi_env_local_scale.md | 23 + mixs6/migs_vi_env_medium.md | 23 + mixs6/migs_vi_env_package.md | 47 + mixs6/migs_vi_estimated_size.md | 40 + mixs6/migs_vi_experimental_factor.md | 40 + mixs6/migs_vi_feat_pred.md | 40 + mixs6/migs_vi_geo_loc_name.md | 23 + mixs6/migs_vi_health_disease_stat.md | 47 + mixs6/migs_vi_host_spec_range.md | 47 + mixs6/migs_vi_investigation_type.md | 40 + mixs6/migs_vi_isol_growth_condt.md | 40 + mixs6/migs_vi_lat_lon.md | 23 + mixs6/migs_vi_lib_layout.md | 40 + mixs6/migs_vi_lib_reads_seqd.md | 40 + mixs6/migs_vi_lib_screen.md | 40 + mixs6/migs_vi_lib_size.md | 40 + mixs6/migs_vi_lib_vector.md | 40 + mixs6/migs_vi_nucl_acid_amp.md | 47 + mixs6/migs_vi_nucl_acid_ext.md | 47 + mixs6/migs_vi_num_replicons.md | 47 + mixs6/migs_vi_number_contig.md | 40 + mixs6/migs_vi_pathogenicity.md | 47 + mixs6/migs_vi_project_name.md | 40 + mixs6/migs_vi_propagation.md | 40 + mixs6/migs_vi_ref_biomaterial.md | 40 + mixs6/migs_vi_ref_db.md | 40 + mixs6/migs_vi_samp_collect_device.md | 40 + mixs6/migs_vi_samp_mat_process.md | 40 + mixs6/migs_vi_samp_size.md | 40 + mixs6/migs_vi_sample_name.md | 40 + mixs6/migs_vi_seq_meth.md | 40 + mixs6/migs_vi_sim_search_meth.md | 40 + mixs6/migs_vi_sop.md | 47 + mixs6/migs_vi_source_mat_id.md | 47 + mixs6/migs_vi_specific_host.md | 47 + mixs6/migs_vi_submitted_to_insdc.md | 40 + mixs6/migs_vi_subspecf_gen_lin.md | 47 + mixs6/migs_vi_tax_class.md | 40 + mixs6/migs_vi_tax_ident.md | 47 + mixs6/migs_vi_url.md | 47 + mixs6/migs_vi_virus_enrich_appr.md | 47 + mixs6/mimag_adapters.md | 47 + mixs6/mimag_annot.md | 40 + mixs6/mimag_assembly_name.md | 47 + mixs6/mimag_assembly_qual.md | 40 + mixs6/mimag_assembly_software.md | 40 + mixs6/mimag_bin_param.md | 40 + mixs6/mimag_bin_software.md | 40 + mixs6/mimag_collection_date.md | 23 + mixs6/mimag_compl_appr.md | 40 + mixs6/mimag_compl_score.md | 40 + mixs6/mimag_compl_software.md | 40 + mixs6/mimag_contam_score.md | 40 + mixs6/mimag_contam_screen_input.md | 40 + mixs6/mimag_contam_screen_param.md | 40 + mixs6/mimag_decontam_software.md | 40 + mixs6/mimag_env_broad_scale.md | 23 + mixs6/mimag_env_local_scale.md | 23 + mixs6/mimag_env_medium.md | 23 + mixs6/mimag_env_package.md | 47 + mixs6/mimag_experimental_factor.md | 47 + mixs6/mimag_feat_pred.md | 40 + mixs6/mimag_geo_loc_name.md | 23 + mixs6/mimag_investigation_type.md | 40 + mixs6/mimag_lat_lon.md | 23 + mixs6/mimag_lib_layout.md | 47 + mixs6/mimag_lib_reads_seqd.md | 47 + mixs6/mimag_lib_screen.md | 47 + mixs6/mimag_lib_size.md | 47 + mixs6/mimag_lib_vector.md | 47 + mixs6/mimag_mag_cov_software.md | 40 + mixs6/mimag_mid.md | 47 + mixs6/mimag_nucl_acid_amp.md | 47 + mixs6/mimag_nucl_acid_ext.md | 47 + mixs6/mimag_number_contig.md | 40 + mixs6/mimag_project_name.md | 40 + mixs6/mimag_reassembly_bin.md | 40 + mixs6/mimag_ref_biomaterial.md | 40 + mixs6/mimag_ref_db.md | 40 + mixs6/mimag_rel_to_oxygen.md | 40 + mixs6/mimag_samp_collect_device.md | 47 + mixs6/mimag_samp_mat_process.md | 47 + mixs6/mimag_samp_size.md | 47 + mixs6/mimag_sample_name.md | 40 + mixs6/mimag_seq_meth.md | 40 + mixs6/mimag_sim_search_meth.md | 40 + mixs6/mimag_size_frac.md | 40 + mixs6/mimag_sop.md | 47 + mixs6/mimag_source_mat_id.md | 47 + mixs6/mimag_submitted_to_insdc.md | 40 + mixs6/mimag_tax_class.md | 40 + mixs6/mimag_tax_ident.md | 40 + mixs6/mimag_trna_ext_software.md | 40 + mixs6/mimag_trnas.md | 40 + mixs6/mimag_url.md | 47 + mixs6/mimag_x_16s_recover.md | 40 + mixs6/mimag_x_16s_recover_software.md | 40 + mixs6/mimarks_c_biotic_relationship.md | 47 + mixs6/mimarks_c_chimera_check.md | 47 + mixs6/mimarks_c_collection_date.md | 23 + mixs6/mimarks_c_env_broad_scale.md | 23 + mixs6/mimarks_c_env_local_scale.md | 23 + mixs6/mimarks_c_env_medium.md | 23 + mixs6/mimarks_c_env_package.md | 47 + mixs6/mimarks_c_experimental_factor.md | 40 + mixs6/mimarks_c_extrachrom_elements.md | 40 + mixs6/mimarks_c_geo_loc_name.md | 23 + mixs6/mimarks_c_investigation_type.md | 40 + mixs6/mimarks_c_isol_growth_condt.md | 40 + mixs6/mimarks_c_lat_lon.md | 23 + mixs6/mimarks_c_nucl_acid_amp.md | 47 + mixs6/mimarks_c_nucl_acid_ext.md | 47 + mixs6/mimarks_c_pcr_cond.md | 47 + mixs6/mimarks_c_pcr_primers.md | 47 + mixs6/mimarks_c_project_name.md | 40 + mixs6/mimarks_c_rel_to_oxygen.md | 47 + mixs6/mimarks_c_samp_collect_device.md | 40 + mixs6/mimarks_c_samp_mat_process.md | 47 + mixs6/mimarks_c_samp_size.md | 40 + mixs6/mimarks_c_sample_name.md | 40 + mixs6/mimarks_c_seq_meth.md | 40 + mixs6/mimarks_c_seq_quality_check.md | 47 + mixs6/mimarks_c_sop.md | 47 + mixs6/mimarks_c_source_mat_id.md | 47 + mixs6/mimarks_c_submitted_to_insdc.md | 40 + mixs6/mimarks_c_subspecf_gen_lin.md | 47 + mixs6/mimarks_c_target_gene.md | 40 + mixs6/mimarks_c_target_subfragment.md | 47 + mixs6/mimarks_c_trophic_level.md | 47 + mixs6/mimarks_c_url.md | 47 + mixs6/mimarks_s_adapters.md | 47 + mixs6/mimarks_s_assembly_software.md | 47 + mixs6/mimarks_s_chimera_check.md | 47 + mixs6/mimarks_s_collection_date.md | 23 + mixs6/mimarks_s_env_broad_scale.md | 23 + mixs6/mimarks_s_env_local_scale.md | 23 + mixs6/mimarks_s_env_medium.md | 23 + mixs6/mimarks_s_env_package.md | 47 + mixs6/mimarks_s_experimental_factor.md | 47 + mixs6/mimarks_s_geo_loc_name.md | 23 + mixs6/mimarks_s_investigation_type.md | 40 + mixs6/mimarks_s_lat_lon.md | 23 + mixs6/mimarks_s_lib_layout.md | 47 + mixs6/mimarks_s_lib_reads_seqd.md | 47 + mixs6/mimarks_s_lib_screen.md | 47 + mixs6/mimarks_s_lib_size.md | 47 + mixs6/mimarks_s_lib_vector.md | 47 + mixs6/mimarks_s_mid.md | 47 + mixs6/mimarks_s_nucl_acid_amp.md | 47 + mixs6/mimarks_s_nucl_acid_ext.md | 47 + mixs6/mimarks_s_pcr_cond.md | 47 + mixs6/mimarks_s_pcr_primers.md | 47 + mixs6/mimarks_s_project_name.md | 40 + mixs6/mimarks_s_rel_to_oxygen.md | 40 + mixs6/mimarks_s_samp_collect_device.md | 47 + mixs6/mimarks_s_samp_mat_process.md | 47 + mixs6/mimarks_s_samp_size.md | 47 + mixs6/mimarks_s_sample_name.md | 40 + mixs6/mimarks_s_seq_meth.md | 40 + mixs6/mimarks_s_seq_quality_check.md | 47 + mixs6/mimarks_s_size_frac.md | 40 + mixs6/mimarks_s_sop.md | 47 + mixs6/mimarks_s_source_mat_id.md | 47 + mixs6/mimarks_s_submitted_to_insdc.md | 40 + mixs6/mimarks_s_target_gene.md | 40 + mixs6/mimarks_s_target_subfragment.md | 47 + mixs6/mimarks_s_url.md | 47 + mixs6/mineral_nutr_regm.md | 22 +- mixs6/misag_adapters.md | 47 + mixs6/misag_annot.md | 40 + mixs6/misag_assembly_name.md | 47 + mixs6/misag_assembly_qual.md | 40 + mixs6/misag_assembly_software.md | 40 + mixs6/misag_collection_date.md | 23 + mixs6/misag_compl_appr.md | 40 + mixs6/misag_compl_score.md | 40 + mixs6/misag_compl_software.md | 40 + mixs6/misag_contam_score.md | 40 + mixs6/misag_contam_screen_input.md | 40 + mixs6/misag_contam_screen_param.md | 40 + mixs6/misag_decontam_software.md | 40 + mixs6/misag_env_broad_scale.md | 23 + mixs6/misag_env_local_scale.md | 23 + mixs6/misag_env_medium.md | 23 + mixs6/misag_env_package.md | 47 + mixs6/misag_experimental_factor.md | 47 + mixs6/misag_feat_pred.md | 40 + mixs6/misag_geo_loc_name.md | 23 + mixs6/misag_investigation_type.md | 40 + mixs6/misag_lat_lon.md | 23 + mixs6/misag_lib_layout.md | 47 + mixs6/misag_lib_reads_seqd.md | 47 + mixs6/misag_lib_screen.md | 47 + mixs6/misag_lib_size.md | 47 + mixs6/misag_lib_vector.md | 47 + mixs6/misag_mid.md | 47 + mixs6/misag_nucl_acid_amp.md | 47 + mixs6/misag_nucl_acid_ext.md | 47 + mixs6/misag_number_contig.md | 40 + mixs6/misag_project_name.md | 40 + mixs6/misag_ref_biomaterial.md | 40 + mixs6/misag_ref_db.md | 40 + mixs6/misag_rel_to_oxygen.md | 40 + mixs6/misag_samp_collect_device.md | 47 + mixs6/misag_samp_mat_process.md | 47 + mixs6/misag_samp_size.md | 47 + mixs6/misag_sample_name.md | 40 + mixs6/misag_seq_meth.md | 40 + mixs6/misag_sim_search_meth.md | 40 + mixs6/misag_single_cell_lysis_appr.md | 40 + mixs6/misag_single_cell_lysis_prot.md | 40 + mixs6/misag_size_frac.md | 40 + mixs6/misag_sop.md | 47 + mixs6/misag_sort_tech.md | 40 + mixs6/misag_source_mat_id.md | 47 + mixs6/misag_submitted_to_insdc.md | 40 + mixs6/misag_tax_class.md | 40 + mixs6/misag_tax_ident.md | 40 + mixs6/misag_trna_ext_software.md | 40 + mixs6/misag_trnas.md | 40 + mixs6/misag_url.md | 47 + mixs6/misag_wga_amp_appr.md | 40 + mixs6/misag_wga_amp_kit.md | 40 + mixs6/misag_x_16s_recover.md | 40 + mixs6/misag_x_16s_recover_software.md | 40 + mixs6/misc_param.md | 352 ++-- mixs6/miuvig_adapters.md | 47 + mixs6/miuvig_annot.md | 40 + mixs6/miuvig_assembly_name.md | 47 + mixs6/miuvig_assembly_qual.md | 40 + mixs6/miuvig_assembly_software.md | 40 + mixs6/miuvig_bin_param.md | 47 + mixs6/miuvig_bin_software.md | 47 + mixs6/miuvig_biotic_relationship.md | 40 + mixs6/miuvig_collection_date.md | 23 + mixs6/miuvig_compl_appr.md | 47 + mixs6/miuvig_compl_score.md | 47 + mixs6/miuvig_compl_software.md | 40 + mixs6/miuvig_detec_type.md | 40 + mixs6/miuvig_env_broad_scale.md | 23 + mixs6/miuvig_env_local_scale.md | 23 + mixs6/miuvig_env_medium.md | 23 + mixs6/miuvig_env_package.md | 47 + mixs6/miuvig_estimated_size.md | 40 + mixs6/miuvig_experimental_factor.md | 47 + mixs6/miuvig_feat_pred.md | 47 + mixs6/miuvig_geo_loc_name.md | 23 + mixs6/miuvig_host_pred_appr.md | 47 + mixs6/miuvig_host_pred_est_acc.md | 47 + mixs6/miuvig_host_spec_range.md | 40 + mixs6/miuvig_investigation_type.md | 40 + mixs6/miuvig_lat_lon.md | 23 + mixs6/miuvig_lib_layout.md | 47 + mixs6/miuvig_lib_reads_seqd.md | 47 + mixs6/miuvig_lib_screen.md | 47 + mixs6/miuvig_lib_size.md | 47 + mixs6/miuvig_lib_vector.md | 47 + mixs6/miuvig_mag_cov_software.md | 40 + mixs6/miuvig_mid.md | 47 + mixs6/miuvig_nucl_acid_amp.md | 47 + mixs6/miuvig_nucl_acid_ext.md | 47 + mixs6/miuvig_number_contig.md | 40 + mixs6/miuvig_pathogenicity.md | 40 + mixs6/miuvig_pred_genome_struc.md | 40 + mixs6/miuvig_pred_genome_type.md | 40 + mixs6/miuvig_project_name.md | 40 + mixs6/miuvig_reassembly_bin.md | 47 + mixs6/miuvig_ref_biomaterial.md | 40 + mixs6/miuvig_ref_db.md | 47 + mixs6/miuvig_samp_collect_device.md | 47 + mixs6/miuvig_samp_mat_process.md | 47 + mixs6/miuvig_samp_size.md | 47 + mixs6/miuvig_sample_name.md | 40 + mixs6/miuvig_seq_meth.md | 40 + mixs6/miuvig_sim_search_meth.md | 47 + mixs6/miuvig_single_cell_lysis_appr.md | 47 + mixs6/miuvig_single_cell_lysis_prot.md | 47 + mixs6/miuvig_size_frac.md | 47 + mixs6/miuvig_sop.md | 47 + mixs6/miuvig_sort_tech.md | 47 + mixs6/miuvig_source_mat_id.md | 47 + mixs6/miuvig_source_uvig.md | 40 + mixs6/miuvig_specific_host.md | 40 + mixs6/miuvig_submitted_to_insdc.md | 40 + mixs6/miuvig_tax_class.md | 47 + mixs6/miuvig_tax_ident.md | 40 + mixs6/miuvig_trna_ext_software.md | 40 + mixs6/miuvig_trnas.md | 40 + mixs6/miuvig_url.md | 47 + mixs6/miuvig_vir_ident_software.md | 40 + mixs6/miuvig_virus_enrich_appr.md | 40 + mixs6/miuvig_votu_class_appr.md | 47 + mixs6/miuvig_votu_db.md | 47 + mixs6/miuvig_votu_seq_comp_appr.md | 47 + mixs6/miuvig_wga_amp_appr.md | 47 + mixs6/miuvig_wga_amp_kit.md | 47 + mixs6/n_alkanes.md | 66 +- mixs6/nitrate.md | 154 +- mixs6/nitrite.md | 132 +- mixs6/nitro.md | 88 +- mixs6/non_mineral_nutr_regm.md | 22 +- mixs6/nose_mouth_teeth_throat_disord.md | 22 +- mixs6/nose_throat_disord.md | 22 +- mixs6/nucl_acid_amp.md | 22 +- mixs6/nucl_acid_ext.md | 22 +- mixs6/num_replicons.md | 6 +- mixs6/number_contig.md | 18 +- mixs6/number_pets.md | 22 +- mixs6/number_plants.md | 22 +- mixs6/number_resident.md | 22 +- mixs6/occup_density_samp.md | 22 +- mixs6/occup_document.md | 22 +- mixs6/occup_samp.md | 22 +- mixs6/org_carb.md | 88 +- mixs6/org_matter.md | 88 +- mixs6/org_nitro.md | 88 +- mixs6/org_particles.md | 22 +- mixs6/organism_count.md | 352 ++-- mixs6/organism_count_qpcr_info.md | 44 +- mixs6/owc_tvdss.md | 22 +- mixs6/oxy_stat_samp.md | 330 ++-- mixs6/oxygen.md | 22 +- mixs6/part_org_carb.md | 66 +- mixs6/part_org_nitro.md | 22 +- mixs6/particle_class.md | 22 +- mixs6/pathogenicity.md | 8 +- mixs6/pcr_cond.md | 4 +- mixs6/pcr_primers.md | 4 +- mixs6/permeability.md | 22 +- mixs6/perturbation.md | 286 ++-- mixs6/pesticide_regm.md | 22 +- mixs6/pet_farm_animal.md | 22 +- mixs6/petroleum_hydrocarb.md | 66 +- mixs6/ph.md | 176 +- mixs6/ph_meth.md | 22 +- mixs6/ph_regm.md | 22 +- mixs6/phaeopigments.md | 66 +- mixs6/phosphate.md | 110 +- mixs6/phosplipid_fatt_acid.md | 88 +- mixs6/photon_flux.md | 22 +- mixs6/plant_growth_med.md | 22 +- mixs6/plant_product.md | 22 +- mixs6/plant_sex.md | 22 +- mixs6/plant_struc.md | 22 +- mixs6/ploidy.md | 2 +- mixs6/pollutants.md | 22 +- mixs6/pool_dna_extracts.md | 22 +- mixs6/porosity.md | 44 +- mixs6/potassium.md | 132 +- mixs6/pour_point.md | 44 +- mixs6/pre_treatment.md | 22 +- mixs6/pred_genome_struc.md | 2 +- mixs6/pred_genome_type.md | 2 +- mixs6/pregnancy.md | 22 +- mixs6/pres_animal.md | 22 +- mixs6/pressure.md | 132 +- mixs6/previous_land_use.md | 22 +- mixs6/previous_land_use_meth.md | 22 +- mixs6/primary_prod.md | 22 +- mixs6/primary_treatment.md | 22 +- mixs6/prod_rate.md | 22 +- mixs6/prod_start_date.md | 22 +- mixs6/profile_position.md | 22 +- mixs6/project_name.md | 22 +- mixs6/propagation.md | 6 +- mixs6/pulmonary_disord.md | 22 +- mixs6/quad_pos.md | 22 +- mixs6/quantityValue__has_numeric_value.md | 22 + mixs6/quantityValue__has_raw_value.md | 22 + mixs6/quantityValue__has_unit.md | 22 + mixs6/radiation_regm.md | 22 +- mixs6/rainfall_regm.md | 22 +- mixs6/reactor_type.md | 22 +- mixs6/reassembly_bin.md | 4 +- mixs6/redox_potential.md | 66 +- mixs6/ref_biomaterial.md | 18 +- mixs6/ref_db.md | 18 +- mixs6/rel_air_humidity.md | 22 +- mixs6/rel_humidity_out.md | 22 +- mixs6/rel_samp_loc.md | 22 +- mixs6/rel_to_oxygen.md | 12 +- mixs6/reservoir.md | 44 +- mixs6/resins_pc.md | 44 +- mixs6/resp_part_matter.md | 22 +- mixs6/room_air_exch_rate.md | 22 +- mixs6/room_architec_element.md | 22 +- mixs6/room_condt.md | 22 +- mixs6/room_connected.md | 22 +- mixs6/room_count.md | 22 +- mixs6/room_dim.md | 22 +- mixs6/room_door_dist.md | 22 +- mixs6/room_door_share.md | 22 +- mixs6/room_hallway.md | 22 +- mixs6/room_loc.md | 22 +- mixs6/room_moist_damage_hist.md | 22 +- mixs6/room_net_area.md | 22 +- mixs6/room_occup.md | 22 +- mixs6/room_samp_pos.md | 22 +- mixs6/room_type.md | 22 +- mixs6/room_vol.md | 22 +- mixs6/room_wall_share.md | 22 +- mixs6/room_window_count.md | 22 +- mixs6/root_cond.md | 22 +- mixs6/root_med_carbon.md | 22 +- mixs6/root_med_macronutr.md | 22 +- mixs6/root_med_micronutr.md | 22 +- mixs6/root_med_ph.md | 22 +- mixs6/root_med_regl.md | 22 +- mixs6/root_med_solid.md | 22 +- mixs6/root_med_suppl.md | 22 +- mixs6/salinity.md | 88 +- mixs6/salinity_meth.md | 22 +- mixs6/salt_regm.md | 22 +- mixs6/samp_capt_status.md | 44 +- mixs6/samp_collect_device.md | 22 +- mixs6/samp_collection_point.md | 22 +- mixs6/samp_dis_stage.md | 44 +- mixs6/samp_floor.md | 22 +- mixs6/samp_loc_corr_rate.md | 22 +- mixs6/samp_mat_process.md | 22 +- mixs6/samp_md.md | 22 +- mixs6/samp_preserv.md | 22 +- mixs6/samp_room_id.md | 22 +- mixs6/samp_salinity.md | 242 +-- mixs6/samp_size.md | 22 +- mixs6/samp_sort_meth.md | 22 +- mixs6/samp_store_dur.md | 330 ++-- mixs6/samp_store_loc.md | 330 ++-- mixs6/samp_store_temp.md | 330 ++-- mixs6/samp_subtype.md | 44 +- mixs6/samp_time_out.md | 22 +- mixs6/samp_transport_cond.md | 44 +- mixs6/samp_tvdss.md | 22 +- mixs6/samp_type.md | 44 +- mixs6/samp_vol_we_dna_ext.md | 352 ++-- mixs6/samp_weather.md | 22 +- mixs6/samp_well_name.md | 44 +- mixs6/sample_name.md | 22 +- mixs6/saturates_pc.md | 44 +- mixs6/season.md | 22 +- mixs6/season_environment.md | 22 +- mixs6/season_precpt.md | 22 +- mixs6/season_temp.md | 22 +- mixs6/season_use.md | 22 +- mixs6/secondary_treatment.md | 22 +- mixs6/sediment_type.md | 22 +- mixs6/seq_meth.md | 22 +- mixs6/seq_quality_check.md | 4 +- mixs6/sewage_type.md | 22 +- mixs6/sexual_act.md | 22 +- mixs6/shading_device_cond.md | 22 +- mixs6/shading_device_loc.md | 22 +- mixs6/shading_device_mat.md | 22 +- mixs6/shading_device_type.md | 22 +- mixs6/shading_device_water_mold.md | 22 +- mixs6/sieving.md | 22 +- mixs6/silicate.md | 88 +- mixs6/sim_search_meth.md | 18 +- mixs6/single_cell_lysis_appr.md | 4 +- mixs6/single_cell_lysis_prot.md | 4 +- mixs6/size_frac.md | 10 +- mixs6/size_frac_low.md | 22 +- mixs6/size_frac_up.md | 22 +- mixs6/slope_aspect.md | 22 +- mixs6/slope_gradient.md | 22 +- mixs6/sludge_retent_time.md | 22 +- mixs6/smoker.md | 22 +- mixs6/sodium.md | 154 +- mixs6/soil_type.md | 22 +- mixs6/soil_type_meth.md | 22 +- mixs6/solar_irradiance.md | 22 +- mixs6/soluble_inorg_mat.md | 22 +- mixs6/soluble_org_mat.md | 22 +- mixs6/soluble_react_phosp.md | 22 +- mixs6/sop.md | 22 +- mixs6/sort_tech.md | 4 +- mixs6/source_mat_id.md | 22 +- mixs6/source_uvig.md | 2 +- mixs6/space_typ_state.md | 22 +- mixs6/special_diet.md | 22 +- mixs6/specific.md | 22 +- mixs6/specific_host.md | 10 +- mixs6/specific_humidity.md | 22 +- mixs6/sr_dep_env.md | 22 +- mixs6/sr_geol_age.md | 22 +- mixs6/sr_kerog_type.md | 22 +- mixs6/sr_lithology.md | 22 +- mixs6/standing_water_regm.md | 22 +- mixs6/store_cond.md | 22 +- mixs6/study_complt_stat.md | 22 +- mixs6/submitted_to_insdc.md | 22 +- mixs6/subspecf_gen_lin.md | 12 +- mixs6/substructure_type.md | 22 +- mixs6/sulfate.md | 132 +- mixs6/sulfate_fw.md | 44 +- mixs6/sulfide.md | 132 +- mixs6/surf_air_cont.md | 22 +- mixs6/surf_humidity.md | 22 +- mixs6/surf_material.md | 22 +- mixs6/surf_moisture.md | 22 +- mixs6/surf_moisture_ph.md | 22 +- mixs6/surf_temp.md | 22 +- mixs6/suspend_part_matter.md | 22 +- mixs6/suspend_solids.md | 66 +- mixs6/tan.md | 44 +- mixs6/target_gene.md | 4 +- mixs6/target_subfragment.md | 4 +- mixs6/tax_class.md | 18 +- mixs6/tax_ident.md | 16 +- mixs6/temp.md | 330 ++-- mixs6/temp_out.md | 22 +- mixs6/tertiary_treatment.md | 22 +- mixs6/texture.md | 22 +- mixs6/texture_meth.md | 22 +- mixs6/tidal_stage.md | 44 +- mixs6/tillage.md | 22 +- mixs6/time_last_toothbrush.md | 22 +- mixs6/time_since_last_wash.md | 22 +- mixs6/tiss_cult_growth_med.md | 22 +- mixs6/toluene.md | 44 +- mixs6/tot_carb.md | 44 +- mixs6/tot_depth_water_col.md | 44 +- mixs6/tot_diss_nitro.md | 22 +- mixs6/tot_inorg_nitro.md | 22 +- mixs6/tot_iron.md | 44 +- mixs6/tot_nitro.md | 88 +- mixs6/tot_nitro_content.md | 66 +- mixs6/tot_nitro_content_meth.md | 22 +- mixs6/tot_org_c_meth.md | 22 +- mixs6/tot_org_carb.md | 66 +- mixs6/tot_part_carb.md | 22 +- mixs6/tot_phosp.md | 66 +- mixs6/tot_phosphate.md | 22 +- mixs6/tot_sulfur.md | 44 +- mixs6/train_line.md | 22 +- mixs6/train_stat_loc.md | 22 +- mixs6/train_stop_loc.md | 22 +- mixs6/travel_out_six_month.md | 22 +- mixs6/trna_ext_software.md | 6 +- mixs6/trnas.md | 6 +- mixs6/trophic_level.md | 6 +- mixs6/turbidity.md | 66 +- mixs6/tvdss_of_hcr_pressure.md | 44 +- mixs6/tvdss_of_hcr_temp.md | 44 +- mixs6/twin_sibling.md | 22 +- mixs6/typ_occup_density.md | 22 +- mixs6/urine_collect_meth.md | 22 +- mixs6/url.md | 22 +- mixs6/urogenit_disord.md | 22 +- mixs6/urogenit_tract_disor.md | 22 +- mixs6/ventilation_rate.md | 22 +- mixs6/ventilation_type.md | 44 +- mixs6/vfa.md | 44 +- mixs6/vfa_fw.md | 44 +- mixs6/vir_ident_software.md | 2 +- mixs6/virus_enrich_appr.md | 4 +- mixs6/vis_media.md | 22 +- mixs6/viscosity.md | 44 +- mixs6/volatile_org_comp.md | 22 +- mixs6/votu_class_appr.md | 2 +- mixs6/votu_db.md | 2 +- mixs6/votu_seq_comp_appr.md | 2 +- mixs6/wall_area.md | 22 +- mixs6/wall_const_type.md | 22 +- mixs6/wall_finish_mat.md | 22 +- mixs6/wall_height.md | 22 +- mixs6/wall_loc.md | 22 +- mixs6/wall_surf_treatment.md | 22 +- mixs6/wall_texture.md | 22 +- mixs6/wall_thermal_mass.md | 22 +- mixs6/wall_water_mold.md | 22 +- mixs6/wastewater_type.md | 22 +- mixs6/water_content.md | 66 +- mixs6/water_content_soil_meth.md | 22 +- mixs6/water_current.md | 44 +- mixs6/water_cut.md | 22 +- mixs6/water_feat_size.md | 22 +- mixs6/water_feat_type.md | 22 +- mixs6/water_production_rate.md | 22 +- mixs6/water_temp_regm.md | 22 +- mixs6/watering_regm.md | 22 +- mixs6/weekday.md | 22 +- mixs6/weight_loss_3_month.md | 22 +- mixs6/wga_amp_appr.md | 4 +- mixs6/wga_amp_kit.md | 4 +- mixs6/win.md | 44 +- mixs6/wind_direction.md | 22 +- mixs6/wind_speed.md | 22 +- mixs6/window_cond.md | 22 +- mixs6/window_cover.md | 22 +- mixs6/window_horiz_pos.md | 22 +- mixs6/window_loc.md | 22 +- mixs6/window_mat.md | 22 +- mixs6/window_open_freq.md | 22 +- mixs6/window_size.md | 22 +- mixs6/window_status.md | 22 +- mixs6/window_type.md | 22 +- mixs6/window_vert_pos.md | 22 +- mixs6/window_water_mold.md | 22 +- mixs6/x_16s_recover.md | 4 +- mixs6/x_16s_recover_software.md | 4 +- mixs6/xylene.md | 44 +- src/schema/mixs.yaml | 1426 +++++++++------- 1639 files changed, 108251 insertions(+), 23602 deletions(-) create mode 100644 mixs6/AirMIGSBacteria.md create mode 100644 mixs6/AirMIGSEukaryote.md create mode 100644 mixs6/AirMIGSPlant.md create mode 100644 mixs6/AirMIGSVirus.md create mode 100644 mixs6/AirMIMARKSSpecimen.md create mode 100644 mixs6/AirMIMARKSSurvey.md create mode 100644 mixs6/BuiltEnvironmentMIGSBacteria.md create mode 100644 mixs6/BuiltEnvironmentMIGSEukaryote.md create mode 100644 mixs6/BuiltEnvironmentMIGSPlant.md create mode 100644 mixs6/BuiltEnvironmentMIGSVirus.md create mode 100644 mixs6/BuiltEnvironmentMIMARKSSpecimen.md create mode 100644 mixs6/BuiltEnvironmentMIMARKSSurvey.md create mode 100644 mixs6/Host-associatedMIGSBacteria.md create mode 100644 mixs6/Host-associatedMIGSEukaryote.md create mode 100644 mixs6/Host-associatedMIGSPlant.md create mode 100644 mixs6/Host-associatedMIGSVirus.md create mode 100644 mixs6/Host-associatedMIMARKSSpecimen.md create mode 100644 mixs6/Host-associatedMIMARKSSurvey.md create mode 100644 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mode 100644 mixs6/mimag_lib_vector.md create mode 100644 mixs6/mimag_mag_cov_software.md create mode 100644 mixs6/mimag_mid.md create mode 100644 mixs6/mimag_nucl_acid_amp.md create mode 100644 mixs6/mimag_nucl_acid_ext.md create mode 100644 mixs6/mimag_number_contig.md create mode 100644 mixs6/mimag_project_name.md create mode 100644 mixs6/mimag_reassembly_bin.md create mode 100644 mixs6/mimag_ref_biomaterial.md create mode 100644 mixs6/mimag_ref_db.md create mode 100644 mixs6/mimag_rel_to_oxygen.md create mode 100644 mixs6/mimag_samp_collect_device.md create mode 100644 mixs6/mimag_samp_mat_process.md create mode 100644 mixs6/mimag_samp_size.md create mode 100644 mixs6/mimag_sample_name.md create mode 100644 mixs6/mimag_seq_meth.md create mode 100644 mixs6/mimag_sim_search_meth.md create mode 100644 mixs6/mimag_size_frac.md create mode 100644 mixs6/mimag_sop.md create mode 100644 mixs6/mimag_source_mat_id.md create mode 100644 mixs6/mimag_submitted_to_insdc.md create mode 100644 mixs6/mimag_tax_class.md create mode 100644 mixs6/mimag_tax_ident.md create mode 100644 mixs6/mimag_trna_ext_software.md create mode 100644 mixs6/mimag_trnas.md create mode 100644 mixs6/mimag_url.md create mode 100644 mixs6/mimag_x_16s_recover.md create mode 100644 mixs6/mimag_x_16s_recover_software.md create mode 100644 mixs6/mimarks_c_biotic_relationship.md create mode 100644 mixs6/mimarks_c_chimera_check.md create mode 100644 mixs6/mimarks_c_collection_date.md create mode 100644 mixs6/mimarks_c_env_broad_scale.md create mode 100644 mixs6/mimarks_c_env_local_scale.md create mode 100644 mixs6/mimarks_c_env_medium.md create mode 100644 mixs6/mimarks_c_env_package.md create mode 100644 mixs6/mimarks_c_experimental_factor.md create mode 100644 mixs6/mimarks_c_extrachrom_elements.md create mode 100644 mixs6/mimarks_c_geo_loc_name.md create mode 100644 mixs6/mimarks_c_investigation_type.md create mode 100644 mixs6/mimarks_c_isol_growth_condt.md create mode 100644 mixs6/mimarks_c_lat_lon.md create mode 100644 mixs6/mimarks_c_nucl_acid_amp.md create mode 100644 mixs6/mimarks_c_nucl_acid_ext.md create mode 100644 mixs6/mimarks_c_pcr_cond.md create mode 100644 mixs6/mimarks_c_pcr_primers.md create mode 100644 mixs6/mimarks_c_project_name.md create mode 100644 mixs6/mimarks_c_rel_to_oxygen.md create mode 100644 mixs6/mimarks_c_samp_collect_device.md create mode 100644 mixs6/mimarks_c_samp_mat_process.md create mode 100644 mixs6/mimarks_c_samp_size.md create mode 100644 mixs6/mimarks_c_sample_name.md create mode 100644 mixs6/mimarks_c_seq_meth.md create mode 100644 mixs6/mimarks_c_seq_quality_check.md create mode 100644 mixs6/mimarks_c_sop.md create mode 100644 mixs6/mimarks_c_source_mat_id.md create mode 100644 mixs6/mimarks_c_submitted_to_insdc.md create mode 100644 mixs6/mimarks_c_subspecf_gen_lin.md create mode 100644 mixs6/mimarks_c_target_gene.md create mode 100644 mixs6/mimarks_c_target_subfragment.md create mode 100644 mixs6/mimarks_c_trophic_level.md create mode 100644 mixs6/mimarks_c_url.md create mode 100644 mixs6/mimarks_s_adapters.md create mode 100644 mixs6/mimarks_s_assembly_software.md create mode 100644 mixs6/mimarks_s_chimera_check.md create mode 100644 mixs6/mimarks_s_collection_date.md create mode 100644 mixs6/mimarks_s_env_broad_scale.md create mode 100644 mixs6/mimarks_s_env_local_scale.md create mode 100644 mixs6/mimarks_s_env_medium.md create mode 100644 mixs6/mimarks_s_env_package.md create mode 100644 mixs6/mimarks_s_experimental_factor.md create mode 100644 mixs6/mimarks_s_geo_loc_name.md create mode 100644 mixs6/mimarks_s_investigation_type.md create mode 100644 mixs6/mimarks_s_lat_lon.md create mode 100644 mixs6/mimarks_s_lib_layout.md create mode 100644 mixs6/mimarks_s_lib_reads_seqd.md create mode 100644 mixs6/mimarks_s_lib_screen.md create mode 100644 mixs6/mimarks_s_lib_size.md create mode 100644 mixs6/mimarks_s_lib_vector.md create mode 100644 mixs6/mimarks_s_mid.md create mode 100644 mixs6/mimarks_s_nucl_acid_amp.md create mode 100644 mixs6/mimarks_s_nucl_acid_ext.md create mode 100644 mixs6/mimarks_s_pcr_cond.md create mode 100644 mixs6/mimarks_s_pcr_primers.md create mode 100644 mixs6/mimarks_s_project_name.md create mode 100644 mixs6/mimarks_s_rel_to_oxygen.md create mode 100644 mixs6/mimarks_s_samp_collect_device.md create mode 100644 mixs6/mimarks_s_samp_mat_process.md create mode 100644 mixs6/mimarks_s_samp_size.md create mode 100644 mixs6/mimarks_s_sample_name.md create mode 100644 mixs6/mimarks_s_seq_meth.md create mode 100644 mixs6/mimarks_s_seq_quality_check.md create mode 100644 mixs6/mimarks_s_size_frac.md create mode 100644 mixs6/mimarks_s_sop.md create mode 100644 mixs6/mimarks_s_source_mat_id.md create mode 100644 mixs6/mimarks_s_submitted_to_insdc.md create mode 100644 mixs6/mimarks_s_target_gene.md create mode 100644 mixs6/mimarks_s_target_subfragment.md create mode 100644 mixs6/mimarks_s_url.md create mode 100644 mixs6/misag_adapters.md create mode 100644 mixs6/misag_annot.md create mode 100644 mixs6/misag_assembly_name.md create mode 100644 mixs6/misag_assembly_qual.md create mode 100644 mixs6/misag_assembly_software.md create mode 100644 mixs6/misag_collection_date.md create mode 100644 mixs6/misag_compl_appr.md create mode 100644 mixs6/misag_compl_score.md create mode 100644 mixs6/misag_compl_software.md create mode 100644 mixs6/misag_contam_score.md create mode 100644 mixs6/misag_contam_screen_input.md create mode 100644 mixs6/misag_contam_screen_param.md create mode 100644 mixs6/misag_decontam_software.md create mode 100644 mixs6/misag_env_broad_scale.md create mode 100644 mixs6/misag_env_local_scale.md create mode 100644 mixs6/misag_env_medium.md create mode 100644 mixs6/misag_env_package.md create mode 100644 mixs6/misag_experimental_factor.md create mode 100644 mixs6/misag_feat_pred.md create mode 100644 mixs6/misag_geo_loc_name.md create mode 100644 mixs6/misag_investigation_type.md create mode 100644 mixs6/misag_lat_lon.md create mode 100644 mixs6/misag_lib_layout.md create mode 100644 mixs6/misag_lib_reads_seqd.md create mode 100644 mixs6/misag_lib_screen.md create mode 100644 mixs6/misag_lib_size.md create mode 100644 mixs6/misag_lib_vector.md create mode 100644 mixs6/misag_mid.md create mode 100644 mixs6/misag_nucl_acid_amp.md create mode 100644 mixs6/misag_nucl_acid_ext.md create mode 100644 mixs6/misag_number_contig.md create mode 100644 mixs6/misag_project_name.md create mode 100644 mixs6/misag_ref_biomaterial.md create mode 100644 mixs6/misag_ref_db.md create mode 100644 mixs6/misag_rel_to_oxygen.md create mode 100644 mixs6/misag_samp_collect_device.md create mode 100644 mixs6/misag_samp_mat_process.md create mode 100644 mixs6/misag_samp_size.md create mode 100644 mixs6/misag_sample_name.md create mode 100644 mixs6/misag_seq_meth.md create mode 100644 mixs6/misag_sim_search_meth.md create mode 100644 mixs6/misag_single_cell_lysis_appr.md create mode 100644 mixs6/misag_single_cell_lysis_prot.md create mode 100644 mixs6/misag_size_frac.md create mode 100644 mixs6/misag_sop.md create mode 100644 mixs6/misag_sort_tech.md create mode 100644 mixs6/misag_source_mat_id.md create mode 100644 mixs6/misag_submitted_to_insdc.md create mode 100644 mixs6/misag_tax_class.md create mode 100644 mixs6/misag_tax_ident.md create mode 100644 mixs6/misag_trna_ext_software.md create mode 100644 mixs6/misag_trnas.md create mode 100644 mixs6/misag_url.md create mode 100644 mixs6/misag_wga_amp_appr.md create mode 100644 mixs6/misag_wga_amp_kit.md create mode 100644 mixs6/misag_x_16s_recover.md create mode 100644 mixs6/misag_x_16s_recover_software.md create mode 100644 mixs6/miuvig_adapters.md create mode 100644 mixs6/miuvig_annot.md create mode 100644 mixs6/miuvig_assembly_name.md create mode 100644 mixs6/miuvig_assembly_qual.md create mode 100644 mixs6/miuvig_assembly_software.md create mode 100644 mixs6/miuvig_bin_param.md create mode 100644 mixs6/miuvig_bin_software.md create mode 100644 mixs6/miuvig_biotic_relationship.md create mode 100644 mixs6/miuvig_collection_date.md create mode 100644 mixs6/miuvig_compl_appr.md create mode 100644 mixs6/miuvig_compl_score.md create mode 100644 mixs6/miuvig_compl_software.md create mode 100644 mixs6/miuvig_detec_type.md create mode 100644 mixs6/miuvig_env_broad_scale.md create mode 100644 mixs6/miuvig_env_local_scale.md create mode 100644 mixs6/miuvig_env_medium.md create mode 100644 mixs6/miuvig_env_package.md create mode 100644 mixs6/miuvig_estimated_size.md create mode 100644 mixs6/miuvig_experimental_factor.md create mode 100644 mixs6/miuvig_feat_pred.md create mode 100644 mixs6/miuvig_geo_loc_name.md create mode 100644 mixs6/miuvig_host_pred_appr.md create mode 100644 mixs6/miuvig_host_pred_est_acc.md create mode 100644 mixs6/miuvig_host_spec_range.md create mode 100644 mixs6/miuvig_investigation_type.md create mode 100644 mixs6/miuvig_lat_lon.md create mode 100644 mixs6/miuvig_lib_layout.md create mode 100644 mixs6/miuvig_lib_reads_seqd.md create mode 100644 mixs6/miuvig_lib_screen.md create mode 100644 mixs6/miuvig_lib_size.md create mode 100644 mixs6/miuvig_lib_vector.md create mode 100644 mixs6/miuvig_mag_cov_software.md create mode 100644 mixs6/miuvig_mid.md create mode 100644 mixs6/miuvig_nucl_acid_amp.md create mode 100644 mixs6/miuvig_nucl_acid_ext.md create mode 100644 mixs6/miuvig_number_contig.md create mode 100644 mixs6/miuvig_pathogenicity.md create mode 100644 mixs6/miuvig_pred_genome_struc.md create mode 100644 mixs6/miuvig_pred_genome_type.md create mode 100644 mixs6/miuvig_project_name.md create mode 100644 mixs6/miuvig_reassembly_bin.md create mode 100644 mixs6/miuvig_ref_biomaterial.md create mode 100644 mixs6/miuvig_ref_db.md create mode 100644 mixs6/miuvig_samp_collect_device.md create mode 100644 mixs6/miuvig_samp_mat_process.md create mode 100644 mixs6/miuvig_samp_size.md create mode 100644 mixs6/miuvig_sample_name.md create mode 100644 mixs6/miuvig_seq_meth.md create mode 100644 mixs6/miuvig_sim_search_meth.md create mode 100644 mixs6/miuvig_single_cell_lysis_appr.md create mode 100644 mixs6/miuvig_single_cell_lysis_prot.md create mode 100644 mixs6/miuvig_size_frac.md create mode 100644 mixs6/miuvig_sop.md create mode 100644 mixs6/miuvig_sort_tech.md create mode 100644 mixs6/miuvig_source_mat_id.md create mode 100644 mixs6/miuvig_source_uvig.md create mode 100644 mixs6/miuvig_specific_host.md create mode 100644 mixs6/miuvig_submitted_to_insdc.md create mode 100644 mixs6/miuvig_tax_class.md create mode 100644 mixs6/miuvig_tax_ident.md create mode 100644 mixs6/miuvig_trna_ext_software.md create mode 100644 mixs6/miuvig_trnas.md create mode 100644 mixs6/miuvig_url.md create mode 100644 mixs6/miuvig_vir_ident_software.md create mode 100644 mixs6/miuvig_virus_enrich_appr.md create mode 100644 mixs6/miuvig_votu_class_appr.md create mode 100644 mixs6/miuvig_votu_db.md create mode 100644 mixs6/miuvig_votu_seq_comp_appr.md create mode 100644 mixs6/miuvig_wga_amp_appr.md create mode 100644 mixs6/miuvig_wga_amp_kit.md create mode 100644 mixs6/quantityValue__has_numeric_value.md create mode 100644 mixs6/quantityValue__has_raw_value.md create mode 100644 mixs6/quantityValue__has_unit.md diff --git a/Makefile b/Makefile index 21e90294..a43c180d 100644 --- a/Makefile +++ b/Makefile @@ -3,6 +3,8 @@ SCHEMA_DIR = $(SRC_DIR)/schema SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml') SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES)) +TARGETDIR = . + SCHEMA_NAME = mixs SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml TGTS = graphql jsonschema docs shex owl csv graphql python @@ -10,11 +12,8 @@ TGTS = graphql jsonschema docs shex owl csv graphql python #GEN_OPTS = --no-mergeimports GEN_OPTS = -all: stage-docs +all: gen-all gen: $(patsubst %,gen-%,$(TGTS)) -clean: - rm -rf target/ - rm -rf docs/ t: echo $(SCHEMA_NAMES) @@ -29,79 +28,65 @@ install: pip install -r requirements.txt tdir-%: - mkdir -p target/$* + mkdir -p $(TARGETDIR)/$* docs: mkdir $@ stage: $(patsubst %,stage-%,$(TGTS)) stage-%: gen-% - cp -pr target/$* . + cp -pr $(TARGETDIR)/$* . ### -- MARKDOWN DOCS -- # Generate documentation ready for mkdocs # TODO: modularize imports -gen-docs: target/docs/index.md +gen-docs: $(TARGETDIR)/mixs6/index.md .PHONY: gen-docs -#copy-src-docs: -# cp $(SRC_DIR)/docs/*md target/docs/ -target/docs/%.md: $(SCHEMA_SRC) tdir-docs - gen-markdown $(GEN_OPTS) --dir target/docs $< -stage-docs: gen-docs - cp -pr target/docs mixs6 - -### -- MARKDOWN DOCS -- -# TODO: modularize imports -gen-python: $(patsubst %, target/python/%.py, $(SCHEMA_NAMES)) -.PHONY: gen-python -target/python/%.py: $(SCHEMA_DIR)/%.yaml tdir-python - gen-py-classes --no-mergeimports $(GEN_OPTS) $< > $@ +$(TARGETDIR)/mixs6/%.md: $(SCHEMA_SRC) + gen-markdown $(GEN_OPTS) --dir $(TARGETDIR)/mixs6 $< ### -- MARKDOWN DOCS -- # TODO: modularize imports. For now imports are merged. -gen-graphql:target/graphql/$(SCHEMA_NAME).graphql -target/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql +gen-graphql:$(TARGETDIR)/graphql/$(SCHEMA_NAME).graphql +$(TARGETDIR)/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql gen-graphql $(GEN_OPTS) $< > $@ ### -- JSON schema -- # TODO: modularize imports. For now imports are merged. -gen-jsonschema: target/jsonschema/$(SCHEMA_NAME).schema.json -target/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema +gen-jsonschema: $(TARGETDIR)/jsonschema/$(SCHEMA_NAME).schema.json +$(TARGETDIR)/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema gen-json-schema $(GEN_OPTS) -t transaction $< > $@ ### -- Shex -- # one file per module -gen-shex: $(patsubst %, target/shex/%.shex, $(SCHEMA_NAMES)) -target/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex +gen-shex: $(patsubst %, $(TARGETDIR)/shex/%.shex, $(SCHEMA_NAMES)) +$(TARGETDIR)/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex gen-shex --no-mergeimports $(GEN_OPTS) $< > $@ ### -- CSV -- # one file per module -gen-csv: $(patsubst %, target/csv/%.csv, $(SCHEMA_NAMES)) -target/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv +gen-csv: $(patsubst %, $(TARGETDIR)/csv/%.csv, $(SCHEMA_NAMES)) +$(TARGETDIR)/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv gen-csv $(GEN_OPTS) $< > $@ ### -- OWL -- # TODO: modularize imports. For now imports are merged. -gen-owl: target/owl/$(SCHEMA_NAME).owl.ttl +gen-owl: $(TARGETDIR)/owl/$(SCHEMA_NAME).owl.ttl .PHONY: gen-owl -target/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl +$(TARGETDIR)/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl gen-owl $(GEN_OPTS) $< > $@ ### -- RDF (direct mapping) -- # TODO: modularize imports. For now imports are merged. -gen-rdf: target/rdf/$(SCHEMA_NAME).ttl -target/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf +gen-rdf: $(TARGETDIR)/rdf/$(SCHEMA_NAME).ttl +$(TARGETDIR)/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf gen-rdf $(GEN_OPTS) $< > $@ ### -- LinkML -- # linkml (copy) # one file per module -gen-linkml: target/linkml/$(SCHEMA_NAME).yaml -target/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml +gen-linkml: $(TARGETDIR)/linkml/$(SCHEMA_NAME).yaml +$(TARGETDIR)/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml cp $< > $@ -# test docs locally. -docserve: - mkdocs serve diff --git a/mixs6/Air.md b/mixs6/Air.md index 6c73d101..6e6c9e3d 100644 --- a/mixs6/Air.md +++ b/mixs6/Air.md @@ -7,21 +7,21 @@ air URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMiuvig],[AirMisag],[AirMimarksS],[AirMimarksC],[AirMimag],[AirMigsVi],[AirMigsPl],[AirMigsOrg],[AirMigsEu],[AirMigsBa],[AirMe],[QuantityValue][MIGSBacteria],[Air]^-[AirMIGSBacteria],[Air],[MIGSBacteria]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSEukaryote.md b/mixs6/AirMIGSEukaryote.md new file mode 100644 index 00000000..1b49ba89 --- /dev/null +++ b/mixs6/AirMIGSEukaryote.md @@ -0,0 +1,395 @@ + +# Class: AirMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + +URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Air]^-[AirMIGSEukaryote],[Air],[MIGSEukaryote]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSPlant.md b/mixs6/AirMIGSPlant.md new file mode 100644 index 00000000..94723967 --- /dev/null +++ b/mixs6/AirMIGSPlant.md @@ -0,0 +1,365 @@ + +# Class: AirMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + +URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSPlant],[Air]^-[AirMIGSPlant],[Air],[MIGSPlant]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIGSVirus.md b/mixs6/AirMIGSVirus.md new file mode 100644 index 00000000..50281d25 --- /dev/null +++ b/mixs6/AirMIGSVirus.md @@ -0,0 +1,390 @@ + +# Class: AirMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + +URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSVirus],[Air]^-[AirMIGSVirus],[Air],[MIGSVirus]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/AirMIMARKSSpecimen.md b/mixs6/AirMIMARKSSpecimen.md new file mode 100644 index 00000000..a475d061 --- /dev/null +++ b/mixs6/AirMIMARKSSpecimen.md @@ -0,0 +1,315 @@ + +# Class: AirMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + +URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Air]^-[AirMIMARKSSpecimen],[Air],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMIMARKSSurvey.md b/mixs6/AirMIMARKSSurvey.md new file mode 100644 index 00000000..7a804a29 --- /dev/null +++ b/mixs6/AirMIMARKSSurvey.md @@ -0,0 +1,295 @@ + +# Class: AirMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + +URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Air]^-[AirMIMARKSSurvey],[Air],[MIMARKSSurvey]) + +## Parents + + * is_a: [Air](Air.md) - air + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from air: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [barometric_press](barometric_press.md) OPT + * Description: Force per unit area exerted against a surface by the weight of air above that surface + * range: [QuantityValue](QuantityValue.md) + * Example: 5 millibar None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [carb_monoxide](carb_monoxide.md) OPT + * Description: Carbon monoxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 parts per million None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [humidity](humidity.md) OPT + * Description: Amount of water vapour in the air, at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 gram per cubic meter None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [oxygen](oxygen.md) OPT + * Description: Oxygen (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 600 parts per million None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pollutants](pollutants.md) OPT + * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + * range: [String](types/String.md) + * Example: lead;0.15 microgram per cubic meter None + * [resp_part_matter](resp_part_matter.md) OPT + * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + * range: [String](types/String.md) + * Example: PM2.5;10 microgram per cubic meter None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [solar_irradiance](solar_irradiance.md) OPT + * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + * range: [QuantityValue](QuantityValue.md) + * Example: 1.36 kilowatts per square meter per day None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [ventilation_rate](ventilation_rate.md) OPT + * Description: Ventilation rate of the system in the sampled premises + * range: [QuantityValue](QuantityValue.md) + * Example: 750 cubic meter per minute None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [volatile_org_comp](volatile_org_comp.md) OPT + * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + * range: [String](types/String.md) + * Example: formaldehyde;500 nanogram per liter None + * [wind_direction](wind_direction.md) OPT + * Description: Wind direction is the direction from which a wind originates + * range: [String](types/String.md) + * Example: Northwest None + * [wind_speed](wind_speed.md) OPT + * Description: Speed of wind measured at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 21 kilometer per hour None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md index f43fbec5..4146ef90 100644 --- a/mixs6/AirMe.md +++ b/mixs6/AirMe.md @@ -1,13 +1,13 @@ -# Class: AirMe +# Class: AirME -Combinatorial checklist for air with me +Combinatorial checklist Metagenome or Environmental with environmental package air -URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) +URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[AirMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Me],[Air]^-[AirMe],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[ME],[Air]^-[AirME],[Air],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -159,172 +159,172 @@ URI: [mixs.vocab:AirMe](https://w3id.org/mixs/vocab/AirMe) * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md index 54cbac53..40a8324c 100644 --- a/mixs6/AirMigsOrg.md +++ b/mixs6/AirMigsOrg.md @@ -1,13 +1,13 @@ -# Class: AirMigsOrg +# Class: AirMIGSOrg -Combinatorial checklist for air with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air -URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) +URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[AirMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsOrg],[Air]^-[AirMigsOrg],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSOrg],[Air]^-[AirMIGSOrg],[Air],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -159,192 +159,192 @@ URI: [mixs.vocab:AirMigsOrg](https://w3id.org/mixs/vocab/AirMigsOrg) * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md index 57e62106..5377572d 100644 --- a/mixs6/AirMimag.md +++ b/mixs6/AirMimag.md @@ -1,13 +1,13 @@ -# Class: AirMimag +# Class: AirMIMAG -Combinatorial checklist for air with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air -URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) +URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[AirMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Mimag],[Air]^-[AirMimag],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMAG],[Air]^-[AirMIMAG],[Air],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -159,252 +159,252 @@ URI: [mixs.vocab:AirMimag](https://w3id.org/mixs/vocab/AirMimag) * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md index a3582fa1..82dccc08 100644 --- a/mixs6/AirMisag.md +++ b/mixs6/AirMisag.md @@ -1,13 +1,13 @@ -# Class: AirMisag +# Class: AirMISAG -Combinatorial checklist for air with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air -URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) +URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[AirMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Misag],[Air]^-[AirMisag],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MISAG],[Air]^-[AirMISAG],[Air],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -159,257 +159,257 @@ URI: [mixs.vocab:AirMisag](https://w3id.org/mixs/vocab/AirMisag) * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md index b855979d..c4a97eb5 100644 --- a/mixs6/AirMiuvig.md +++ b/mixs6/AirMiuvig.md @@ -1,13 +1,13 @@ -# Class: AirMiuvig +# Class: AirMIUVIG -Combinatorial checklist for air with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air -URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) +URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[AirMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[Miuvig],[Air]^-[AirMiuvig],[Air]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIUVIG],[Air]^-[AirMIUVIG],[Air],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -159,322 +159,322 @@ URI: [mixs.vocab:AirMiuvig](https://w3id.org/mixs/vocab/AirMiuvig) * range: [QuantityValue](QuantityValue.md) * Example: 21 kilometer per hour None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironment.md b/mixs6/BuiltEnvironment.md index c836e5b9..c921c955 100644 --- a/mixs6/BuiltEnvironment.md +++ b/mixs6/BuiltEnvironment.md @@ -7,21 +7,21 @@ built environment URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMiuvig],[BuiltEnvironmentMisag],[BuiltEnvironmentMimarksS],[BuiltEnvironmentMimarksC],[BuiltEnvironmentMimag],[BuiltEnvironmentMigsVi],[BuiltEnvironmentMigsPl],[BuiltEnvironmentMigsOrg],[BuiltEnvironmentMigsEu],[BuiltEnvironmentMigsBa],[BuiltEnvironmentMe],[QuantityValue][MIGSBacteria],[BuiltEnvironment]^-[BuiltEnvironmentMIGSBacteria],[BuiltEnvironment],[MIGSBacteria]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSEukaryote.md b/mixs6/BuiltEnvironmentMIGSEukaryote.md new file mode 100644 index 00000000..9918f0a8 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSEukaryote.md @@ -0,0 +1,935 @@ + +# Class: BuiltEnvironmentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSEukaryote],[BuiltEnvironment]^-[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironment],[MIGSEukaryote]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSPlant.md b/mixs6/BuiltEnvironmentMIGSPlant.md new file mode 100644 index 00000000..ee3f07a0 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSPlant.md @@ -0,0 +1,905 @@ + +# Class: BuiltEnvironmentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSPlant],[BuiltEnvironment]^-[BuiltEnvironmentMIGSPlant],[BuiltEnvironment],[MIGSPlant]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIGSVirus.md b/mixs6/BuiltEnvironmentMIGSVirus.md new file mode 100644 index 00000000..15207d05 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIGSVirus.md @@ -0,0 +1,930 @@ + +# Class: BuiltEnvironmentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSVirus],[BuiltEnvironment]^-[BuiltEnvironmentMIGSVirus],[BuiltEnvironment],[MIGSVirus]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/BuiltEnvironmentMIMARKSSpecimen.md b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md new file mode 100644 index 00000000..13f82861 --- /dev/null +++ b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md @@ -0,0 +1,855 @@ + +# Class: BuiltEnvironmentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironment],[MIMARKSSpecimen]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMIMARKSSurvey.md b/mixs6/BuiltEnvironmentMIMARKSSurvey.md new file mode 100644 index 00000000..353f9a7b --- /dev/null +++ b/mixs6/BuiltEnvironmentMIMARKSSurvey.md @@ -0,0 +1,835 @@ + +# Class: BuiltEnvironmentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + +URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSurvey],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironment],[MIMARKSSurvey]) + +## Parents + + * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from built environment: + + * [abs_air_humidity](abs_air_humidity.md) OPT + * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + * range: [QuantityValue](QuantityValue.md) + * Example: 9 gram per gram None + * [address](address.md) OPT + * Description: The street name and building number where the sampling occurred. + * range: [String](types/String.md) + * Example: None + * [adj_room](adj_room.md) OPT + * Description: List of rooms (room number, room name) immediately adjacent to the sampling room + * range: [String](types/String.md) + * Example: None + * [aero_struc](aero_struc.md) OPT + * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + * range: [String](types/String.md) + * Example: plane None + * [air_temp](air_temp.md) OPT + * Description: Temperature of the air at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 20 degree Celsius None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amount_light](amount_light.md) OPT + * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [arch_struc](arch_struc.md) OPT + * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction + * range: + * Example: shed None + * [avg_dew_point](avg_dew_point.md) OPT + * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 25.5 degree Celsius None + * [avg_occup](avg_occup.md) OPT + * Description: Daily average occupancy of room + * range: [Double](types/Double.md) + * Example: 2 None + * [avg_temp](avg_temp.md) OPT + * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [bathroom_count](bathroom_count.md) OPT + * Description: The number of bathrooms in the building + * range: [String](types/String.md) + * Example: 1 None + * [bedroom_count](bedroom_count.md) OPT + * Description: The number of bedrooms in the building + * range: [String](types/String.md) + * Example: 2 None + * [build_docs](build_docs.md) OPT + * Description: The building design, construction and operation documents + * range: + * Example: maintenance plans None + * [build_occup_type](build_occup_type.md) OPT + * Description: The primary function for which a building or discrete part of a building is intended to be used + * range: + * Example: market None + * [building_setting](building_setting.md) OPT + * Description: A location (geography) where a building is set + * range: + * Example: rural None + * [built_struc_age](built_struc_age.md) OPT + * Description: The age of the built structure since construction + * range: [QuantityValue](QuantityValue.md) + * Example: 15 None + * [built_struc_set](built_struc_set.md) OPT + * Description: The characterization of the location of the built structure as high or low human density + * range: [String](types/String.md) + * Example: rural None + * [built_struc_type](built_struc_type.md) OPT + * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + * range: [String](types/String.md) + * Example: None + * [carb_dioxide](carb_dioxide.md) OPT + * Description: Carbon dioxide (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 410 parts per million None + * [ceil_area](ceil_area.md) OPT + * Description: The area of the ceiling space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: 25 square meter None + * [ceil_cond](ceil_cond.md) OPT + * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [ceil_finish_mat](ceil_finish_mat.md) OPT + * Description: The type of material used to finish a ceiling + * range: + * Example: stucco None + * [ceil_struc](ceil_struc.md) OPT + * Description: The construction format of the ceiling + * range: [String](types/String.md) + * Example: concrete None + * [ceil_texture](ceil_texture.md) OPT + * Description: The feel, appearance, or consistency of a ceiling surface + * range: + * Example: popcorn None + * [ceil_thermal_mass](ceil_thermal_mass.md) OPT + * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [ceil_type](ceil_type.md) OPT + * Description: The type of ceiling according to the ceiling's appearance or construction + * range: + * Example: coffered None + * [ceil_water_mold](ceil_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the ceiling + * range: [String](types/String.md) + * Example: presence of mold visible None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cool_syst_id](cool_syst_id.md) OPT + * Description: The cooling system identifier + * range: [String](types/String.md) + * Example: 12345 None + * [date_last_rain](date_last_rain.md) OPT + * Description: The date of the last time it rained + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dew_point](dew_point.md) OPT + * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + * range: [QuantityValue](QuantityValue.md) + * Example: 22 degree Celsius None + * [door_comp_type](door_comp_type.md) OPT + * Description: The composite type of the door + * range: + * Example: revolving None + * [door_cond](door_cond.md) OPT + * Description: The phsical condition of the door + * range: + * Example: new None + * [door_direct](door_direct.md) OPT + * Description: The direction the door opens + * range: + * Example: inward None + * [door_loc](door_loc.md) OPT + * Description: The relative location of the door in the room + * range: + * Example: north None + * [door_mat](door_mat.md) OPT + * Description: The material the door is composed of + * range: + * Example: wood None + * [door_move](door_move.md) OPT + * Description: The type of movement of the door + * range: + * Example: swinging None + * [door_size](door_size.md) OPT + * Description: The size of the door + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 square meter None + * [door_type](door_type.md) OPT + * Description: The type of door material + * range: + * Example: wooden None + * [door_type_metal](door_type_metal.md) OPT + * Description: The type of metal door + * range: + * Example: hollow None + * [door_type_wood](door_type_wood.md) OPT + * Description: The type of wood door + * range: + * Example: battened None + * [door_water_mold](door_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a door + * range: [String](types/String.md) + * Example: presence of mold visible None + * [drawings](drawings.md) OPT + * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + * range: + * Example: sketch None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [elevator](elevator.md) OPT + * Description: The number of elevators within the built structure + * range: [String](types/String.md) + * Example: 2 None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [escalator](escalator.md) OPT + * Description: The number of escalators within the built structure + * range: [String](types/String.md) + * Example: 4 None + * [exp_duct](exp_duct.md) OPT + * Description: The amount of exposed ductwork in the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [exp_pipe](exp_pipe.md) OPT + * Description: The number of exposed pipes in the room + * range: [String](types/String.md) + * Example: None + * [ext_door](ext_door.md) OPT + * Description: The number of exterior doors in the built structure + * range: [String](types/String.md) + * Example: None + * [ext_wall_orient](ext_wall_orient.md) OPT + * Description: The orientation of the exterior wall + * range: + * Example: northwest None + * [ext_window_orient](ext_window_orient.md) OPT + * Description: The compass direction the exterior window of the room is facing + * range: + * Example: southwest None + * [filter_type](filter_type.md) OPT + * Description: A device which removes solid particulates or airborne molecular contaminants + * range: + * Example: HEPA None + * [fireplace_type](fireplace_type.md) OPT + * Description: A firebox with chimney + * range: [String](types/String.md) + * Example: wood burning None + * [floor_age](floor_age.md) OPT + * Description: The time period since installment of the carpet or flooring + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_area](floor_area.md) OPT + * Description: The area of the floor space within the room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_cond](floor_cond.md) OPT + * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: new None + * [floor_count](floor_count.md) OPT + * Description: The number of floors in the building, including basements and mechanical penthouse + * range: [String](types/String.md) + * Example: None + * [floor_finish_mat](floor_finish_mat.md) OPT + * Description: The floor covering type; the finished surface that is walked on + * range: + * Example: carpet None + * [floor_struc](floor_struc.md) OPT + * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed + * range: + * Example: concrete None + * [floor_thermal_mass](floor_thermal_mass.md) OPT + * Description: The ability of the floor to provide inertia against temperature fluctuations + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [floor_water_mold](floor_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew in a room + * range: + * Example: ceiling discoloration None + * [freq_clean](freq_clean.md) OPT + * Description: The number of times the building is cleaned per week + * range: [String](types/String.md) + * Example: None + * [freq_cook](freq_cook.md) OPT + * Description: The number of times a meal is cooked per week + * range: [String](types/String.md) + * Example: None + * [furniture](furniture.md) OPT + * Description: The types of furniture present in the sampled room + * range: + * Example: chair None + * [gender_restroom](gender_restroom.md) OPT + * Description: The gender type of the restroom + * range: [String](types/String.md) + * Example: male None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hall_count](hall_count.md) OPT + * Description: The total count of hallways and cooridors in the built structure + * range: [String](types/String.md) + * Example: None + * [handidness](handidness.md) OPT + * Description: The handidness of the individual sampled + * range: + * Example: right handedness None + * [heat_cool_type](heat_cool_type.md) OPT + * Description: Methods of conditioning or heating a room or building + * range: + * Example: heat pump None + * [heat_deliv_loc](heat_deliv_loc.md) OPT + * Description: The location of heat delivery within the room + * range: + * Example: north None + * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT + * Description: The method by which the heat is delivered through the system + * range: [String](types/String.md) + * Example: radiant None + * [heat_system_id](heat_system_id.md) OPT + * Description: The heating system identifier + * range: [String](types/String.md) + * Example: None + * [height_carper_fiber](height_carper_fiber.md) OPT + * Description: The average carpet fiber height in the indoor environment + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [indoor_space](indoor_space.md) OPT + * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + * range: + * Example: foyer None + * [indoor_surf](indoor_surf.md) OPT + * Description: Type of indoor surface + * range: + * Example: wall None + * [inside_lux](inside_lux.md) OPT + * Description: The recorded value at sampling time (power density) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [int_wall_cond](int_wall_cond.md) OPT + * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + * range: + * Example: damaged None + * [last_clean](last_clean.md) OPT + * Description: The last time the floor was cleaned (swept, mopped, vacuumed) + * range: [String](types/String.md) + * Example: 2018-05-11:T14:30Z None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_type](light_type.md) OPT + * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + * range: + * Example: desk lamp None + * [max_occup](max_occup.md) OPT + * Description: The maximum amount of people allowed in the indoor environment + * range: [String](types/String.md) + * Example: None + * [mech_struc](mech_struc.md) OPT + * Description: mechanical structure: a moving structure + * range: + * Example: elevator None + * [number_pets](number_pets.md) OPT + * Description: The number of pets residing in the sampled space + * range: [String](types/String.md) + * Example: None + * [number_plants](number_plants.md) OPT + * Description: The number of plant(s) in the sampling space + * range: [String](types/String.md) + * Example: None + * [number_resident](number_resident.md) OPT + * Description: The number of individuals currently occupying in the sampling location + * range: [String](types/String.md) + * Example: None + * [occup_density_samp](occup_density_samp.md) OPT + * Description: Average number of occupants at time of sampling per square footage + * range: [Double](types/Double.md) + * Example: None + * [occup_document](occup_document.md) OPT + * Description: The type of documentation of occupancy + * range: + * Example: estimate None + * [occup_samp](occup_samp.md) OPT + * Description: Number of occupants present at time of sample within the given space + * range: [String](types/String.md) + * Example: 10 None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [pres_animal](pres_animal.md) OPT + * Description: The number and type of animals present in the sampling space + * range: + * Example: cat;5 None + * [quad_pos](quad_pos.md) OPT + * Description: The quadrant position of the sampling room within the building + * range: + * Example: West side None + * [rel_air_humidity](rel_air_humidity.md) OPT + * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + * range: [QuantityValue](QuantityValue.md) + * Example: 80% None + * [rel_humidity_out](rel_humidity_out.md) OPT + * Description: The recorded outside relative humidity value at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 12 per kilogram of air None + * [rel_samp_loc](rel_samp_loc.md) OPT + * Description: The sampling location within the train car + * range: + * Example: center of car None + * [room_air_exch_rate](room_air_exch_rate.md) OPT + * Description: The rate at which outside air replaces indoor air in a given space + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [room_architec_element](room_architec_element.md) OPT + * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + * range: [String](types/String.md) + * Example: None + * [room_condt](room_condt.md) OPT + * Description: The condition of the room at the time of sampling + * range: + * Example: new None + * [room_connected](room_connected.md) OPT + * Description: List of rooms connected to the sampling room by a doorway + * range: + * Example: office None + * [room_count](room_count.md) OPT + * Description: The total count of rooms in the built structure including all room types + * range: [String](types/String.md) + * Example: None + * [room_dim](room_dim.md) OPT + * Description: The length, width and height of sampling room + * range: [String](types/String.md) + * Example: None + * [room_door_dist](room_door_dist.md) OPT + * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + * range: [String](types/String.md) + * Example: None + * [room_door_share](room_door_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a door with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_hallway](room_hallway.md) OPT + * Description: List of room(s) (room number, room name) located in the same hallway as sampling room + * range: [String](types/String.md) + * Example: None + * [room_loc](room_loc.md) OPT + * Description: The position of the room within the building + * range: + * Example: interior room None + * [room_moist_damage_hist](room_moist_damage_hist.md) OPT + * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + * range: [String](types/String.md) + * Example: None + * [room_net_area](room_net_area.md) OPT + * Description: The net floor area of sampling room. Net area excludes wall thicknesses + * range: [String](types/String.md) + * Example: None + * [room_occup](room_occup.md) OPT + * Description: Count of room occupancy at time of sampling + * range: [String](types/String.md) + * Example: None + * [room_samp_pos](room_samp_pos.md) OPT + * Description: The horizontal sampling position in the room relative to architectural elements + * range: + * Example: south corner None + * [room_type](room_type.md) OPT + * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + * range: + * Example: bathroom None + * [room_vol](room_vol.md) OPT + * Description: Volume of sampling room + * range: [String](types/String.md) + * Example: None + * [room_wall_share](room_wall_share.md) OPT + * Description: List of room(s) (room number, room name) sharing a wall with the sampling room + * range: [String](types/String.md) + * Example: None + * [room_window_count](room_window_count.md) OPT + * Description: Number of windows in the room + * range: [String](types/String.md) + * Example: None + * [samp_floor](samp_floor.md) OPT + * Description: The floor of the building, where the sampling room is located + * range: + * Example: 4th floor None + * [samp_room_id](samp_room_id.md) OPT + * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans + * range: [String](types/String.md) + * Example: None + * [samp_sort_meth](samp_sort_meth.md) OPT + * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + * range: [String](types/String.md) + * Example: None + * [samp_time_out](samp_time_out.md) OPT + * Description: The recent and long term history of outside sampling + * range: [Double](types/Double.md) + * Example: None + * [samp_weather](samp_weather.md) OPT + * Description: The weather on the sampling day + * range: + * Example: foggy None + * [season](season.md) OPT + * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + * range: [String](types/String.md) + * Example: autumn [NCIT:C94733] None + * [season_use](season_use.md) OPT + * Description: The seasons the space is occupied + * range: + * Example: Winter None + * [shading_device_cond](shading_device_cond.md) OPT + * Description: The physical condition of the shading device at the time of sampling + * range: + * Example: new None + * [shading_device_loc](shading_device_loc.md) OPT + * Description: The location of the shading device in relation to the built structure + * range: [String](types/String.md) + * Example: exterior None + * [shading_device_mat](shading_device_mat.md) OPT + * Description: The material the shading device is composed of + * range: [String](types/String.md) + * Example: None + * [shading_device_type](shading_device_type.md) OPT + * Description: The type of shading device + * range: + * Example: slatted aluminum awning None + * [shading_device_water_mold](shading_device_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the shading device + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [space_typ_state](space_typ_state.md) OPT + * Description: Customary or normal state of the space + * range: [String](types/String.md) + * Example: typically occupied None + * [specific](specific.md) OPT + * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents + * range: + * Example: construction None + * [specific_humidity](specific_humidity.md) OPT + * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + * range: [QuantityValue](QuantityValue.md) + * Example: 15 per kilogram of air None + * [substructure_type](substructure_type.md) OPT + * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + * range: + * Example: basement None + * [surf_air_cont](surf_air_cont.md) OPT + * Description: Contaminant identified on surface + * range: + * Example: radon None + * [surf_humidity](surf_humidity.md) OPT + * Description: Surfaces: water activity as a function of air and material moisture + * range: [QuantityValue](QuantityValue.md) + * Example: 10% None + * [surf_material](surf_material.md) OPT + * Description: Surface materials at the point of sampling + * range: + * Example: wood None + * [surf_moisture](surf_moisture.md) OPT + * Description: Water held on a surface + * range: [QuantityValue](QuantityValue.md) + * Example: 0.01 gram per square meter None + * [surf_moisture_ph](surf_moisture_ph.md) OPT + * Description: ph measurement of surface + * range: [Double](types/Double.md) + * Example: 7 None + * [surf_temp](surf_temp.md) OPT + * Description: Temperature of the surface at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [temp_out](temp_out.md) OPT + * Description: The recorded temperature value at sampling time outside + * range: [QuantityValue](QuantityValue.md) + * Example: 5 degree Celsius None + * [train_line](train_line.md) OPT + * Description: The subway line name + * range: + * Example: red None + * [train_stat_loc](train_stat_loc.md) OPT + * Description: The train station collection location + * range: + * Example: forest hills None + * [train_stop_loc](train_stop_loc.md) OPT + * Description: The train stop collection location + * range: + * Example: end None + * [typ_occup_density](typ_occup_density.md) OPT + * Description: Customary or normal density of occupants + * range: [Double](types/Double.md) + * Example: 25 None + * [ventilation_type](ventilation_type.md) OPT + * Description: Ventilation system used in the sampled premises + * range: [String](types/String.md) + * Example: Operable windows None + * [vis_media](vis_media.md) OPT + * Description: The building visual media + * range: + * Example: 3D scans None + * [wall_area](wall_area.md) OPT + * Description: The total area of the sampled room's walls + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_const_type](wall_const_type.md) OPT + * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + * range: + * Example: fire resistive None + * [wall_finish_mat](wall_finish_mat.md) OPT + * Description: The material utilized to finish the outer most layer of the wall + * range: + * Example: wood None + * [wall_height](wall_height.md) OPT + * Description: The average height of the walls in the sampled room + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_loc](wall_loc.md) OPT + * Description: The relative location of the wall within the room + * range: + * Example: north None + * [wall_surf_treatment](wall_surf_treatment.md) OPT + * Description: The surface treatment of interior wall + * range: + * Example: paneling None + * [wall_texture](wall_texture.md) OPT + * Description: The feel, appearance, or consistency of a wall surface + * range: + * Example: popcorn None + * [wall_thermal_mass](wall_thermal_mass.md) OPT + * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wall_water_mold](wall_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on a wall + * range: [String](types/String.md) + * Example: no presence of mold visible None + * [water_feat_size](water_feat_size.md) OPT + * Description: The size of the water feature + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_feat_type](water_feat_type.md) OPT + * Description: The type of water feature present within the building being sampled + * range: + * Example: stream None + * [weekday](weekday.md) OPT + * Description: The day of the week when sampling occurred + * range: + * Example: Sunday None + * [window_cond](window_cond.md) OPT + * Description: The physical condition of the window at the time of sampling + * range: + * Example: rupture None + * [window_cover](window_cover.md) OPT + * Description: The type of window covering + * range: + * Example: curtains None + * [window_horiz_pos](window_horiz_pos.md) OPT + * Description: The horizontal position of the window on the wall + * range: + * Example: middle None + * [window_loc](window_loc.md) OPT + * Description: The relative location of the window within the room + * range: + * Example: west None + * [window_mat](window_mat.md) OPT + * Description: The type of material used to finish a window + * range: + * Example: wood None + * [window_open_freq](window_open_freq.md) OPT + * Description: The number of times windows are opened per week + * range: [String](types/String.md) + * Example: None + * [window_size](window_size.md) OPT + * Description: The window's length and width + * range: [String](types/String.md) + * Example: None + * [window_status](window_status.md) OPT + * Description: Defines whether the windows were open or closed during environmental testing + * range: [String](types/String.md) + * Example: open None + * [window_type](window_type.md) OPT + * Description: The type of windows + * range: + * Example: fixed window None + * [window_vert_pos](window_vert_pos.md) OPT + * Description: The vertical position of the window on the wall + * range: + * Example: middle None + * [window_water_mold](window_water_mold.md) OPT + * Description: Signs of the presence of mold or mildew on the window. + * range: [String](types/String.md) + * Example: no presence of mold visible None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMe.md b/mixs6/BuiltEnvironmentMe.md index 4b33e069..527b7d0c 100644 --- a/mixs6/BuiltEnvironmentMe.md +++ b/mixs6/BuiltEnvironmentMe.md @@ -1,13 +1,13 @@ -# Class: BuiltEnvironmentMe +# Class: BuiltEnvironmentME -Combinatorial checklist for built environment with me +Combinatorial checklist Metagenome or Environmental with environmental package built environment -URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmentMe) +URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[BuiltEnvironmentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Me],[BuiltEnvironment]^-[BuiltEnvironmentMe],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[ME],[BuiltEnvironment]^-[BuiltEnvironmentME],[BuiltEnvironment],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -699,172 +699,172 @@ URI: [mixs.vocab:BuiltEnvironmentMe](https://w3id.org/mixs/vocab/BuiltEnvironmen * range: [String](types/String.md) * Example: no presence of mold visible None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsOrg.md b/mixs6/BuiltEnvironmentMigsOrg.md index 7827e881..99550dc9 100644 --- a/mixs6/BuiltEnvironmentMigsOrg.md +++ b/mixs6/BuiltEnvironmentMigsOrg.md @@ -1,13 +1,13 @@ -# Class: BuiltEnvironmentMigsOrg +# Class: BuiltEnvironmentMIGSOrg -Combinatorial checklist for built environment with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment -URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsOrg) +URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[BuiltEnvironmentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsOrg],[BuiltEnvironment]^-[BuiltEnvironmentMigsOrg],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSOrg],[BuiltEnvironment]^-[BuiltEnvironmentMIGSOrg],[BuiltEnvironment],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -699,192 +699,192 @@ URI: [mixs.vocab:BuiltEnvironmentMigsOrg](https://w3id.org/mixs/vocab/BuiltEnvir * range: [String](types/String.md) * Example: no presence of mold visible None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimag.md b/mixs6/BuiltEnvironmentMimag.md index 602bb639..3794f823 100644 --- a/mixs6/BuiltEnvironmentMimag.md +++ b/mixs6/BuiltEnvironmentMimag.md @@ -1,13 +1,13 @@ -# Class: BuiltEnvironmentMimag +# Class: BuiltEnvironmentMIMAG -Combinatorial checklist for built environment with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment -URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnvironmentMimag) +URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[BuiltEnvironmentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Mimag],[BuiltEnvironment]^-[BuiltEnvironmentMimag],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMAG],[BuiltEnvironment]^-[BuiltEnvironmentMIMAG],[BuiltEnvironment],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -699,252 +699,252 @@ URI: [mixs.vocab:BuiltEnvironmentMimag](https://w3id.org/mixs/vocab/BuiltEnviron * range: [String](types/String.md) * Example: no presence of mold visible None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMisag.md b/mixs6/BuiltEnvironmentMisag.md index ea0bec0d..be839ce8 100644 --- a/mixs6/BuiltEnvironmentMisag.md +++ b/mixs6/BuiltEnvironmentMisag.md @@ -1,13 +1,13 @@ -# Class: BuiltEnvironmentMisag +# Class: BuiltEnvironmentMISAG -Combinatorial checklist for built environment with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment -URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnvironmentMisag) +URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[BuiltEnvironmentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Misag],[BuiltEnvironment]^-[BuiltEnvironmentMisag],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MISAG],[BuiltEnvironment]^-[BuiltEnvironmentMISAG],[BuiltEnvironment],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -699,257 +699,257 @@ URI: [mixs.vocab:BuiltEnvironmentMisag](https://w3id.org/mixs/vocab/BuiltEnviron * range: [String](types/String.md) * Example: no presence of mold visible None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMiuvig.md b/mixs6/BuiltEnvironmentMiuvig.md index a1905895..8a08aebc 100644 --- a/mixs6/BuiltEnvironmentMiuvig.md +++ b/mixs6/BuiltEnvironmentMiuvig.md @@ -1,13 +1,13 @@ -# Class: BuiltEnvironmentMiuvig +# Class: BuiltEnvironmentMIUVIG -Combinatorial checklist for built environment with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment -URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnvironmentMiuvig) +URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[BuiltEnvironmentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[Miuvig],[BuiltEnvironment]^-[BuiltEnvironmentMiuvig],[BuiltEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIUVIG],[BuiltEnvironment]^-[BuiltEnvironmentMIUVIG],[BuiltEnvironment],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -699,322 +699,322 @@ URI: [mixs.vocab:BuiltEnvironmentMiuvig](https://w3id.org/mixs/vocab/BuiltEnviro * range: [String](types/String.md) * Example: no presence of mold visible None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Host-associated.md b/mixs6/Host-associated.md index 5f438a70..fac780fd 100644 --- a/mixs6/Host-associated.md +++ b/mixs6/Host-associated.md @@ -7,21 +7,21 @@ host-associated URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMiuvig],[Host-associatedMisag],[Host-associatedMimarksS],[Host-associatedMimarksC],[Host-associatedMimag],[Host-associatedMigsVi],[Host-associatedMigsPl],[Host-associatedMigsOrg],[Host-associatedMigsEu],[Host-associatedMigsBa],[Host-associatedMe],[QuantityValue][MIGSBacteria],[Host-associated]^-[Host-associatedMIGSBacteria],[Host-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSEukaryote.md b/mixs6/Host-associatedMIGSEukaryote.md new file mode 100644 index 00000000..63032bb0 --- /dev/null +++ b/mixs6/Host-associatedMIGSEukaryote.md @@ -0,0 +1,475 @@ + +# Class: Host-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Host-associated]^-[Host-associatedMIGSEukaryote],[Host-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSPlant.md b/mixs6/Host-associatedMIGSPlant.md new file mode 100644 index 00000000..f2f3498d --- /dev/null +++ b/mixs6/Host-associatedMIGSPlant.md @@ -0,0 +1,445 @@ + +# Class: Host-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Host-associated]^-[Host-associatedMIGSPlant],[Host-associated],[MIGSPlant]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIGSVirus.md b/mixs6/Host-associatedMIGSVirus.md new file mode 100644 index 00000000..3da0b62d --- /dev/null +++ b/mixs6/Host-associatedMIGSVirus.md @@ -0,0 +1,470 @@ + +# Class: Host-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Host-associated]^-[Host-associatedMIGSVirus],[Host-associated],[MIGSVirus]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Host-associatedMIMARKSSpecimen.md b/mixs6/Host-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..08ab1057 --- /dev/null +++ b/mixs6/Host-associatedMIMARKSSpecimen.md @@ -0,0 +1,395 @@ + +# Class: Host-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Host-associated]^-[Host-associatedMIMARKSSpecimen],[Host-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMIMARKSSurvey.md b/mixs6/Host-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..593b685b --- /dev/null +++ b/mixs6/Host-associatedMIMARKSSurvey.md @@ -0,0 +1,375 @@ + +# Class: Host-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + +URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Host-associated]^-[Host-associatedMIMARKSSurvey],[Host-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Host-associated](Host-associated.md) - host-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from host-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravidity](gravidity.md) OPT + * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + * range: [String](types/String.md) + * Example: yes;due date:2018-05-11 None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_blood_press_diast](host_blood_press_diast.md) OPT + * Description: Resting diastolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_blood_press_syst](host_blood_press_syst.md) OPT + * Description: Resting systolic blood pressure, measured as mm mercury + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [host_body_habitat](host_body_habitat.md) OPT + * Description: Original body habitat where the sample was obtained from + * range: [String](types/String.md) + * Example: nasopharynx None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_color](host_color.md) OPT + * Description: The color of host + * range: [String](types/String.md) + * Example: None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_growth_cond](host_growth_cond.md) OPT + * Description: Literature reference giving growth conditions of the host + * range: [String](types/String.md) + * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_shape](host_shape.md) OPT + * Description: Morphological shape of host + * range: [String](types/String.md) + * Example: round None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_substrate](host_substrate.md) OPT + * Description: The growth substrate of the host + * range: [String](types/String.md) + * Example: rock None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMe.md b/mixs6/Host-associatedMe.md index 38a32a28..f07b4bb6 100644 --- a/mixs6/Host-associatedMe.md +++ b/mixs6/Host-associatedMe.md @@ -1,13 +1,13 @@ -# Class: Host-associatedMe +# Class: Host-associatedME -Combinatorial checklist for host-associated with me +Combinatorial checklist Metagenome or Environmental with environmental package host-associated -URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedMe) +URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Host-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Host-associated]^-[Host-associatedMe],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Host-associated]^-[Host-associatedME],[Host-associated],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -239,172 +239,172 @@ URI: [mixs.vocab:Host-associatedMe](https://w3id.org/mixs/vocab/Host-associatedM * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsOrg.md b/mixs6/Host-associatedMigsOrg.md index 8d5603c2..2d62128d 100644 --- a/mixs6/Host-associatedMigsOrg.md +++ b/mixs6/Host-associatedMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Host-associatedMigsOrg +# Class: Host-associatedMIGSOrg -Combinatorial checklist for host-associated with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated -URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associatedMigsOrg) +URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Host-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Host-associated]^-[Host-associatedMigsOrg],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Host-associated]^-[Host-associatedMIGSOrg],[Host-associated],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -239,192 +239,192 @@ URI: [mixs.vocab:Host-associatedMigsOrg](https://w3id.org/mixs/vocab/Host-associ * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimag.md b/mixs6/Host-associatedMimag.md index 422afd1b..c6287d88 100644 --- a/mixs6/Host-associatedMimag.md +++ b/mixs6/Host-associatedMimag.md @@ -1,13 +1,13 @@ -# Class: Host-associatedMimag +# Class: Host-associatedMIMAG -Combinatorial checklist for host-associated with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated -URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associatedMimag) +URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Host-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Host-associated]^-[Host-associatedMimag],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Host-associated]^-[Host-associatedMIMAG],[Host-associated],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -239,252 +239,252 @@ URI: [mixs.vocab:Host-associatedMimag](https://w3id.org/mixs/vocab/Host-associat * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMisag.md b/mixs6/Host-associatedMisag.md index bdb4dd4b..7ed6c9cd 100644 --- a/mixs6/Host-associatedMisag.md +++ b/mixs6/Host-associatedMisag.md @@ -1,13 +1,13 @@ -# Class: Host-associatedMisag +# Class: Host-associatedMISAG -Combinatorial checklist for host-associated with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated -URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associatedMisag) +URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Host-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Host-associated]^-[Host-associatedMisag],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Host-associated]^-[Host-associatedMISAG],[Host-associated],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -239,257 +239,257 @@ URI: [mixs.vocab:Host-associatedMisag](https://w3id.org/mixs/vocab/Host-associat * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMiuvig.md b/mixs6/Host-associatedMiuvig.md index 9260f3cd..4fe1924c 100644 --- a/mixs6/Host-associatedMiuvig.md +++ b/mixs6/Host-associatedMiuvig.md @@ -1,13 +1,13 @@ -# Class: Host-associatedMiuvig +# Class: Host-associatedMIUVIG -Combinatorial checklist for host-associated with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated -URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associatedMiuvig) +URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Host-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Host-associated]^-[Host-associatedMiuvig],[Host-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Host-associated]^-[Host-associatedMIUVIG],[Host-associated],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -239,322 +239,322 @@ URI: [mixs.vocab:Host-associatedMiuvig](https://w3id.org/mixs/vocab/Host-associa * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-associated.md b/mixs6/Human-associated.md index 0b21f326..de763b3e 100644 --- a/mixs6/Human-associated.md +++ b/mixs6/Human-associated.md @@ -7,21 +7,21 @@ human-associated URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMiuvig],[Human-associatedMisag],[Human-associatedMimarksS],[Human-associatedMimarksC],[Human-associatedMimag],[Human-associatedMigsVi],[Human-associatedMigsPl],[Human-associatedMigsOrg],[Human-associatedMigsEu],[Human-associatedMigsBa],[Human-associatedMe],[QuantityValue][MIGSBacteria],[Human-associated]^-[Human-associatedMIGSBacteria],[Human-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSEukaryote.md b/mixs6/Human-associatedMIGSEukaryote.md new file mode 100644 index 00000000..53b53776 --- /dev/null +++ b/mixs6/Human-associatedMIGSEukaryote.md @@ -0,0 +1,491 @@ + +# Class: Human-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Human-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-associated]^-[Human-associatedMIGSEukaryote],[Human-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSPlant.md b/mixs6/Human-associatedMIGSPlant.md new file mode 100644 index 00000000..c6c2b181 --- /dev/null +++ b/mixs6/Human-associatedMIGSPlant.md @@ -0,0 +1,461 @@ + +# Class: Human-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-associated]^-[Human-associatedMIGSPlant],[Human-associated],[MIGSPlant]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSVirus.md b/mixs6/Human-associatedMIGSVirus.md new file mode 100644 index 00000000..307515c0 --- /dev/null +++ b/mixs6/Human-associatedMIGSVirus.md @@ -0,0 +1,486 @@ + +# Class: Human-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-associated]^-[Human-associatedMIGSVirus],[Human-associated],[MIGSVirus]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-associatedMIMARKSSpecimen.md b/mixs6/Human-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..0bf183e9 --- /dev/null +++ b/mixs6/Human-associatedMIMARKSSpecimen.md @@ -0,0 +1,411 @@ + +# Class: Human-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-associated]^-[Human-associatedMIMARKSSpecimen],[Human-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIMARKSSurvey.md b/mixs6/Human-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..5e7a87ce --- /dev/null +++ b/mixs6/Human-associatedMIMARKSSurvey.md @@ -0,0 +1,391 @@ + +# Class: Human-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + +URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-associated]^-[Human-associatedMIMARKSSurvey],[Human-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-associated](Human-associated.md) - human-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-associated: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [amniotic_fluid_color](amniotic_fluid_color.md) OPT + * Description: Specification of the color of the amniotic fluid sample + * range: [String](types/String.md) + * Example: None + * [blood_blood_disord](blood_blood_disord.md) OPT + * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diet_last_six_month](diet_last_six_month.md) OPT + * Description: Specification of major diet changes in the last six months, if yes the change should be specified + * range: [String](types/String.md) + * Example: yes;vegetarian diet None + * [drug_usage](drug_usage.md) OPT + * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used + * range: + * Example: Lipitor;2/day None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [foetal_health_stat](foetal_health_stat.md) OPT + * Description: Specification of foetal health status, should also include abortion + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gestation_state](gestation_state.md) OPT + * Description: Specification of the gestation state + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_hiv_stat](host_hiv_stat.md) OPT + * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + * range: [String](types/String.md) + * Example: yes;yes None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [maternal_health_stat](maternal_health_stat.md) OPT + * Description: Specification of the maternal health status + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_throat_disord](nose_throat_disord.md) OPT + * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pet_farm_animal](pet_farm_animal.md) OPT + * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + * range: [String](types/String.md) + * Example: yes; 5 cats None + * [pulmonary_disord](pulmonary_disord.md) OPT + * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [smoker](smoker.md) OPT + * Description: Specification of smoking status + * range: [String](types/String.md) + * Example: yes None + * [study_complt_stat](study_complt_stat.md) OPT + * Description: Specification of study completion status, if no the reason should be specified + * range: + * Example: no;non-compliance None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [travel_out_six_month](travel_out_six_month.md) OPT + * Description: Specification of the countries travelled in the last six months; can include multiple travels + * range: [String](types/String.md) + * Example: None + * [twin_sibling](twin_sibling.md) OPT + * Description: Specification of twin sibling presence + * range: [String](types/String.md) + * Example: yes None + * [urine_collect_meth](urine_collect_meth.md) OPT + * Description: Specification of urine collection method + * range: [String](types/String.md) + * Example: catheter None + * [urogenit_tract_disor](urogenit_tract_disor.md) OPT + * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + * [weight_loss_3_month](weight_loss_3_month.md) OPT + * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + * range: [String](types/String.md) + * Example: yes;5 kilogram None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMe.md b/mixs6/Human-associatedMe.md index e7515f51..d1899efa 100644 --- a/mixs6/Human-associatedMe.md +++ b/mixs6/Human-associatedMe.md @@ -1,13 +1,13 @@ -# Class: Human-associatedMe +# Class: Human-associatedME -Combinatorial checklist for human-associated with me +Combinatorial checklist Metagenome or Environmental with environmental package human-associated -URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associatedMe) +URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-associated]^-[Human-associatedMe],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-associated]^-[Human-associatedME],[Human-associated],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -255,172 +255,172 @@ URI: [mixs.vocab:Human-associatedMe](https://w3id.org/mixs/vocab/Human-associate * range: [String](types/String.md) * Example: yes;5 kilogram None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsOrg.md b/mixs6/Human-associatedMigsOrg.md index bcd015d4..72f24c92 100644 --- a/mixs6/Human-associatedMigsOrg.md +++ b/mixs6/Human-associatedMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Human-associatedMigsOrg +# Class: Human-associatedMIGSOrg -Combinatorial checklist for human-associated with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated -URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-associatedMigsOrg) +URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-associated]^-[Human-associatedMigsOrg],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-associated]^-[Human-associatedMIGSOrg],[Human-associated],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -255,192 +255,192 @@ URI: [mixs.vocab:Human-associatedMigsOrg](https://w3id.org/mixs/vocab/Human-asso * range: [String](types/String.md) * Example: yes;5 kilogram None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimag.md b/mixs6/Human-associatedMimag.md index 2876429e..89d666bc 100644 --- a/mixs6/Human-associatedMimag.md +++ b/mixs6/Human-associatedMimag.md @@ -1,13 +1,13 @@ -# Class: Human-associatedMimag +# Class: Human-associatedMIMAG -Combinatorial checklist for human-associated with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated -URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associatedMimag) +URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-associated]^-[Human-associatedMimag],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-associated]^-[Human-associatedMIMAG],[Human-associated],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -255,252 +255,252 @@ URI: [mixs.vocab:Human-associatedMimag](https://w3id.org/mixs/vocab/Human-associ * range: [String](types/String.md) * Example: yes;5 kilogram None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMisag.md b/mixs6/Human-associatedMisag.md index 073a1419..5082bd1b 100644 --- a/mixs6/Human-associatedMisag.md +++ b/mixs6/Human-associatedMisag.md @@ -1,13 +1,13 @@ -# Class: Human-associatedMisag +# Class: Human-associatedMISAG -Combinatorial checklist for human-associated with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated -URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associatedMisag) +URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-associated]^-[Human-associatedMisag],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-associated]^-[Human-associatedMISAG],[Human-associated],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -255,257 +255,257 @@ URI: [mixs.vocab:Human-associatedMisag](https://w3id.org/mixs/vocab/Human-associ * range: [String](types/String.md) * Example: yes;5 kilogram None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMiuvig.md b/mixs6/Human-associatedMiuvig.md index a695973c..c3e9f591 100644 --- a/mixs6/Human-associatedMiuvig.md +++ b/mixs6/Human-associatedMiuvig.md @@ -1,13 +1,13 @@ -# Class: Human-associatedMiuvig +# Class: Human-associatedMIUVIG -Combinatorial checklist for human-associated with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated -URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-associatedMiuvig) +URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-associated]^-[Human-associatedMiuvig],[Human-associated]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-associated]^-[Human-associatedMIUVIG],[Human-associated],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -255,322 +255,322 @@ URI: [mixs.vocab:Human-associatedMiuvig](https://w3id.org/mixs/vocab/Human-assoc * range: [String](types/String.md) * Example: yes;5 kilogram None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-gut.md b/mixs6/Human-gut.md index bc2dd462..fb95a39c 100644 --- a/mixs6/Human-gut.md +++ b/mixs6/Human-gut.md @@ -7,21 +7,21 @@ human-gut URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMiuvig],[Human-gutMisag],[Human-gutMimarksS],[Human-gutMimarksC],[Human-gutMimag],[Human-gutMigsVi],[Human-gutMigsPl],[Human-gutMigsOrg],[Human-gutMigsEu],[Human-gutMigsBa],[Human-gutMe],[QuantityValue][MIGSBacteria],[Human-gut]^-[Human-gutMIGSBacteria],[Human-gut],[MIGSBacteria]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSEukaryote.md b/mixs6/Human-gutMIGSEukaryote.md new file mode 100644 index 00000000..595740be --- /dev/null +++ b/mixs6/Human-gutMIGSEukaryote.md @@ -0,0 +1,431 @@ + +# Class: Human-gutMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-gut]^-[Human-gutMIGSEukaryote],[Human-gut],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSPlant.md b/mixs6/Human-gutMIGSPlant.md new file mode 100644 index 00000000..c82bf631 --- /dev/null +++ b/mixs6/Human-gutMIGSPlant.md @@ -0,0 +1,401 @@ + +# Class: Human-gutMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-gut]^-[Human-gutMIGSPlant],[Human-gut],[MIGSPlant]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIGSVirus.md b/mixs6/Human-gutMIGSVirus.md new file mode 100644 index 00000000..9b3d9077 --- /dev/null +++ b/mixs6/Human-gutMIGSVirus.md @@ -0,0 +1,426 @@ + +# Class: Human-gutMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-gut]^-[Human-gutMIGSVirus],[Human-gut],[MIGSVirus]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-gutMIMARKSSpecimen.md b/mixs6/Human-gutMIMARKSSpecimen.md new file mode 100644 index 00000000..3cb70198 --- /dev/null +++ b/mixs6/Human-gutMIMARKSSpecimen.md @@ -0,0 +1,351 @@ + +# Class: Human-gutMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gutMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-gut]^-[Human-gutMIMARKSSpecimen],[Human-gut],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMIMARKSSurvey.md b/mixs6/Human-gutMIMARKSSurvey.md new file mode 100644 index 00000000..1e3d22bb --- /dev/null +++ b/mixs6/Human-gutMIMARKSSurvey.md @@ -0,0 +1,331 @@ + +# Class: Human-gutMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + +URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-gut]^-[Human-gutMIMARKSSurvey],[Human-gut],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-gut](Human-gut.md) - human-gut + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-gut: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gastrointest_disord](gastrointest_disord.md) OPT + * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [liver_disord](liver_disord.md) OPT + * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). + * range: [String](types/String.md) + * Example: None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [special_diet](special_diet.md) OPT + * Description: Specification of special diet; can include multiple special diets + * range: + * Example: other:vegan None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-gutMe.md b/mixs6/Human-gutMe.md index d7e5ca7a..495caf06 100644 --- a/mixs6/Human-gutMe.md +++ b/mixs6/Human-gutMe.md @@ -1,13 +1,13 @@ -# Class: Human-gutMe +# Class: Human-gutME -Combinatorial checklist for human-gut with me +Combinatorial checklist Metagenome or Environmental with environmental package human-gut -URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) +URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-gutMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-gut]^-[Human-gutMe],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-gut]^-[Human-gutME],[Human-gut],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -195,172 +195,172 @@ URI: [mixs.vocab:Human-gutMe](https://w3id.org/mixs/vocab/Human-gutMe) * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsOrg.md b/mixs6/Human-gutMigsOrg.md index 794c99b7..fd219851 100644 --- a/mixs6/Human-gutMigsOrg.md +++ b/mixs6/Human-gutMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Human-gutMigsOrg +# Class: Human-gutMIGSOrg -Combinatorial checklist for human-gut with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut -URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) +URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-gutMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-gut]^-[Human-gutMigsOrg],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-gut]^-[Human-gutMIGSOrg],[Human-gut],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -195,192 +195,192 @@ URI: [mixs.vocab:Human-gutMigsOrg](https://w3id.org/mixs/vocab/Human-gutMigsOrg) * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimag.md b/mixs6/Human-gutMimag.md index b8c7ab64..bf877e07 100644 --- a/mixs6/Human-gutMimag.md +++ b/mixs6/Human-gutMimag.md @@ -1,13 +1,13 @@ -# Class: Human-gutMimag +# Class: Human-gutMIMAG -Combinatorial checklist for human-gut with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut -URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) +URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-gutMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-gut]^-[Human-gutMimag],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-gut]^-[Human-gutMIMAG],[Human-gut],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -195,252 +195,252 @@ URI: [mixs.vocab:Human-gutMimag](https://w3id.org/mixs/vocab/Human-gutMimag) * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-gutMisag.md b/mixs6/Human-gutMisag.md index b7abd73d..55ed35a9 100644 --- a/mixs6/Human-gutMisag.md +++ b/mixs6/Human-gutMisag.md @@ -1,13 +1,13 @@ -# Class: Human-gutMisag +# Class: Human-gutMISAG -Combinatorial checklist for human-gut with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut -URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) +URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-gutMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-gut]^-[Human-gutMisag],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-gut]^-[Human-gutMISAG],[Human-gut],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -195,257 +195,257 @@ URI: [mixs.vocab:Human-gutMisag](https://w3id.org/mixs/vocab/Human-gutMisag) * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-gutMiuvig.md b/mixs6/Human-gutMiuvig.md index b79c93ec..d425d6a3 100644 --- a/mixs6/Human-gutMiuvig.md +++ b/mixs6/Human-gutMiuvig.md @@ -1,13 +1,13 @@ -# Class: Human-gutMiuvig +# Class: Human-gutMIUVIG -Combinatorial checklist for human-gut with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut -URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) +URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-gutMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-gut]^-[Human-gutMiuvig],[Human-gut]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-gut]^-[Human-gutMIUVIG],[Human-gut],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -195,322 +195,322 @@ URI: [mixs.vocab:Human-gutMiuvig](https://w3id.org/mixs/vocab/Human-gutMiuvig) * range: [QuantityValue](QuantityValue.md) * Example: 25 degree Celsius None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-oral.md b/mixs6/Human-oral.md index 267dbefb..494084b7 100644 --- a/mixs6/Human-oral.md +++ b/mixs6/Human-oral.md @@ -7,21 +7,21 @@ human-oral URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMiuvig],[Human-oralMisag],[Human-oralMimarksS],[Human-oralMimarksC],[Human-oralMimag],[Human-oralMigsVi],[Human-oralMigsPl],[Human-oralMigsOrg],[Human-oralMigsEu],[Human-oralMigsBa],[Human-oralMe],[QuantityValue][MIGSBacteria],[Human-oral]^-[Human-oralMIGSBacteria],[Human-oral],[MIGSBacteria]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSEukaryote.md b/mixs6/Human-oralMIGSEukaryote.md new file mode 100644 index 00000000..d86053cc --- /dev/null +++ b/mixs6/Human-oralMIGSEukaryote.md @@ -0,0 +1,427 @@ + +# Class: Human-oralMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oralMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-oral]^-[Human-oralMIGSEukaryote],[Human-oral],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSPlant.md b/mixs6/Human-oralMIGSPlant.md new file mode 100644 index 00000000..057ef81f --- /dev/null +++ b/mixs6/Human-oralMIGSPlant.md @@ -0,0 +1,397 @@ + +# Class: Human-oralMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-oral]^-[Human-oralMIGSPlant],[Human-oral],[MIGSPlant]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIGSVirus.md b/mixs6/Human-oralMIGSVirus.md new file mode 100644 index 00000000..6e6be11b --- /dev/null +++ b/mixs6/Human-oralMIGSVirus.md @@ -0,0 +1,422 @@ + +# Class: Human-oralMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-oral]^-[Human-oralMIGSVirus],[Human-oral],[MIGSVirus]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-oralMIMARKSSpecimen.md b/mixs6/Human-oralMIMARKSSpecimen.md new file mode 100644 index 00000000..b7f7c8ff --- /dev/null +++ b/mixs6/Human-oralMIMARKSSpecimen.md @@ -0,0 +1,347 @@ + +# Class: Human-oralMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-oralMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-oral]^-[Human-oralMIMARKSSpecimen],[Human-oral],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMIMARKSSurvey.md b/mixs6/Human-oralMIMARKSSurvey.md new file mode 100644 index 00000000..d593eb7e --- /dev/null +++ b/mixs6/Human-oralMIMARKSSurvey.md @@ -0,0 +1,327 @@ + +# Class: Human-oralMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + +URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oralMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-oral]^-[Human-oralMIMARKSSurvey],[Human-oral],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-oral](Human-oral.md) - human-oral + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-oral: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT + * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_last_toothbrush](time_last_toothbrush.md) OPT + * Description: Specification of the time since last toothbrushing + * range: [String](types/String.md) + * Example: P2H45M None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-oralMe.md b/mixs6/Human-oralMe.md index ba99823d..dc681564 100644 --- a/mixs6/Human-oralMe.md +++ b/mixs6/Human-oralMe.md @@ -1,13 +1,13 @@ -# Class: Human-oralMe +# Class: Human-oralME -Combinatorial checklist for human-oral with me +Combinatorial checklist Metagenome or Environmental with environmental package human-oral -URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) +URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-oralMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-oral]^-[Human-oralMe],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-oral]^-[Human-oralME],[Human-oral],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -191,172 +191,172 @@ URI: [mixs.vocab:Human-oralMe](https://w3id.org/mixs/vocab/Human-oralMe) * range: [String](types/String.md) * Example: P2H45M None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsOrg.md b/mixs6/Human-oralMigsOrg.md index 36c3a9c3..238fac59 100644 --- a/mixs6/Human-oralMigsOrg.md +++ b/mixs6/Human-oralMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Human-oralMigsOrg +# Class: Human-oralMIGSOrg -Combinatorial checklist for human-oral with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral -URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOrg) +URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-oralMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-oral]^-[Human-oralMigsOrg],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-oral]^-[Human-oralMIGSOrg],[Human-oral],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -191,192 +191,192 @@ URI: [mixs.vocab:Human-oralMigsOrg](https://w3id.org/mixs/vocab/Human-oralMigsOr * range: [String](types/String.md) * Example: P2H45M None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimag.md b/mixs6/Human-oralMimag.md index e5236953..e742203b 100644 --- a/mixs6/Human-oralMimag.md +++ b/mixs6/Human-oralMimag.md @@ -1,13 +1,13 @@ -# Class: Human-oralMimag +# Class: Human-oralMIMAG -Combinatorial checklist for human-oral with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral -URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) +URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-oralMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-oral]^-[Human-oralMimag],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-oral]^-[Human-oralMIMAG],[Human-oral],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -191,252 +191,252 @@ URI: [mixs.vocab:Human-oralMimag](https://w3id.org/mixs/vocab/Human-oralMimag) * range: [String](types/String.md) * Example: P2H45M None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-oralMisag.md b/mixs6/Human-oralMisag.md index 9aa69691..52b2b00c 100644 --- a/mixs6/Human-oralMisag.md +++ b/mixs6/Human-oralMisag.md @@ -1,13 +1,13 @@ -# Class: Human-oralMisag +# Class: Human-oralMISAG -Combinatorial checklist for human-oral with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral -URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) +URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-oralMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-oral]^-[Human-oralMisag],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-oral]^-[Human-oralMISAG],[Human-oral],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -191,257 +191,257 @@ URI: [mixs.vocab:Human-oralMisag](https://w3id.org/mixs/vocab/Human-oralMisag) * range: [String](types/String.md) * Example: P2H45M None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-oralMiuvig.md b/mixs6/Human-oralMiuvig.md index 0b4ce634..1b4e2fc8 100644 --- a/mixs6/Human-oralMiuvig.md +++ b/mixs6/Human-oralMiuvig.md @@ -1,13 +1,13 @@ -# Class: Human-oralMiuvig +# Class: Human-oralMIUVIG -Combinatorial checklist for human-oral with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral -URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) +URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-oralMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-oral]^-[Human-oralMiuvig],[Human-oral]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-oral]^-[Human-oralMIUVIG],[Human-oral],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -191,322 +191,322 @@ URI: [mixs.vocab:Human-oralMiuvig](https://w3id.org/mixs/vocab/Human-oralMiuvig) * range: [String](types/String.md) * Example: P2H45M None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-skin.md b/mixs6/Human-skin.md index 33246725..ea8f4915 100644 --- a/mixs6/Human-skin.md +++ b/mixs6/Human-skin.md @@ -7,21 +7,21 @@ human-skin URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMiuvig],[Human-skinMisag],[Human-skinMimarksS],[Human-skinMimarksC],[Human-skinMimag],[Human-skinMigsVi],[Human-skinMigsPl],[Human-skinMigsOrg],[Human-skinMigsEu],[Human-skinMigsBa],[Human-skinMe],[QuantityValue][MIGSBacteria],[Human-skin]^-[Human-skinMIGSBacteria],[Human-skin],[MIGSBacteria]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSEukaryote.md b/mixs6/Human-skinMIGSEukaryote.md new file mode 100644 index 00000000..d01d6c01 --- /dev/null +++ b/mixs6/Human-skinMIGSEukaryote.md @@ -0,0 +1,431 @@ + +# Class: Human-skinMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skinMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-skin]^-[Human-skinMIGSEukaryote],[Human-skin],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSPlant.md b/mixs6/Human-skinMIGSPlant.md new file mode 100644 index 00000000..c03995ac --- /dev/null +++ b/mixs6/Human-skinMIGSPlant.md @@ -0,0 +1,401 @@ + +# Class: Human-skinMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-skin]^-[Human-skinMIGSPlant],[Human-skin],[MIGSPlant]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIGSVirus.md b/mixs6/Human-skinMIGSVirus.md new file mode 100644 index 00000000..254b1110 --- /dev/null +++ b/mixs6/Human-skinMIGSVirus.md @@ -0,0 +1,426 @@ + +# Class: Human-skinMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-skin]^-[Human-skinMIGSVirus],[Human-skin],[MIGSVirus]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-skinMIMARKSSpecimen.md b/mixs6/Human-skinMIMARKSSpecimen.md new file mode 100644 index 00000000..a8ba6df6 --- /dev/null +++ b/mixs6/Human-skinMIMARKSSpecimen.md @@ -0,0 +1,351 @@ + +# Class: Human-skinMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-skinMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-skin]^-[Human-skinMIMARKSSpecimen],[Human-skin],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMIMARKSSurvey.md b/mixs6/Human-skinMIMARKSSurvey.md new file mode 100644 index 00000000..c1172644 --- /dev/null +++ b/mixs6/Human-skinMIMARKSSurvey.md @@ -0,0 +1,331 @@ + +# Class: Human-skinMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + +URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skinMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-skin]^-[Human-skinMIMARKSSurvey],[Human-skin],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-skin](Human-skin.md) - human-skin + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-skin: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [dermatology_disord](dermatology_disord.md) OPT + * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). + * range: [String](types/String.md) + * Example: None + * [dominant_hand](dominant_hand.md) OPT + * Description: Dominant hand of the subject + * range: + * Example: right None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [time_since_last_wash](time_since_last_wash.md) OPT + * Description: Specification of the time since last wash + * range: [String](types/String.md) + * Example: P1D None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-skinMe.md b/mixs6/Human-skinMe.md index dfdfd495..37d87ed5 100644 --- a/mixs6/Human-skinMe.md +++ b/mixs6/Human-skinMe.md @@ -1,13 +1,13 @@ -# Class: Human-skinMe +# Class: Human-skinME -Combinatorial checklist for human-skin with me +Combinatorial checklist Metagenome or Environmental with environmental package human-skin -URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) +URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-skinMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-skin]^-[Human-skinMe],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-skin]^-[Human-skinME],[Human-skin],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -195,172 +195,172 @@ URI: [mixs.vocab:Human-skinMe](https://w3id.org/mixs/vocab/Human-skinMe) * range: [String](types/String.md) * Example: P1D None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsOrg.md b/mixs6/Human-skinMigsOrg.md index f039e57e..9ffda114 100644 --- a/mixs6/Human-skinMigsOrg.md +++ b/mixs6/Human-skinMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Human-skinMigsOrg +# Class: Human-skinMIGSOrg -Combinatorial checklist for human-skin with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin -URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOrg) +URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-skinMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-skin]^-[Human-skinMigsOrg],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-skin]^-[Human-skinMIGSOrg],[Human-skin],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -195,192 +195,192 @@ URI: [mixs.vocab:Human-skinMigsOrg](https://w3id.org/mixs/vocab/Human-skinMigsOr * range: [String](types/String.md) * Example: P1D None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimag.md b/mixs6/Human-skinMimag.md index 8e5432c4..be36689d 100644 --- a/mixs6/Human-skinMimag.md +++ b/mixs6/Human-skinMimag.md @@ -1,13 +1,13 @@ -# Class: Human-skinMimag +# Class: Human-skinMIMAG -Combinatorial checklist for human-skin with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin -URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) +URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-skinMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-skin]^-[Human-skinMimag],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-skin]^-[Human-skinMIMAG],[Human-skin],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -195,252 +195,252 @@ URI: [mixs.vocab:Human-skinMimag](https://w3id.org/mixs/vocab/Human-skinMimag) * range: [String](types/String.md) * Example: P1D None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-skinMisag.md b/mixs6/Human-skinMisag.md index 248f0747..03a35d80 100644 --- a/mixs6/Human-skinMisag.md +++ b/mixs6/Human-skinMisag.md @@ -1,13 +1,13 @@ -# Class: Human-skinMisag +# Class: Human-skinMISAG -Combinatorial checklist for human-skin with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin -URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) +URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-skinMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-skin]^-[Human-skinMisag],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-skin]^-[Human-skinMISAG],[Human-skin],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -195,257 +195,257 @@ URI: [mixs.vocab:Human-skinMisag](https://w3id.org/mixs/vocab/Human-skinMisag) * range: [String](types/String.md) * Example: P1D None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-skinMiuvig.md b/mixs6/Human-skinMiuvig.md index aea1554a..5a87a7bd 100644 --- a/mixs6/Human-skinMiuvig.md +++ b/mixs6/Human-skinMiuvig.md @@ -1,13 +1,13 @@ -# Class: Human-skinMiuvig +# Class: Human-skinMIUVIG -Combinatorial checklist for human-skin with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin -URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) +URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-skinMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-skin]^-[Human-skinMiuvig],[Human-skin]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-skin]^-[Human-skinMIUVIG],[Human-skin],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -195,322 +195,322 @@ URI: [mixs.vocab:Human-skinMiuvig](https://w3id.org/mixs/vocab/Human-skinMiuvig) * range: [String](types/String.md) * Example: P1D None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-vaginal.md b/mixs6/Human-vaginal.md index 77f37d11..e1e8a7da 100644 --- a/mixs6/Human-vaginal.md +++ b/mixs6/Human-vaginal.md @@ -7,21 +7,21 @@ human-vaginal URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMiuvig],[Human-vaginalMisag],[Human-vaginalMimarksS],[Human-vaginalMimarksC],[Human-vaginalMimag],[Human-vaginalMigsVi],[Human-vaginalMigsPl],[Human-vaginalMigsOrg],[Human-vaginalMigsEu],[Human-vaginalMigsBa],[Human-vaginalMe],[QuantityValue][MIGSBacteria],[Human-vaginal]^-[Human-vaginalMIGSBacteria],[Human-vaginal],[MIGSBacteria]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSEukaryote.md b/mixs6/Human-vaginalMIGSEukaryote.md new file mode 100644 index 00000000..ffc385cf --- /dev/null +++ b/mixs6/Human-vaginalMIGSEukaryote.md @@ -0,0 +1,459 @@ + +# Class: Human-vaginalMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-vaginalMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-vaginal]^-[Human-vaginalMIGSEukaryote],[Human-vaginal],[MIGSEukaryote]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSPlant.md b/mixs6/Human-vaginalMIGSPlant.md new file mode 100644 index 00000000..1a14ee95 --- /dev/null +++ b/mixs6/Human-vaginalMIGSPlant.md @@ -0,0 +1,429 @@ + +# Class: Human-vaginalMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vaginalMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-vaginal]^-[Human-vaginalMIGSPlant],[Human-vaginal],[MIGSPlant]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIGSVirus.md b/mixs6/Human-vaginalMIGSVirus.md new file mode 100644 index 00000000..9721fc60 --- /dev/null +++ b/mixs6/Human-vaginalMIGSVirus.md @@ -0,0 +1,454 @@ + +# Class: Human-vaginalMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vaginalMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-vaginal]^-[Human-vaginalMIGSVirus],[Human-vaginal],[MIGSVirus]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Human-vaginalMIMARKSSpecimen.md b/mixs6/Human-vaginalMIMARKSSpecimen.md new file mode 100644 index 00000000..3fea70e3 --- /dev/null +++ b/mixs6/Human-vaginalMIMARKSSpecimen.md @@ -0,0 +1,379 @@ + +# Class: Human-vaginalMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-vaginal]^-[Human-vaginalMIMARKSSpecimen],[Human-vaginal],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMIMARKSSurvey.md b/mixs6/Human-vaginalMIMARKSSurvey.md new file mode 100644 index 00000000..c72d8a9d --- /dev/null +++ b/mixs6/Human-vaginalMIMARKSSurvey.md @@ -0,0 +1,359 @@ + +# Class: Human-vaginalMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + +URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-vaginal]^-[Human-vaginalMIMARKSSurvey],[Human-vaginal],[MIMARKSSurvey]) + +## Parents + + * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from human-vaginal: + + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [birth_control](birth_control.md) OPT + * Description: Specification of birth control medication used + * range: [String](types/String.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [douche](douche.md) OPT + * Description: Date of most recent douche + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gynecologic_disord](gynecologic_disord.md) OPT + * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). + * range: [String](types/String.md) + * Example: None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_body_mass_index](host_body_mass_index.md) OPT + * Description: Body mass index, calculated as weight/(height)squared + * range: [QuantityValue](QuantityValue.md) + * Example: 22 kilogram per square meter None + * [host_body_product](host_body_product.md) OPT + * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + * range: [String](types/String.md) + * Example: Portion of mucus [fma66938] None + * [host_body_site](host_body_site.md) OPT + * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + * range: [String](types/String.md) + * Example: gill [UBERON:0002535] None + * [host_body_temp](host_body_temp.md) OPT + * Description: Core body temperature of the host when sample was collected + * range: [QuantityValue](QuantityValue.md) + * Example: 15 degree Celsius None + * [host_diet](host_diet.md) OPT + * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + * range: [String](types/String.md) + * Example: herbivore None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_family_relationship](host_family_relationship.md) OPT + * Description: Relationships to other hosts in the same study; can include multiple relationships + * range: [String](types/String.md) + * Example: offspring;Mussel25 None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_last_meal](host_last_meal.md) OPT + * Description: Content of last meal and time since feeding; can include multiple values + * range: [String](types/String.md) + * Example: corn feed;P2H None + * [host_occupation](host_occupation.md) OPT + * Description: Most frequent job performed by subject + * range: [String](types/String.md) + * Example: veterinary None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_pulse](host_pulse.md) OPT + * Description: Resting pulse, measured as beats per minute + * range: [QuantityValue](QuantityValue.md) + * Example: 65 beats per minute None + * [host_sex](host_sex.md) OPT + * Description: Physical sex of the host + * range: + * Example: female None + * [host_subject_id](host_subject_id.md) OPT + * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 + * range: [String](types/String.md) + * Example: MPI123 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [hrt](hrt.md) OPT + * Description: Whether subject had hormone replacement theraphy, and if yes start date + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [hysterectomy](hysterectomy.md) OPT + * Description: Specification of whether hysterectomy was performed + * range: [String](types/String.md) + * Example: no None + * [ihmc_ethnicity](ihmc_ethnicity.md) OPT + * Description: Ethnicity of the subject + * range: [String](types/String.md) + * Example: caucasian None + * [ihmc_medication_code](ihmc_medication_code.md) OPT + * Description: Can include multiple medication codes + * range: [String](types/String.md) + * Example: 810 None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [medic_hist_perform](medic_hist_perform.md) OPT + * Description: Whether full medical history was collected + * range: [String](types/String.md) + * Example: TRUE None + * [menarche](menarche.md) OPT + * Description: Date of most recent menstruation + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [menopause](menopause.md) OPT + * Description: Date of onset of menopause + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pregnancy](pregnancy.md) OPT + * Description: Date due of pregnancy + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sexual_act](sexual_act.md) OPT + * Description: Current sexual partner and frequency of sex + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [urogenit_disord](urogenit_disord.md) OPT + * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMe.md b/mixs6/Human-vaginalMe.md index fd9e0b5e..e223eff2 100644 --- a/mixs6/Human-vaginalMe.md +++ b/mixs6/Human-vaginalMe.md @@ -1,13 +1,13 @@ -# Class: Human-vaginalMe +# Class: Human-vaginalME -Combinatorial checklist for human-vaginal with me +Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal -URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) +URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[Human-vaginalMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Human-vaginal]^-[Human-vaginalMe],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-vaginal]^-[Human-vaginalME],[Human-vaginal],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -223,172 +223,172 @@ URI: [mixs.vocab:Human-vaginalMe](https://w3id.org/mixs/vocab/Human-vaginalMe) * range: [String](types/String.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsOrg.md b/mixs6/Human-vaginalMigsOrg.md index a959ed25..4a7b14a0 100644 --- a/mixs6/Human-vaginalMigsOrg.md +++ b/mixs6/Human-vaginalMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Human-vaginalMigsOrg +# Class: Human-vaginalMIGSOrg -Combinatorial checklist for human-vaginal with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal -URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginalMigsOrg) +URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginalMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[Human-vaginalMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Human-vaginal]^-[Human-vaginalMigsOrg],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-vaginal]^-[Human-vaginalMIGSOrg],[Human-vaginal],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -223,192 +223,192 @@ URI: [mixs.vocab:Human-vaginalMigsOrg](https://w3id.org/mixs/vocab/Human-vaginal * range: [String](types/String.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimag.md b/mixs6/Human-vaginalMimag.md index aae33fc9..4302412f 100644 --- a/mixs6/Human-vaginalMimag.md +++ b/mixs6/Human-vaginalMimag.md @@ -1,13 +1,13 @@ -# Class: Human-vaginalMimag +# Class: Human-vaginalMIMAG -Combinatorial checklist for human-vaginal with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal -URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMimag) +URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[Human-vaginalMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Human-vaginal]^-[Human-vaginalMimag],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-vaginal]^-[Human-vaginalMIMAG],[Human-vaginal],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -223,252 +223,252 @@ URI: [mixs.vocab:Human-vaginalMimag](https://w3id.org/mixs/vocab/Human-vaginalMi * range: [String](types/String.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMisag.md b/mixs6/Human-vaginalMisag.md index 75bc2671..417f4119 100644 --- a/mixs6/Human-vaginalMisag.md +++ b/mixs6/Human-vaginalMisag.md @@ -1,13 +1,13 @@ -# Class: Human-vaginalMisag +# Class: Human-vaginalMISAG -Combinatorial checklist for human-vaginal with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal -URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMisag) +URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[Human-vaginalMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Human-vaginal]^-[Human-vaginalMisag],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-vaginal]^-[Human-vaginalMISAG],[Human-vaginal],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -223,257 +223,257 @@ URI: [mixs.vocab:Human-vaginalMisag](https://w3id.org/mixs/vocab/Human-vaginalMi * range: [String](types/String.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMiuvig.md b/mixs6/Human-vaginalMiuvig.md index 291113b7..ae693081 100644 --- a/mixs6/Human-vaginalMiuvig.md +++ b/mixs6/Human-vaginalMiuvig.md @@ -1,13 +1,13 @@ -# Class: Human-vaginalMiuvig +# Class: Human-vaginalMIUVIG -Combinatorial checklist for human-vaginal with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal -URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalMiuvig) +URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[Human-vaginalMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Human-vaginal]^-[Human-vaginalMiuvig],[Human-vaginal]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-vaginal]^-[Human-vaginalMIUVIG],[Human-vaginal],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -223,322 +223,322 @@ URI: [mixs.vocab:Human-vaginalMiuvig](https://w3id.org/mixs/vocab/Human-vaginalM * range: [String](types/String.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-cores.md b/mixs6/HydrocarbonResources-cores.md index 081e6f24..d9e848fc 100644 --- a/mixs6/HydrocarbonResources-cores.md +++ b/mixs6/HydrocarbonResources-cores.md @@ -7,21 +7,21 @@ hydrocarbon resources-cores URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/HydrocarbonResources-cores) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-coresMisag],[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-coresMimag],[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-coresMe],[QuantityValue][MIGSBacteria],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-cores],[MIGSBacteria]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSEukaryote.md b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md new file mode 100644 index 00000000..93acfdc3 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md @@ -0,0 +1,611 @@ + +# Class: HydrocarbonResources-coresMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-cores],[MIGSEukaryote]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSPlant.md b/mixs6/HydrocarbonResources-coresMIGSPlant.md new file mode 100644 index 00000000..fa429282 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSPlant.md @@ -0,0 +1,581 @@ + +# Class: HydrocarbonResources-coresMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-cores],[MIGSPlant]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIGSVirus.md b/mixs6/HydrocarbonResources-coresMIGSVirus.md new file mode 100644 index 00000000..0755dac1 --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIGSVirus.md @@ -0,0 +1,606 @@ + +# Class: HydrocarbonResources-coresMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-cores],[MIGSVirus]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md new file mode 100644 index 00000000..cc5db42c --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md @@ -0,0 +1,531 @@ + +# Class: HydrocarbonResources-coresMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-cores],[MIMARKSSpecimen]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md new file mode 100644 index 00000000..7b52aead --- /dev/null +++ b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md @@ -0,0 +1,511 @@ + +# Class: HydrocarbonResources-coresMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + +URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-cores],[MIMARKSSurvey]) + +## Parents + + * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from hydrocarbon resources-cores: + + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [owc_tvdss](owc_tvdss.md) OPT + * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [permeability](permeability.md) OPT + * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) + * range: [String](types/String.md) + * Example: None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_md](samp_md.md) OPT + * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: 1534 meter;MSL None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_tvdss](samp_tvdss.md) OPT + * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + * range: [String](types/String.md) + * Example: None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sr_dep_env](sr_dep_env.md) OPT + * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Marine None + * [sr_geol_age](sr_geol_age.md) OPT + * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [sr_kerog_type](sr_kerog_type.md) OPT + * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Type IV None + * [sr_lithology](sr_lithology.md) OPT + * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Coal None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMe.md b/mixs6/HydrocarbonResources-coresMe.md index 1bee79d9..4baecfc7 100644 --- a/mixs6/HydrocarbonResources-coresMe.md +++ b/mixs6/HydrocarbonResources-coresMe.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-coresMe +# Class: HydrocarbonResources-coresME -Combinatorial checklist for hydrocarbon resources-cores with me +Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores -URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMe) +URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/HydrocarbonResources-coresME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[HydrocarbonResources-coresMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMe],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresME],[HydrocarbonResources-cores],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -375,172 +375,172 @@ URI: [mixs.vocab:HydrocarbonResources-coresMe](https://w3id.org/mixs/vocab/Hydro * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsOrg.md b/mixs6/HydrocarbonResources-coresMigsOrg.md index cadcc628..551bf9d2 100644 --- a/mixs6/HydrocarbonResources-coresMigsOrg.md +++ b/mixs6/HydrocarbonResources-coresMigsOrg.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-coresMigsOrg +# Class: HydrocarbonResources-coresMIGSOrg -Combinatorial checklist for hydrocarbon resources-cores with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores -URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsOrg) +URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[HydrocarbonResources-coresMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsOrg],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-cores],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -375,192 +375,192 @@ URI: [mixs.vocab:HydrocarbonResources-coresMigsOrg](https://w3id.org/mixs/vocab/ * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimag.md b/mixs6/HydrocarbonResources-coresMimag.md index 3d8a7582..91b80179 100644 --- a/mixs6/HydrocarbonResources-coresMimag.md +++ b/mixs6/HydrocarbonResources-coresMimag.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-coresMimag +# Class: HydrocarbonResources-coresMIMAG -Combinatorial checklist for hydrocarbon resources-cores with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores -URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimag) +URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[HydrocarbonResources-coresMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimag],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-cores],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -375,252 +375,252 @@ URI: [mixs.vocab:HydrocarbonResources-coresMimag](https://w3id.org/mixs/vocab/Hy * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMisag.md b/mixs6/HydrocarbonResources-coresMisag.md index 74062409..1d73cdf3 100644 --- a/mixs6/HydrocarbonResources-coresMisag.md +++ b/mixs6/HydrocarbonResources-coresMisag.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-coresMisag +# Class: HydrocarbonResources-coresMISAG -Combinatorial checklist for hydrocarbon resources-cores with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores -URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMisag) +URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[HydrocarbonResources-coresMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMisag],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMISAG],[HydrocarbonResources-cores],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -375,257 +375,257 @@ URI: [mixs.vocab:HydrocarbonResources-coresMisag](https://w3id.org/mixs/vocab/Hy * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMiuvig.md b/mixs6/HydrocarbonResources-coresMiuvig.md index 0735fde7..37ece903 100644 --- a/mixs6/HydrocarbonResources-coresMiuvig.md +++ b/mixs6/HydrocarbonResources-coresMiuvig.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-coresMiuvig +# Class: HydrocarbonResources-coresMIUVIG -Combinatorial checklist for hydrocarbon resources-cores with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores -URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMiuvig) +URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[HydrocarbonResources-coresMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMiuvig],[HydrocarbonResources-cores]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-cores],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -375,322 +375,322 @@ URI: [mixs.vocab:HydrocarbonResources-coresMiuvig](https://w3id.org/mixs/vocab/H * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabs.md b/mixs6/HydrocarbonResources-fluidsSwabs.md index 389af4da..5cf4ceda 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabs.md +++ b/mixs6/HydrocarbonResources-fluidsSwabs.md @@ -7,21 +7,21 @@ hydrocarbon resources-fluids/swabs URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabs) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabsMe],[QuantityValue][MIGSBacteria],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabs],[MIGSBacteria]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md new file mode 100644 index 00000000..31cfff37 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md @@ -0,0 +1,631 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabs],[MIGSEukaryote]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md new file mode 100644 index 00000000..2bc7867e --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md @@ -0,0 +1,601 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabs],[MIGSPlant]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md new file mode 100644 index 00000000..e29a98fd --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md @@ -0,0 +1,626 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabs],[MIGSVirus]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md new file mode 100644 index 00000000..86e209c8 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md @@ -0,0 +1,551 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs],[MIMARKSSpecimen]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md new file mode 100644 index 00000000..85fb4d46 --- /dev/null +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md @@ -0,0 +1,531 @@ + +# Class: HydrocarbonResources-fluidsSwabsMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabs],[MIMARKSSurvey]) + +## Parents + + * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from hydrocarbon resources-fluids_swabs: + + * [add_recov_method](add_recov_method.md) OPT + * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Polymer Addition;2018-06-21T14:30Z None + * [additional_info](additional_info.md) OPT + * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + * range: [String](types/String.md) + * Example: None + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [api](api.md) OPT + * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [aromatics_pc](aromatics_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [asphaltenes_pc](asphaltenes_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [basin](basin.md) OPT + * Description: Name of the basin (e.g. Campos) + * range: [String](types/String.md) + * Example: None + * [benzene](benzene.md) OPT + * Description: Concentration of benzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [biocide](biocide.md) OPT + * Description: List of biocides (commercial name of product and supplier) and date of administration + * range: [String](types/String.md) + * Example: ALPHA 1427;Baker Hughes;2008-01-23 None + * [biocide_admin_method](biocide_admin_method.md) OPT + * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + * range: [String](types/String.md) + * Example: None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_treatment](chem_treatment.md) OPT + * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + * range: [String](types/String.md) + * Example: ACCENT 1125;DOW;2010-11-17 None + * [chem_treatment_method](chem_treatment_method.md) OPT + * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + * range: [String](types/String.md) + * Example: None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depos_env](depos_env.md) OPT + * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Continental - Alluvial None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_iron](diss_iron.md) OPT + * Description: Concentration of dissolved iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT + * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [ethylbenzene](ethylbenzene.md) OPT + * Description: Concentration of ethylbenzene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [field](field.md) OPT + * Description: Name of the hydrocarbon field (e.g. Albacora) + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [hc_produced](hc_produced.md) OPT + * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Gas None + * [hcr](hcr.md) OPT + * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Oil Sand None + * [hcr_fw_salinity](hcr_fw_salinity.md) OPT + * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [hcr_geol_age](hcr_geol_age.md) OPT + * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Silurian None + * [hcr_pressure](hcr_pressure.md) OPT + * Description: Original pressure of the hydrocarbon resource + * range: [String](types/String.md) + * Example: None + * [hcr_temp](hcr_temp.md) OPT + * Description: Original temperature of the hydrocarbon resource + * range: [String](types/String.md) + * Example: 150-295 degree Celsius None + * [iw_bt_date_well](iw_bt_date_well.md) OPT + * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [iwf](iwf.md) OPT + * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [lithology](lithology.md) OPT + * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: Volcanic None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT + * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) + * range: [String](types/String.md) + * Example: None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pour_point](pour_point.md) OPT + * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [prod_rate](prod_rate.md) OPT + * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [prod_start_date](prod_start_date.md) OPT + * Description: Date of field's first production + * range: [String](types/String.md) + * Example: 2018-05-11 None + * [reservoir](reservoir.md) OPT + * Description: Name of the reservoir (e.g. Carapebus) + * range: [String](types/String.md) + * Example: None + * [resins_pc](resins_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [samp_collection_point](samp_collection_point.md) OPT + * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + * range: + * Example: well None + * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT + * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + * range: [String](types/String.md) + * Example: None + * [samp_preserv](samp_preserv.md) OPT + * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_subtype](samp_subtype.md) OPT + * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + * range: + * Example: biofilm None + * [samp_transport_cond](samp_transport_cond.md) OPT + * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + * range: [String](types/String.md) + * Example: 5 days;-20 degree Celsius None + * [samp_type](samp_type.md) OPT + * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field + * range: + * Example: solid deposit None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [samp_well_name](samp_well_name.md) OPT + * Description: Name of the well (e.g. BXA1123) where sample was taken + * range: [String](types/String.md) + * Example: None + * [saturates_pc](saturates_pc.md) OPT + * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) + * range: [String](types/String.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfate_fw](sulfate_fw.md) OPT + * Description: Original sulfate concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [tan](tan.md) OPT + * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [toluene](toluene.md) OPT + * Description: Concentration of toluene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_iron](tot_iron.md) OPT + * Description: Concentration of total iron in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [tot_sulfur](tot_sulfur.md) OPT + * Description: Concentration of total sulfur in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa](vfa.md) OPT + * Description: Concentration of Volatile Fatty Acids in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [vfa_fw](vfa_fw.md) OPT + * Description: Original volatile fatty acid concentration in the hydrocarbon resource + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [viscosity](viscosity.md) OPT + * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + * range: [String](types/String.md) + * Example: None + * [water_cut](water_cut.md) OPT + * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_production_rate](water_production_rate.md) OPT + * Description: Water production rates per well (e.g. 987 m3 / day) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [win](win.md) OPT + * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) + * range: [String](types/String.md) + * Example: None + * [xylene](xylene.md) OPT + * Description: Concentration of xylene in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMe.md b/mixs6/HydrocarbonResources-fluidsSwabsMe.md index f0e9bf2c..5fe771c0 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMe.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMe.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-fluidsSwabsMe +# Class: HydrocarbonResources-fluidsSwabsME -Combinatorial checklist for hydrocarbon resources-fluids_swabs with me +Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMe) +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Me],[HydrocarbonResources-fluidsSwabsMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-fluidsSwabs],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -395,172 +395,172 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMe](https://w3id.org/mixs/vocab * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md index 4b979239..5eb54cd7 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-fluidsSwabsMigsOrg +# Class: HydrocarbonResources-fluidsSwabsMIGSOrg -Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsOrg) +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabs],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -395,192 +395,192 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsOrg](https://w3id.org/mixs/ * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md index af71dc40..70a887fe 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-fluidsSwabsMimag +# Class: HydrocarbonResources-fluidsSwabsMIMAG -Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimag) +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[HydrocarbonResources-fluidsSwabsMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabs],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -395,252 +395,252 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimag](https://w3id.org/mixs/vo * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md index 45e33445..f193ea6e 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-fluidsSwabsMisag +# Class: HydrocarbonResources-fluidsSwabsMISAG -Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMisag) +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[HydrocarbonResources-fluidsSwabsMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabs],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -395,257 +395,257 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMisag](https://w3id.org/mixs/vo * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md index 02056f3c..01959d2a 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md @@ -1,13 +1,13 @@ -# Class: HydrocarbonResources-fluidsSwabsMiuvig +# Class: HydrocarbonResources-fluidsSwabsMIUVIG -Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMiuvig) +URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-fluidsSwabs]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabs],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -395,322 +395,322 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMiuvig](https://w3id.org/mixs/v * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MIGSBacteria.md b/mixs6/MIGSBacteria.md new file mode 100644 index 00000000..e37ee90d --- /dev/null +++ b/mixs6/MIGSBacteria.md @@ -0,0 +1,152 @@ + +# Class: MIGSBacteria + + +Minimal Information about a Genome Sequence: cultured bacteria/archaea + +URI: [mixs.vocab:MIGSBacteria](https://w3id.org/mixs/vocab/MIGSBacteria) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSBacteria],[WastewaterSludgeMIGSBacteria]uses%20-.->[MIGSBacteria],[SoilMIGSBacteria]uses%20-.->[MIGSBacteria],[SedimentMIGSBacteria]uses%20-.->[MIGSBacteria],[Plant-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilmMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-coresMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-vaginalMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-skinMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-oralMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-gutMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[Host-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[BuiltEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[AirMIGSBacteria]uses%20-.->[MIGSBacteria],[WaterMIGSBacteria],[WastewaterSludgeMIGSBacteria],[SoilMIGSBacteria],[SedimentMIGSBacteria],[Plant-associatedMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MicrobialMatBiofilmMIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-coresMIGSBacteria],[Human-vaginalMIGSBacteria],[Human-skinMIGSBacteria],[Human-oralMIGSBacteria],[Human-gutMIGSBacteria],[Human-associatedMIGSBacteria],[Host-associatedMIGSBacteria],[BuiltEnvironmentMIGSBacteria],[AirMIGSBacteria]) + +## Mixin for + + * [AirMIGSBacteria](AirMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SoilMIGSBacteria](SoilMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WaterMIGSBacteria](WaterMIGSBacteria.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.ba | + diff --git a/mixs6/MIGSEukaryote.md b/mixs6/MIGSEukaryote.md new file mode 100644 index 00000000..a55e5022 --- /dev/null +++ b/mixs6/MIGSEukaryote.md @@ -0,0 +1,152 @@ + +# Class: MIGSEukaryote + + +Minimal Information about a Genome Sequence: eukaryote + +URI: [mixs.vocab:MIGSEukaryote](https://w3id.org/mixs/vocab/MIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSEukaryote],[WastewaterSludgeMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SoilMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SedimentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Plant-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-vaginalMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-skinMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-oralMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-gutMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Host-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[BuiltEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[AirMIGSEukaryote]uses%20-.->[MIGSEukaryote],[WaterMIGSEukaryote],[WastewaterSludgeMIGSEukaryote],[SoilMIGSEukaryote],[SedimentMIGSEukaryote],[Plant-associatedMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote],[Human-vaginalMIGSEukaryote],[Human-skinMIGSEukaryote],[Human-oralMIGSEukaryote],[Human-gutMIGSEukaryote],[Human-associatedMIGSEukaryote],[Host-associatedMIGSEukaryote],[BuiltEnvironmentMIGSEukaryote],[AirMIGSEukaryote]) + +## Mixin for + + * [AirMIGSEukaryote](AirMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.eu | + diff --git a/mixs6/MIGSPlant.md b/mixs6/MIGSPlant.md new file mode 100644 index 00000000..e8d9992e --- /dev/null +++ b/mixs6/MIGSPlant.md @@ -0,0 +1,140 @@ + +# Class: MIGSPlant + + +Minimal Information about a Genome Sequence: plant + +URI: [mixs.vocab:MIGSPlant](https://w3id.org/mixs/vocab/MIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSPlant],[WastewaterSludgeMIGSPlant]uses%20-.->[MIGSPlant],[SoilMIGSPlant]uses%20-.->[MIGSPlant],[SedimentMIGSPlant]uses%20-.->[MIGSPlant],[Plant-associatedMIGSPlant]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[MicrobialMatBiofilmMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-coresMIGSPlant]uses%20-.->[MIGSPlant],[Human-vaginalMIGSPlant]uses%20-.->[MIGSPlant],[Human-skinMIGSPlant]uses%20-.->[MIGSPlant],[Human-oralMIGSPlant]uses%20-.->[MIGSPlant],[Human-gutMIGSPlant]uses%20-.->[MIGSPlant],[Human-associatedMIGSPlant]uses%20-.->[MIGSPlant],[Host-associatedMIGSPlant]uses%20-.->[MIGSPlant],[BuiltEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[AirMIGSPlant]uses%20-.->[MIGSPlant],[WaterMIGSPlant],[WastewaterSludgeMIGSPlant],[SoilMIGSPlant],[SedimentMIGSPlant],[Plant-associatedMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MicrobialMatBiofilmMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-coresMIGSPlant],[Human-vaginalMIGSPlant],[Human-skinMIGSPlant],[Human-oralMIGSPlant],[Human-gutMIGSPlant],[Human-associatedMIGSPlant],[Host-associatedMIGSPlant],[BuiltEnvironmentMIGSPlant],[AirMIGSPlant]) + +## Mixin for + + * [AirMIGSPlant](AirMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + * [SedimentMIGSPlant](SedimentMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + * [SoilMIGSPlant](SoilMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + * [WaterMIGSPlant](WaterMIGSPlant.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.pl | + diff --git a/mixs6/MIGSVirus.md b/mixs6/MIGSVirus.md new file mode 100644 index 00000000..74641603 --- /dev/null +++ b/mixs6/MIGSVirus.md @@ -0,0 +1,150 @@ + +# Class: MIGSVirus + + +Minimal Information about a Genome Sequence: cultured bacteria/archaea + +URI: [mixs.vocab:MIGSVirus](https://w3id.org/mixs/vocab/MIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSVirus],[WastewaterSludgeMIGSVirus]uses%20-.->[MIGSVirus],[SoilMIGSVirus]uses%20-.->[MIGSVirus],[SedimentMIGSVirus]uses%20-.->[MIGSVirus],[Plant-associatedMIGSVirus]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[MicrobialMatBiofilmMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-coresMIGSVirus]uses%20-.->[MIGSVirus],[Human-vaginalMIGSVirus]uses%20-.->[MIGSVirus],[Human-skinMIGSVirus]uses%20-.->[MIGSVirus],[Human-oralMIGSVirus]uses%20-.->[MIGSVirus],[Human-gutMIGSVirus]uses%20-.->[MIGSVirus],[Human-associatedMIGSVirus]uses%20-.->[MIGSVirus],[Host-associatedMIGSVirus]uses%20-.->[MIGSVirus],[BuiltEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[AirMIGSVirus]uses%20-.->[MIGSVirus],[WaterMIGSVirus],[WastewaterSludgeMIGSVirus],[SoilMIGSVirus],[SedimentMIGSVirus],[Plant-associatedMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MicrobialMatBiofilmMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-coresMIGSVirus],[Human-vaginalMIGSVirus],[Human-skinMIGSVirus],[Human-oralMIGSVirus],[Human-gutMIGSVirus],[Human-associatedMIGSVirus],[Host-associatedMIGSVirus],[BuiltEnvironmentMIGSVirus],[AirMIGSVirus]) + +## Mixin for + + * [AirMIGSVirus](AirMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [SedimentMIGSVirus](SedimentMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SoilMIGSVirus](SoilMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WaterMIGSVirus](WaterMIGSVirus.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.ba | + diff --git a/mixs6/MIGS_bacteria_adapters.md b/mixs6/MIGS_bacteria_adapters.md new file mode 100644 index 00000000..530ada43 --- /dev/null +++ b/mixs6/MIGS_bacteria_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_adapters + + + + +URI: [mixs.vocab:MIGS_bacteria_adapters](https://w3id.org/mixs/vocab/MIGS_bacteria_adapters) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_annot.md b/mixs6/MIGS_bacteria_annot.md new file mode 100644 index 00000000..ba2250ae --- /dev/null +++ b/mixs6/MIGS_bacteria_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_annot + + + + +URI: [mixs.vocab:MIGS_bacteria_annot](https://w3id.org/mixs/vocab/MIGS_bacteria_annot) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_assembly_name.md b/mixs6/MIGS_bacteria_assembly_name.md new file mode 100644 index 00000000..4840fe88 --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_assembly_name + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_name](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_assembly_qual.md b/mixs6/MIGS_bacteria_assembly_qual.md new file mode 100644 index 00000000..ca60c110 --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_assembly_qual + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_qual](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_qual) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_assembly_software.md b/mixs6/MIGS_bacteria_assembly_software.md new file mode 100644 index 00000000..a3929cfd --- /dev/null +++ b/mixs6/MIGS_bacteria_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_assembly_software + + + + +URI: [mixs.vocab:MIGS_bacteria_assembly_software](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_software) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_biotic_relationship.md b/mixs6/MIGS_bacteria_biotic_relationship.md new file mode 100644 index 00000000..b93d07c6 --- /dev/null +++ b/mixs6/MIGS_bacteria_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_bacteria_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_bacteria_biotic_relationship) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_collection_date.md b/mixs6/MIGS_bacteria_collection_date.md new file mode 100644 index 00000000..949a5a6f --- /dev/null +++ b/mixs6/MIGS_bacteria_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_collection_date + + + + +URI: [mixs.vocab:MIGS_bacteria_collection_date](https://w3id.org/mixs/vocab/MIGS_bacteria_collection_date) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_compl_score.md b/mixs6/MIGS_bacteria_compl_score.md new file mode 100644 index 00000000..e7449551 --- /dev/null +++ b/mixs6/MIGS_bacteria_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_compl_score + + + + +URI: [mixs.vocab:MIGS_bacteria_compl_score](https://w3id.org/mixs/vocab/MIGS_bacteria_compl_score) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_compl_software.md b/mixs6/MIGS_bacteria_compl_software.md new file mode 100644 index 00000000..30a096ec --- /dev/null +++ b/mixs6/MIGS_bacteria_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_compl_software + + + + +URI: [mixs.vocab:MIGS_bacteria_compl_software](https://w3id.org/mixs/vocab/MIGS_bacteria_compl_software) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_encoded_traits.md b/mixs6/MIGS_bacteria_encoded_traits.md new file mode 100644 index 00000000..6f2c8cef --- /dev/null +++ b/mixs6/MIGS_bacteria_encoded_traits.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_encoded_traits + + + + +URI: [mixs.vocab:MIGS_bacteria_encoded_traits](https://w3id.org/mixs/vocab/MIGS_bacteria_encoded_traits) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_broad_scale.md b/mixs6/MIGS_bacteria_env_broad_scale.md new file mode 100644 index 00000000..f1d226fb --- /dev/null +++ b/mixs6/MIGS_bacteria_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_bacteria_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_bacteria_env_broad_scale) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_local_scale.md b/mixs6/MIGS_bacteria_env_local_scale.md new file mode 100644 index 00000000..f1b4fbcf --- /dev/null +++ b/mixs6/MIGS_bacteria_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_local_scale + + + + +URI: [mixs.vocab:MIGS_bacteria_env_local_scale](https://w3id.org/mixs/vocab/MIGS_bacteria_env_local_scale) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_medium.md b/mixs6/MIGS_bacteria_env_medium.md new file mode 100644 index 00000000..ed3db8c9 --- /dev/null +++ b/mixs6/MIGS_bacteria_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_env_medium + + + + +URI: [mixs.vocab:MIGS_bacteria_env_medium](https://w3id.org/mixs/vocab/MIGS_bacteria_env_medium) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_env_package.md b/mixs6/MIGS_bacteria_env_package.md new file mode 100644 index 00000000..20b75103 --- /dev/null +++ b/mixs6/MIGS_bacteria_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_env_package + + + + +URI: [mixs.vocab:MIGS_bacteria_env_package](https://w3id.org/mixs/vocab/MIGS_bacteria_env_package) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_estimated_size.md b/mixs6/MIGS_bacteria_estimated_size.md new file mode 100644 index 00000000..7eb1f474 --- /dev/null +++ b/mixs6/MIGS_bacteria_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_estimated_size + + + + +URI: [mixs.vocab:MIGS_bacteria_estimated_size](https://w3id.org/mixs/vocab/MIGS_bacteria_estimated_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_experimental_factor.md b/mixs6/MIGS_bacteria_experimental_factor.md new file mode 100644 index 00000000..6ba4686f --- /dev/null +++ b/mixs6/MIGS_bacteria_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_experimental_factor + + + + +URI: [mixs.vocab:MIGS_bacteria_experimental_factor](https://w3id.org/mixs/vocab/MIGS_bacteria_experimental_factor) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_extrachrom_elements.md b/mixs6/MIGS_bacteria_extrachrom_elements.md new file mode 100644 index 00000000..f2b616c5 --- /dev/null +++ b/mixs6/MIGS_bacteria_extrachrom_elements.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_bacteria_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_bacteria_extrachrom_elements) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_feat_pred.md b/mixs6/MIGS_bacteria_feat_pred.md new file mode 100644 index 00000000..e68bea98 --- /dev/null +++ b/mixs6/MIGS_bacteria_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_feat_pred + + + + +URI: [mixs.vocab:MIGS_bacteria_feat_pred](https://w3id.org/mixs/vocab/MIGS_bacteria_feat_pred) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_geo_loc_name.md b/mixs6/MIGS_bacteria_geo_loc_name.md new file mode 100644 index 00000000..12b29dc6 --- /dev/null +++ b/mixs6/MIGS_bacteria_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_bacteria_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_bacteria_geo_loc_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_health_disease_stat.md b/mixs6/MIGS_bacteria_health_disease_stat.md new file mode 100644 index 00000000..050830a8 --- /dev/null +++ b/mixs6/MIGS_bacteria_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_bacteria_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_bacteria_health_disease_stat) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_host_spec_range.md b/mixs6/MIGS_bacteria_host_spec_range.md new file mode 100644 index 00000000..01e1272c --- /dev/null +++ b/mixs6/MIGS_bacteria_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_host_spec_range + + + + +URI: [mixs.vocab:MIGS_bacteria_host_spec_range](https://w3id.org/mixs/vocab/MIGS_bacteria_host_spec_range) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_investigation_type.md b/mixs6/MIGS_bacteria_investigation_type.md new file mode 100644 index 00000000..f1778d90 --- /dev/null +++ b/mixs6/MIGS_bacteria_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_investigation_type + + + + +URI: [mixs.vocab:MIGS_bacteria_investigation_type](https://w3id.org/mixs/vocab/MIGS_bacteria_investigation_type) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_isol_growth_condt.md b/mixs6/MIGS_bacteria_isol_growth_condt.md new file mode 100644 index 00000000..a8b860f4 --- /dev/null +++ b/mixs6/MIGS_bacteria_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_bacteria_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_bacteria_isol_growth_condt) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lat_lon.md b/mixs6/MIGS_bacteria_lat_lon.md new file mode 100644 index 00000000..0a32974d --- /dev/null +++ b/mixs6/MIGS_bacteria_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_bacteria_lat_lon + + + + +URI: [mixs.vocab:MIGS_bacteria_lat_lon](https://w3id.org/mixs/vocab/MIGS_bacteria_lat_lon) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_layout.md b/mixs6/MIGS_bacteria_lib_layout.md new file mode 100644 index 00000000..44eaa376 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_layout + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_layout](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_layout) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_reads_seqd.md b/mixs6/MIGS_bacteria_lib_reads_seqd.md new file mode 100644 index 00000000..dbb90ba1 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_reads_seqd) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_screen.md b/mixs6/MIGS_bacteria_lib_screen.md new file mode 100644 index 00000000..3cb6fb63 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_screen + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_screen](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_screen) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_size.md b/mixs6/MIGS_bacteria_lib_size.md new file mode 100644 index 00000000..a4cc3d07 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_size + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_size](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_lib_vector.md b/mixs6/MIGS_bacteria_lib_vector.md new file mode 100644 index 00000000..3ef72937 --- /dev/null +++ b/mixs6/MIGS_bacteria_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_lib_vector + + + + +URI: [mixs.vocab:MIGS_bacteria_lib_vector](https://w3id.org/mixs/vocab/MIGS_bacteria_lib_vector) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_nucl_acid_amp.md b/mixs6/MIGS_bacteria_nucl_acid_amp.md new file mode 100644 index 00000000..f14fab06 --- /dev/null +++ b/mixs6/MIGS_bacteria_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_bacteria_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_bacteria_nucl_acid_amp) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_nucl_acid_ext.md b/mixs6/MIGS_bacteria_nucl_acid_ext.md new file mode 100644 index 00000000..989e74d3 --- /dev/null +++ b/mixs6/MIGS_bacteria_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_bacteria_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_bacteria_nucl_acid_ext) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_num_replicons.md b/mixs6/MIGS_bacteria_num_replicons.md new file mode 100644 index 00000000..86077b1b --- /dev/null +++ b/mixs6/MIGS_bacteria_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_num_replicons + + + + +URI: [mixs.vocab:MIGS_bacteria_num_replicons](https://w3id.org/mixs/vocab/MIGS_bacteria_num_replicons) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_number_contig.md b/mixs6/MIGS_bacteria_number_contig.md new file mode 100644 index 00000000..ffdcfccb --- /dev/null +++ b/mixs6/MIGS_bacteria_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_number_contig + + + + +URI: [mixs.vocab:MIGS_bacteria_number_contig](https://w3id.org/mixs/vocab/MIGS_bacteria_number_contig) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_pathogenicity.md b/mixs6/MIGS_bacteria_pathogenicity.md new file mode 100644 index 00000000..2448a700 --- /dev/null +++ b/mixs6/MIGS_bacteria_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_pathogenicity + + + + +URI: [mixs.vocab:MIGS_bacteria_pathogenicity](https://w3id.org/mixs/vocab/MIGS_bacteria_pathogenicity) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_project_name.md b/mixs6/MIGS_bacteria_project_name.md new file mode 100644 index 00000000..851f2d86 --- /dev/null +++ b/mixs6/MIGS_bacteria_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_project_name + + + + +URI: [mixs.vocab:MIGS_bacteria_project_name](https://w3id.org/mixs/vocab/MIGS_bacteria_project_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_ref_biomaterial.md b/mixs6/MIGS_bacteria_ref_biomaterial.md new file mode 100644 index 00000000..06813701 --- /dev/null +++ b/mixs6/MIGS_bacteria_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_bacteria_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_bacteria_ref_biomaterial) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_ref_db.md b/mixs6/MIGS_bacteria_ref_db.md new file mode 100644 index 00000000..d9f9d9c4 --- /dev/null +++ b/mixs6/MIGS_bacteria_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_ref_db + + + + +URI: [mixs.vocab:MIGS_bacteria_ref_db](https://w3id.org/mixs/vocab/MIGS_bacteria_ref_db) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_rel_to_oxygen.md b/mixs6/MIGS_bacteria_rel_to_oxygen.md new file mode 100644 index 00000000..17434d02 --- /dev/null +++ b/mixs6/MIGS_bacteria_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_rel_to_oxygen + + + + +URI: [mixs.vocab:MIGS_bacteria_rel_to_oxygen](https://w3id.org/mixs/vocab/MIGS_bacteria_rel_to_oxygen) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_samp_collect_device.md b/mixs6/MIGS_bacteria_samp_collect_device.md new file mode 100644 index 00000000..df27ec0a --- /dev/null +++ b/mixs6/MIGS_bacteria_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_samp_collect_device + + + + +URI: [mixs.vocab:MIGS_bacteria_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_collect_device) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_samp_mat_process.md b/mixs6/MIGS_bacteria_samp_mat_process.md new file mode 100644 index 00000000..2f443358 --- /dev/null +++ b/mixs6/MIGS_bacteria_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_bacteria_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_mat_process) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_samp_size.md b/mixs6/MIGS_bacteria_samp_size.md new file mode 100644 index 00000000..bf67e5c2 --- /dev/null +++ b/mixs6/MIGS_bacteria_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_samp_size + + + + +URI: [mixs.vocab:MIGS_bacteria_samp_size](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_size) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sample_name.md b/mixs6/MIGS_bacteria_sample_name.md new file mode 100644 index 00000000..b26a9d24 --- /dev/null +++ b/mixs6/MIGS_bacteria_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sample_name + + + + +URI: [mixs.vocab:MIGS_bacteria_sample_name](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_name) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_seq_meth.md b/mixs6/MIGS_bacteria_seq_meth.md new file mode 100644 index 00000000..7c6dac2d --- /dev/null +++ b/mixs6/MIGS_bacteria_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_seq_meth + + + + +URI: [mixs.vocab:MIGS_bacteria_seq_meth](https://w3id.org/mixs/vocab/MIGS_bacteria_seq_meth) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sim_search_meth.md b/mixs6/MIGS_bacteria_sim_search_meth.md new file mode 100644 index 00000000..df0061d6 --- /dev/null +++ b/mixs6/MIGS_bacteria_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_bacteria_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_bacteria_sim_search_meth) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sop.md b/mixs6/MIGS_bacteria_sop.md new file mode 100644 index 00000000..30544a2c --- /dev/null +++ b/mixs6/MIGS_bacteria_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_sop + + + + +URI: [mixs.vocab:MIGS_bacteria_sop](https://w3id.org/mixs/vocab/MIGS_bacteria_sop) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_source_mat_id.md b/mixs6/MIGS_bacteria_source_mat_id.md new file mode 100644 index 00000000..f327f648 --- /dev/null +++ b/mixs6/MIGS_bacteria_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_source_mat_id + + + + +URI: [mixs.vocab:MIGS_bacteria_source_mat_id](https://w3id.org/mixs/vocab/MIGS_bacteria_source_mat_id) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_specific_host.md b/mixs6/MIGS_bacteria_specific_host.md new file mode 100644 index 00000000..53a9def4 --- /dev/null +++ b/mixs6/MIGS_bacteria_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_specific_host + + + + +URI: [mixs.vocab:MIGS_bacteria_specific_host](https://w3id.org/mixs/vocab/MIGS_bacteria_specific_host) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_submitted_to_insdc.md b/mixs6/MIGS_bacteria_submitted_to_insdc.md new file mode 100644 index 00000000..43216416 --- /dev/null +++ b/mixs6/MIGS_bacteria_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_bacteria_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_bacteria_submitted_to_insdc) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_subspecf_gen_lin.md b/mixs6/MIGS_bacteria_subspecf_gen_lin.md new file mode 100644 index 00000000..a8a8397c --- /dev/null +++ b/mixs6/MIGS_bacteria_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_bacteria_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_bacteria_subspecf_gen_lin) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_tax_class.md b/mixs6/MIGS_bacteria_tax_class.md new file mode 100644 index 00000000..21493ae4 --- /dev/null +++ b/mixs6/MIGS_bacteria_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_tax_class + + + + +URI: [mixs.vocab:MIGS_bacteria_tax_class](https://w3id.org/mixs/vocab/MIGS_bacteria_tax_class) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_tax_ident.md b/mixs6/MIGS_bacteria_tax_ident.md new file mode 100644 index 00000000..b3b5da8f --- /dev/null +++ b/mixs6/MIGS_bacteria_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_tax_ident + + + + +URI: [mixs.vocab:MIGS_bacteria_tax_ident](https://w3id.org/mixs/vocab/MIGS_bacteria_tax_ident) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_trophic_level.md b/mixs6/MIGS_bacteria_trophic_level.md new file mode 100644 index 00000000..9c41c1ea --- /dev/null +++ b/mixs6/MIGS_bacteria_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_trophic_level + + + + +URI: [mixs.vocab:MIGS_bacteria_trophic_level](https://w3id.org/mixs/vocab/MIGS_bacteria_trophic_level) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_bacteria_url.md b/mixs6/MIGS_bacteria_url.md new file mode 100644 index 00000000..139e1745 --- /dev/null +++ b/mixs6/MIGS_bacteria_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_bacteria_url + + + + +URI: [mixs.vocab:MIGS_bacteria_url](https://w3id.org/mixs/vocab/MIGS_bacteria_url) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_adapters.md b/mixs6/MIGS_eukaryote_adapters.md new file mode 100644 index 00000000..eb7a03b6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_adapters + + + + +URI: [mixs.vocab:MIGS_eukaryote_adapters](https://w3id.org/mixs/vocab/MIGS_eukaryote_adapters) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_annot.md b/mixs6/MIGS_eukaryote_annot.md new file mode 100644 index 00000000..4e4c0c3c --- /dev/null +++ b/mixs6/MIGS_eukaryote_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_annot + + + + +URI: [mixs.vocab:MIGS_eukaryote_annot](https://w3id.org/mixs/vocab/MIGS_eukaryote_annot) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_assembly_name.md b/mixs6/MIGS_eukaryote_assembly_name.md new file mode 100644 index 00000000..ca703149 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_assembly_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_assembly_qual.md b/mixs6/MIGS_eukaryote_assembly_qual.md new file mode 100644 index 00000000..5457dd91 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_assembly_qual + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_qual](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_qual) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_assembly_software.md b/mixs6/MIGS_eukaryote_assembly_software.md new file mode 100644 index 00000000..d8dd4870 --- /dev/null +++ b/mixs6/MIGS_eukaryote_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_assembly_software + + + + +URI: [mixs.vocab:MIGS_eukaryote_assembly_software](https://w3id.org/mixs/vocab/MIGS_eukaryote_assembly_software) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_biotic_relationship.md b/mixs6/MIGS_eukaryote_biotic_relationship.md new file mode 100644 index 00000000..84b9eb08 --- /dev/null +++ b/mixs6/MIGS_eukaryote_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_eukaryote_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_eukaryote_biotic_relationship) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_collection_date.md b/mixs6/MIGS_eukaryote_collection_date.md new file mode 100644 index 00000000..567b02ff --- /dev/null +++ b/mixs6/MIGS_eukaryote_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_collection_date + + + + +URI: [mixs.vocab:MIGS_eukaryote_collection_date](https://w3id.org/mixs/vocab/MIGS_eukaryote_collection_date) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_compl_score.md b/mixs6/MIGS_eukaryote_compl_score.md new file mode 100644 index 00000000..837de7d1 --- /dev/null +++ b/mixs6/MIGS_eukaryote_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_compl_score + + + + +URI: [mixs.vocab:MIGS_eukaryote_compl_score](https://w3id.org/mixs/vocab/MIGS_eukaryote_compl_score) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_compl_software.md b/mixs6/MIGS_eukaryote_compl_software.md new file mode 100644 index 00000000..a0d5e8e6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_compl_software + + + + +URI: [mixs.vocab:MIGS_eukaryote_compl_software](https://w3id.org/mixs/vocab/MIGS_eukaryote_compl_software) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_broad_scale.md b/mixs6/MIGS_eukaryote_env_broad_scale.md new file mode 100644 index 00000000..06026e2f --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_broad_scale) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_local_scale.md b/mixs6/MIGS_eukaryote_env_local_scale.md new file mode 100644 index 00000000..00638ff7 --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_local_scale + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_local_scale](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_local_scale) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_medium.md b/mixs6/MIGS_eukaryote_env_medium.md new file mode 100644 index 00000000..44572961 --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_env_medium + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_medium](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_medium) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_env_package.md b/mixs6/MIGS_eukaryote_env_package.md new file mode 100644 index 00000000..ca40b85c --- /dev/null +++ b/mixs6/MIGS_eukaryote_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_env_package + + + + +URI: [mixs.vocab:MIGS_eukaryote_env_package](https://w3id.org/mixs/vocab/MIGS_eukaryote_env_package) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_estimated_size.md b/mixs6/MIGS_eukaryote_estimated_size.md new file mode 100644 index 00000000..815d5701 --- /dev/null +++ b/mixs6/MIGS_eukaryote_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_estimated_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_estimated_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_estimated_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_experimental_factor.md b/mixs6/MIGS_eukaryote_experimental_factor.md new file mode 100644 index 00000000..7fb090b6 --- /dev/null +++ b/mixs6/MIGS_eukaryote_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_experimental_factor + + + + +URI: [mixs.vocab:MIGS_eukaryote_experimental_factor](https://w3id.org/mixs/vocab/MIGS_eukaryote_experimental_factor) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_extrachrom_elements.md b/mixs6/MIGS_eukaryote_extrachrom_elements.md new file mode 100644 index 00000000..f40ede50 --- /dev/null +++ b/mixs6/MIGS_eukaryote_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_eukaryote_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_eukaryote_extrachrom_elements) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_feat_pred.md b/mixs6/MIGS_eukaryote_feat_pred.md new file mode 100644 index 00000000..5dfaf9ea --- /dev/null +++ b/mixs6/MIGS_eukaryote_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_feat_pred + + + + +URI: [mixs.vocab:MIGS_eukaryote_feat_pred](https://w3id.org/mixs/vocab/MIGS_eukaryote_feat_pred) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_geo_loc_name.md b/mixs6/MIGS_eukaryote_geo_loc_name.md new file mode 100644 index 00000000..5f31bb2f --- /dev/null +++ b/mixs6/MIGS_eukaryote_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_geo_loc_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_health_disease_stat.md b/mixs6/MIGS_eukaryote_health_disease_stat.md new file mode 100644 index 00000000..24329f53 --- /dev/null +++ b/mixs6/MIGS_eukaryote_health_disease_stat.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_eukaryote_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_eukaryote_health_disease_stat) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_host_spec_range.md b/mixs6/MIGS_eukaryote_host_spec_range.md new file mode 100644 index 00000000..8d6780e2 --- /dev/null +++ b/mixs6/MIGS_eukaryote_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_host_spec_range + + + + +URI: [mixs.vocab:MIGS_eukaryote_host_spec_range](https://w3id.org/mixs/vocab/MIGS_eukaryote_host_spec_range) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_investigation_type.md b/mixs6/MIGS_eukaryote_investigation_type.md new file mode 100644 index 00000000..29dea620 --- /dev/null +++ b/mixs6/MIGS_eukaryote_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_investigation_type + + + + +URI: [mixs.vocab:MIGS_eukaryote_investigation_type](https://w3id.org/mixs/vocab/MIGS_eukaryote_investigation_type) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_isol_growth_condt.md b/mixs6/MIGS_eukaryote_isol_growth_condt.md new file mode 100644 index 00000000..dfe519a3 --- /dev/null +++ b/mixs6/MIGS_eukaryote_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_eukaryote_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_eukaryote_isol_growth_condt) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lat_lon.md b/mixs6/MIGS_eukaryote_lat_lon.md new file mode 100644 index 00000000..f583d145 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_eukaryote_lat_lon + + + + +URI: [mixs.vocab:MIGS_eukaryote_lat_lon](https://w3id.org/mixs/vocab/MIGS_eukaryote_lat_lon) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_layout.md b/mixs6/MIGS_eukaryote_lib_layout.md new file mode 100644 index 00000000..f9a7a1ac --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_layout + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_layout](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_layout) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_reads_seqd.md b/mixs6/MIGS_eukaryote_lib_reads_seqd.md new file mode 100644 index 00000000..a3941435 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_reads_seqd) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_screen.md b/mixs6/MIGS_eukaryote_lib_screen.md new file mode 100644 index 00000000..a142cbc0 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_screen + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_screen](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_screen) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_size.md b/mixs6/MIGS_eukaryote_lib_size.md new file mode 100644 index 00000000..4ca7b8a2 --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_lib_vector.md b/mixs6/MIGS_eukaryote_lib_vector.md new file mode 100644 index 00000000..b686f06d --- /dev/null +++ b/mixs6/MIGS_eukaryote_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_lib_vector + + + + +URI: [mixs.vocab:MIGS_eukaryote_lib_vector](https://w3id.org/mixs/vocab/MIGS_eukaryote_lib_vector) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_nucl_acid_amp.md b/mixs6/MIGS_eukaryote_nucl_acid_amp.md new file mode 100644 index 00000000..13f5f670 --- /dev/null +++ b/mixs6/MIGS_eukaryote_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_eukaryote_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_eukaryote_nucl_acid_amp) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_nucl_acid_ext.md b/mixs6/MIGS_eukaryote_nucl_acid_ext.md new file mode 100644 index 00000000..4c34e35d --- /dev/null +++ b/mixs6/MIGS_eukaryote_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_eukaryote_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_eukaryote_nucl_acid_ext) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_num_replicons.md b/mixs6/MIGS_eukaryote_num_replicons.md new file mode 100644 index 00000000..ca4149ed --- /dev/null +++ b/mixs6/MIGS_eukaryote_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_num_replicons + + + + +URI: [mixs.vocab:MIGS_eukaryote_num_replicons](https://w3id.org/mixs/vocab/MIGS_eukaryote_num_replicons) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_number_contig.md b/mixs6/MIGS_eukaryote_number_contig.md new file mode 100644 index 00000000..30721565 --- /dev/null +++ b/mixs6/MIGS_eukaryote_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_number_contig + + + + +URI: [mixs.vocab:MIGS_eukaryote_number_contig](https://w3id.org/mixs/vocab/MIGS_eukaryote_number_contig) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_pathogenicity.md b/mixs6/MIGS_eukaryote_pathogenicity.md new file mode 100644 index 00000000..df21c4e5 --- /dev/null +++ b/mixs6/MIGS_eukaryote_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_pathogenicity + + + + +URI: [mixs.vocab:MIGS_eukaryote_pathogenicity](https://w3id.org/mixs/vocab/MIGS_eukaryote_pathogenicity) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_ploidy.md b/mixs6/MIGS_eukaryote_ploidy.md new file mode 100644 index 00000000..bc4f92f7 --- /dev/null +++ b/mixs6/MIGS_eukaryote_ploidy.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ploidy + + + + +URI: [mixs.vocab:MIGS_eukaryote_ploidy](https://w3id.org/mixs/vocab/MIGS_eukaryote_ploidy) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ploidy](ploidy.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_project_name.md b/mixs6/MIGS_eukaryote_project_name.md new file mode 100644 index 00000000..b9b44f2e --- /dev/null +++ b/mixs6/MIGS_eukaryote_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_project_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_project_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_project_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_propagation.md b/mixs6/MIGS_eukaryote_propagation.md new file mode 100644 index 00000000..df273139 --- /dev/null +++ b/mixs6/MIGS_eukaryote_propagation.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_propagation + + + + +URI: [mixs.vocab:MIGS_eukaryote_propagation](https://w3id.org/mixs/vocab/MIGS_eukaryote_propagation) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_ref_biomaterial.md b/mixs6/MIGS_eukaryote_ref_biomaterial.md new file mode 100644 index 00000000..dedde21b --- /dev/null +++ b/mixs6/MIGS_eukaryote_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_eukaryote_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_eukaryote_ref_biomaterial) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_ref_db.md b/mixs6/MIGS_eukaryote_ref_db.md new file mode 100644 index 00000000..9759e30b --- /dev/null +++ b/mixs6/MIGS_eukaryote_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_ref_db + + + + +URI: [mixs.vocab:MIGS_eukaryote_ref_db](https://w3id.org/mixs/vocab/MIGS_eukaryote_ref_db) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_samp_collect_device.md b/mixs6/MIGS_eukaryote_samp_collect_device.md new file mode 100644 index 00000000..87e93bee --- /dev/null +++ b/mixs6/MIGS_eukaryote_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_samp_collect_device + + + + +URI: [mixs.vocab:MIGS_eukaryote_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_collect_device) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_samp_mat_process.md b/mixs6/MIGS_eukaryote_samp_mat_process.md new file mode 100644 index 00000000..e920d891 --- /dev/null +++ b/mixs6/MIGS_eukaryote_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_eukaryote_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_mat_process) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_samp_size.md b/mixs6/MIGS_eukaryote_samp_size.md new file mode 100644 index 00000000..d542b487 --- /dev/null +++ b/mixs6/MIGS_eukaryote_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_samp_size + + + + +URI: [mixs.vocab:MIGS_eukaryote_samp_size](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_size) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sample_name.md b/mixs6/MIGS_eukaryote_sample_name.md new file mode 100644 index 00000000..570ab29f --- /dev/null +++ b/mixs6/MIGS_eukaryote_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sample_name + + + + +URI: [mixs.vocab:MIGS_eukaryote_sample_name](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_name) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_seq_meth.md b/mixs6/MIGS_eukaryote_seq_meth.md new file mode 100644 index 00000000..d4b9d8e9 --- /dev/null +++ b/mixs6/MIGS_eukaryote_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_seq_meth + + + + +URI: [mixs.vocab:MIGS_eukaryote_seq_meth](https://w3id.org/mixs/vocab/MIGS_eukaryote_seq_meth) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sim_search_meth.md b/mixs6/MIGS_eukaryote_sim_search_meth.md new file mode 100644 index 00000000..c8c0d433 --- /dev/null +++ b/mixs6/MIGS_eukaryote_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_eukaryote_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_eukaryote_sim_search_meth) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sop.md b/mixs6/MIGS_eukaryote_sop.md new file mode 100644 index 00000000..fcd5ebf1 --- /dev/null +++ b/mixs6/MIGS_eukaryote_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_sop + + + + +URI: [mixs.vocab:MIGS_eukaryote_sop](https://w3id.org/mixs/vocab/MIGS_eukaryote_sop) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_source_mat_id.md b/mixs6/MIGS_eukaryote_source_mat_id.md new file mode 100644 index 00000000..89ed35a9 --- /dev/null +++ b/mixs6/MIGS_eukaryote_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_source_mat_id + + + + +URI: [mixs.vocab:MIGS_eukaryote_source_mat_id](https://w3id.org/mixs/vocab/MIGS_eukaryote_source_mat_id) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_specific_host.md b/mixs6/MIGS_eukaryote_specific_host.md new file mode 100644 index 00000000..dcde77ac --- /dev/null +++ b/mixs6/MIGS_eukaryote_specific_host.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_specific_host + + + + +URI: [mixs.vocab:MIGS_eukaryote_specific_host](https://w3id.org/mixs/vocab/MIGS_eukaryote_specific_host) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_submitted_to_insdc.md b/mixs6/MIGS_eukaryote_submitted_to_insdc.md new file mode 100644 index 00000000..c2c80a75 --- /dev/null +++ b/mixs6/MIGS_eukaryote_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_eukaryote_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_eukaryote_submitted_to_insdc) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_subspecf_gen_lin.md b/mixs6/MIGS_eukaryote_subspecf_gen_lin.md new file mode 100644 index 00000000..8877899c --- /dev/null +++ b/mixs6/MIGS_eukaryote_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_eukaryote_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_eukaryote_subspecf_gen_lin) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_tax_class.md b/mixs6/MIGS_eukaryote_tax_class.md new file mode 100644 index 00000000..b1655e70 --- /dev/null +++ b/mixs6/MIGS_eukaryote_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_tax_class + + + + +URI: [mixs.vocab:MIGS_eukaryote_tax_class](https://w3id.org/mixs/vocab/MIGS_eukaryote_tax_class) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_tax_ident.md b/mixs6/MIGS_eukaryote_tax_ident.md new file mode 100644 index 00000000..43f86760 --- /dev/null +++ b/mixs6/MIGS_eukaryote_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_tax_ident + + + + +URI: [mixs.vocab:MIGS_eukaryote_tax_ident](https://w3id.org/mixs/vocab/MIGS_eukaryote_tax_ident) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_trophic_level.md b/mixs6/MIGS_eukaryote_trophic_level.md new file mode 100644 index 00000000..a64dcb5a --- /dev/null +++ b/mixs6/MIGS_eukaryote_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_trophic_level + + + + +URI: [mixs.vocab:MIGS_eukaryote_trophic_level](https://w3id.org/mixs/vocab/MIGS_eukaryote_trophic_level) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_eukaryote_url.md b/mixs6/MIGS_eukaryote_url.md new file mode 100644 index 00000000..9af82372 --- /dev/null +++ b/mixs6/MIGS_eukaryote_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_eukaryote_url + + + + +URI: [mixs.vocab:MIGS_eukaryote_url](https://w3id.org/mixs/vocab/MIGS_eukaryote_url) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_adapters.md b/mixs6/MIGS_plant_adapters.md new file mode 100644 index 00000000..b9b79fc9 --- /dev/null +++ b/mixs6/MIGS_plant_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_adapters + + + + +URI: [mixs.vocab:MIGS_plant_adapters](https://w3id.org/mixs/vocab/MIGS_plant_adapters) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_annot.md b/mixs6/MIGS_plant_annot.md new file mode 100644 index 00000000..dd3c6fac --- /dev/null +++ b/mixs6/MIGS_plant_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_annot + + + + +URI: [mixs.vocab:MIGS_plant_annot](https://w3id.org/mixs/vocab/MIGS_plant_annot) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_assembly_name.md b/mixs6/MIGS_plant_assembly_name.md new file mode 100644 index 00000000..a14795dd --- /dev/null +++ b/mixs6/MIGS_plant_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_assembly_name + + + + +URI: [mixs.vocab:MIGS_plant_assembly_name](https://w3id.org/mixs/vocab/MIGS_plant_assembly_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_assembly_qual.md b/mixs6/MIGS_plant_assembly_qual.md new file mode 100644 index 00000000..7d5dda42 --- /dev/null +++ b/mixs6/MIGS_plant_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_assembly_qual + + + + +URI: [mixs.vocab:MIGS_plant_assembly_qual](https://w3id.org/mixs/vocab/MIGS_plant_assembly_qual) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_assembly_software.md b/mixs6/MIGS_plant_assembly_software.md new file mode 100644 index 00000000..89589ab7 --- /dev/null +++ b/mixs6/MIGS_plant_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_assembly_software + + + + +URI: [mixs.vocab:MIGS_plant_assembly_software](https://w3id.org/mixs/vocab/MIGS_plant_assembly_software) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_collection_date.md b/mixs6/MIGS_plant_collection_date.md new file mode 100644 index 00000000..b8b90631 --- /dev/null +++ b/mixs6/MIGS_plant_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_collection_date + + + + +URI: [mixs.vocab:MIGS_plant_collection_date](https://w3id.org/mixs/vocab/MIGS_plant_collection_date) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_compl_score.md b/mixs6/MIGS_plant_compl_score.md new file mode 100644 index 00000000..2f90e44d --- /dev/null +++ b/mixs6/MIGS_plant_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_compl_score + + + + +URI: [mixs.vocab:MIGS_plant_compl_score](https://w3id.org/mixs/vocab/MIGS_plant_compl_score) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_compl_software.md b/mixs6/MIGS_plant_compl_software.md new file mode 100644 index 00000000..b369a96d --- /dev/null +++ b/mixs6/MIGS_plant_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_compl_software + + + + +URI: [mixs.vocab:MIGS_plant_compl_software](https://w3id.org/mixs/vocab/MIGS_plant_compl_software) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_encoded_traits.md b/mixs6/MIGS_plant_encoded_traits.md new file mode 100644 index 00000000..953db827 --- /dev/null +++ b/mixs6/MIGS_plant_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_encoded_traits + + + + +URI: [mixs.vocab:MIGS_plant_encoded_traits](https://w3id.org/mixs/vocab/MIGS_plant_encoded_traits) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_env_broad_scale.md b/mixs6/MIGS_plant_env_broad_scale.md new file mode 100644 index 00000000..f3f6b225 --- /dev/null +++ b/mixs6/MIGS_plant_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_plant_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_plant_env_broad_scale) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_local_scale.md b/mixs6/MIGS_plant_env_local_scale.md new file mode 100644 index 00000000..f97a444b --- /dev/null +++ b/mixs6/MIGS_plant_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_local_scale + + + + +URI: [mixs.vocab:MIGS_plant_env_local_scale](https://w3id.org/mixs/vocab/MIGS_plant_env_local_scale) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_medium.md b/mixs6/MIGS_plant_env_medium.md new file mode 100644 index 00000000..c1e6c02f --- /dev/null +++ b/mixs6/MIGS_plant_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_env_medium + + + + +URI: [mixs.vocab:MIGS_plant_env_medium](https://w3id.org/mixs/vocab/MIGS_plant_env_medium) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_env_package.md b/mixs6/MIGS_plant_env_package.md new file mode 100644 index 00000000..1c332eb2 --- /dev/null +++ b/mixs6/MIGS_plant_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_env_package + + + + +URI: [mixs.vocab:MIGS_plant_env_package](https://w3id.org/mixs/vocab/MIGS_plant_env_package) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_estimated_size.md b/mixs6/MIGS_plant_estimated_size.md new file mode 100644 index 00000000..3e506e0d --- /dev/null +++ b/mixs6/MIGS_plant_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_estimated_size + + + + +URI: [mixs.vocab:MIGS_plant_estimated_size](https://w3id.org/mixs/vocab/MIGS_plant_estimated_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_experimental_factor.md b/mixs6/MIGS_plant_experimental_factor.md new file mode 100644 index 00000000..2045f70b --- /dev/null +++ b/mixs6/MIGS_plant_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_experimental_factor + + + + +URI: [mixs.vocab:MIGS_plant_experimental_factor](https://w3id.org/mixs/vocab/MIGS_plant_experimental_factor) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_feat_pred.md b/mixs6/MIGS_plant_feat_pred.md new file mode 100644 index 00000000..b4146b1a --- /dev/null +++ b/mixs6/MIGS_plant_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_feat_pred + + + + +URI: [mixs.vocab:MIGS_plant_feat_pred](https://w3id.org/mixs/vocab/MIGS_plant_feat_pred) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_geo_loc_name.md b/mixs6/MIGS_plant_geo_loc_name.md new file mode 100644 index 00000000..6122fb42 --- /dev/null +++ b/mixs6/MIGS_plant_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_plant_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_plant_geo_loc_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_host_spec_range.md b/mixs6/MIGS_plant_host_spec_range.md new file mode 100644 index 00000000..986f5845 --- /dev/null +++ b/mixs6/MIGS_plant_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_host_spec_range + + + + +URI: [mixs.vocab:MIGS_plant_host_spec_range](https://w3id.org/mixs/vocab/MIGS_plant_host_spec_range) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_investigation_type.md b/mixs6/MIGS_plant_investigation_type.md new file mode 100644 index 00000000..05ca7ce2 --- /dev/null +++ b/mixs6/MIGS_plant_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_investigation_type + + + + +URI: [mixs.vocab:MIGS_plant_investigation_type](https://w3id.org/mixs/vocab/MIGS_plant_investigation_type) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_isol_growth_condt.md b/mixs6/MIGS_plant_isol_growth_condt.md new file mode 100644 index 00000000..a1ad3590 --- /dev/null +++ b/mixs6/MIGS_plant_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_plant_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_plant_isol_growth_condt) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lat_lon.md b/mixs6/MIGS_plant_lat_lon.md new file mode 100644 index 00000000..93a3b91b --- /dev/null +++ b/mixs6/MIGS_plant_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_plant_lat_lon + + + + +URI: [mixs.vocab:MIGS_plant_lat_lon](https://w3id.org/mixs/vocab/MIGS_plant_lat_lon) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_layout.md b/mixs6/MIGS_plant_lib_layout.md new file mode 100644 index 00000000..dc22b890 --- /dev/null +++ b/mixs6/MIGS_plant_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_layout + + + + +URI: [mixs.vocab:MIGS_plant_lib_layout](https://w3id.org/mixs/vocab/MIGS_plant_lib_layout) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_reads_seqd.md b/mixs6/MIGS_plant_lib_reads_seqd.md new file mode 100644 index 00000000..71af3d1b --- /dev/null +++ b/mixs6/MIGS_plant_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_plant_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_plant_lib_reads_seqd) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_screen.md b/mixs6/MIGS_plant_lib_screen.md new file mode 100644 index 00000000..83a688b9 --- /dev/null +++ b/mixs6/MIGS_plant_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_screen + + + + +URI: [mixs.vocab:MIGS_plant_lib_screen](https://w3id.org/mixs/vocab/MIGS_plant_lib_screen) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_size.md b/mixs6/MIGS_plant_lib_size.md new file mode 100644 index 00000000..8a271c88 --- /dev/null +++ b/mixs6/MIGS_plant_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_size + + + + +URI: [mixs.vocab:MIGS_plant_lib_size](https://w3id.org/mixs/vocab/MIGS_plant_lib_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_lib_vector.md b/mixs6/MIGS_plant_lib_vector.md new file mode 100644 index 00000000..51ee6bf3 --- /dev/null +++ b/mixs6/MIGS_plant_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_lib_vector + + + + +URI: [mixs.vocab:MIGS_plant_lib_vector](https://w3id.org/mixs/vocab/MIGS_plant_lib_vector) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_nucl_acid_amp.md b/mixs6/MIGS_plant_nucl_acid_amp.md new file mode 100644 index 00000000..ceb8ceb1 --- /dev/null +++ b/mixs6/MIGS_plant_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_plant_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_plant_nucl_acid_amp) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_nucl_acid_ext.md b/mixs6/MIGS_plant_nucl_acid_ext.md new file mode 100644 index 00000000..0a15a1ff --- /dev/null +++ b/mixs6/MIGS_plant_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_plant_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_plant_nucl_acid_ext) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_number_contig.md b/mixs6/MIGS_plant_number_contig.md new file mode 100644 index 00000000..e6d8bceb --- /dev/null +++ b/mixs6/MIGS_plant_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_number_contig + + + + +URI: [mixs.vocab:MIGS_plant_number_contig](https://w3id.org/mixs/vocab/MIGS_plant_number_contig) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_project_name.md b/mixs6/MIGS_plant_project_name.md new file mode 100644 index 00000000..66133a7c --- /dev/null +++ b/mixs6/MIGS_plant_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_project_name + + + + +URI: [mixs.vocab:MIGS_plant_project_name](https://w3id.org/mixs/vocab/MIGS_plant_project_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_propagation.md b/mixs6/MIGS_plant_propagation.md new file mode 100644 index 00000000..e7014b7a --- /dev/null +++ b/mixs6/MIGS_plant_propagation.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_propagation + + + + +URI: [mixs.vocab:MIGS_plant_propagation](https://w3id.org/mixs/vocab/MIGS_plant_propagation) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_ref_biomaterial.md b/mixs6/MIGS_plant_ref_biomaterial.md new file mode 100644 index 00000000..762537d4 --- /dev/null +++ b/mixs6/MIGS_plant_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_plant_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_plant_ref_biomaterial) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_ref_db.md b/mixs6/MIGS_plant_ref_db.md new file mode 100644 index 00000000..817da0d8 --- /dev/null +++ b/mixs6/MIGS_plant_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_ref_db + + + + +URI: [mixs.vocab:MIGS_plant_ref_db](https://w3id.org/mixs/vocab/MIGS_plant_ref_db) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_samp_collect_device.md b/mixs6/MIGS_plant_samp_collect_device.md new file mode 100644 index 00000000..bc4a1ab6 --- /dev/null +++ b/mixs6/MIGS_plant_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_samp_collect_device + + + + +URI: [mixs.vocab:MIGS_plant_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_plant_samp_collect_device) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_samp_mat_process.md b/mixs6/MIGS_plant_samp_mat_process.md new file mode 100644 index 00000000..d7f7bb5f --- /dev/null +++ b/mixs6/MIGS_plant_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_plant_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_plant_samp_mat_process) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_samp_size.md b/mixs6/MIGS_plant_samp_size.md new file mode 100644 index 00000000..6a08be13 --- /dev/null +++ b/mixs6/MIGS_plant_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_samp_size + + + + +URI: [mixs.vocab:MIGS_plant_samp_size](https://w3id.org/mixs/vocab/MIGS_plant_samp_size) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sample_name.md b/mixs6/MIGS_plant_sample_name.md new file mode 100644 index 00000000..b0389a89 --- /dev/null +++ b/mixs6/MIGS_plant_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sample_name + + + + +URI: [mixs.vocab:MIGS_plant_sample_name](https://w3id.org/mixs/vocab/MIGS_plant_sample_name) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_seq_meth.md b/mixs6/MIGS_plant_seq_meth.md new file mode 100644 index 00000000..8588e681 --- /dev/null +++ b/mixs6/MIGS_plant_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_seq_meth + + + + +URI: [mixs.vocab:MIGS_plant_seq_meth](https://w3id.org/mixs/vocab/MIGS_plant_seq_meth) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sim_search_meth.md b/mixs6/MIGS_plant_sim_search_meth.md new file mode 100644 index 00000000..de0f4f75 --- /dev/null +++ b/mixs6/MIGS_plant_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_plant_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_plant_sim_search_meth) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sop.md b/mixs6/MIGS_plant_sop.md new file mode 100644 index 00000000..b64e28c5 --- /dev/null +++ b/mixs6/MIGS_plant_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_sop + + + + +URI: [mixs.vocab:MIGS_plant_sop](https://w3id.org/mixs/vocab/MIGS_plant_sop) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_source_mat_id.md b/mixs6/MIGS_plant_source_mat_id.md new file mode 100644 index 00000000..be275e0a --- /dev/null +++ b/mixs6/MIGS_plant_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_source_mat_id + + + + +URI: [mixs.vocab:MIGS_plant_source_mat_id](https://w3id.org/mixs/vocab/MIGS_plant_source_mat_id) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_specific_host.md b/mixs6/MIGS_plant_specific_host.md new file mode 100644 index 00000000..2668f9b3 --- /dev/null +++ b/mixs6/MIGS_plant_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_specific_host + + + + +URI: [mixs.vocab:MIGS_plant_specific_host](https://w3id.org/mixs/vocab/MIGS_plant_specific_host) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_submitted_to_insdc.md b/mixs6/MIGS_plant_submitted_to_insdc.md new file mode 100644 index 00000000..80dc3910 --- /dev/null +++ b/mixs6/MIGS_plant_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_plant_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_plant_submitted_to_insdc) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_subspecf_gen_lin.md b/mixs6/MIGS_plant_subspecf_gen_lin.md new file mode 100644 index 00000000..917376da --- /dev/null +++ b/mixs6/MIGS_plant_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_plant_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_plant_subspecf_gen_lin) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_tax_class.md b/mixs6/MIGS_plant_tax_class.md new file mode 100644 index 00000000..fdd028f7 --- /dev/null +++ b/mixs6/MIGS_plant_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_tax_class + + + + +URI: [mixs.vocab:MIGS_plant_tax_class](https://w3id.org/mixs/vocab/MIGS_plant_tax_class) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_tax_ident.md b/mixs6/MIGS_plant_tax_ident.md new file mode 100644 index 00000000..b248a803 --- /dev/null +++ b/mixs6/MIGS_plant_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_tax_ident + + + + +URI: [mixs.vocab:MIGS_plant_tax_ident](https://w3id.org/mixs/vocab/MIGS_plant_tax_ident) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_plant_url.md b/mixs6/MIGS_plant_url.md new file mode 100644 index 00000000..3319deb6 --- /dev/null +++ b/mixs6/MIGS_plant_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_plant_url + + + + +URI: [mixs.vocab:MIGS_plant_url](https://w3id.org/mixs/vocab/MIGS_plant_url) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_adapters.md b/mixs6/MIGS_virus_adapters.md new file mode 100644 index 00000000..3af4bb77 --- /dev/null +++ b/mixs6/MIGS_virus_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_adapters + + + + +URI: [mixs.vocab:MIGS_virus_adapters](https://w3id.org/mixs/vocab/MIGS_virus_adapters) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_annot.md b/mixs6/MIGS_virus_annot.md new file mode 100644 index 00000000..83ddd3ec --- /dev/null +++ b/mixs6/MIGS_virus_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_annot + + + + +URI: [mixs.vocab:MIGS_virus_annot](https://w3id.org/mixs/vocab/MIGS_virus_annot) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_assembly_name.md b/mixs6/MIGS_virus_assembly_name.md new file mode 100644 index 00000000..a1fbc0f7 --- /dev/null +++ b/mixs6/MIGS_virus_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_assembly_name + + + + +URI: [mixs.vocab:MIGS_virus_assembly_name](https://w3id.org/mixs/vocab/MIGS_virus_assembly_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_assembly_qual.md b/mixs6/MIGS_virus_assembly_qual.md new file mode 100644 index 00000000..076e135b --- /dev/null +++ b/mixs6/MIGS_virus_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_assembly_qual + + + + +URI: [mixs.vocab:MIGS_virus_assembly_qual](https://w3id.org/mixs/vocab/MIGS_virus_assembly_qual) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_assembly_software.md b/mixs6/MIGS_virus_assembly_software.md new file mode 100644 index 00000000..d3cb98a2 --- /dev/null +++ b/mixs6/MIGS_virus_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_assembly_software + + + + +URI: [mixs.vocab:MIGS_virus_assembly_software](https://w3id.org/mixs/vocab/MIGS_virus_assembly_software) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_biotic_relationship.md b/mixs6/MIGS_virus_biotic_relationship.md new file mode 100644 index 00000000..b0ab80c6 --- /dev/null +++ b/mixs6/MIGS_virus_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_biotic_relationship + + + + +URI: [mixs.vocab:MIGS_virus_biotic_relationship](https://w3id.org/mixs/vocab/MIGS_virus_biotic_relationship) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_collection_date.md b/mixs6/MIGS_virus_collection_date.md new file mode 100644 index 00000000..6d76d920 --- /dev/null +++ b/mixs6/MIGS_virus_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_collection_date + + + + +URI: [mixs.vocab:MIGS_virus_collection_date](https://w3id.org/mixs/vocab/MIGS_virus_collection_date) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_compl_score.md b/mixs6/MIGS_virus_compl_score.md new file mode 100644 index 00000000..8c26a4a7 --- /dev/null +++ b/mixs6/MIGS_virus_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_compl_score + + + + +URI: [mixs.vocab:MIGS_virus_compl_score](https://w3id.org/mixs/vocab/MIGS_virus_compl_score) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_compl_software.md b/mixs6/MIGS_virus_compl_software.md new file mode 100644 index 00000000..a25b73e0 --- /dev/null +++ b/mixs6/MIGS_virus_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_compl_software + + + + +URI: [mixs.vocab:MIGS_virus_compl_software](https://w3id.org/mixs/vocab/MIGS_virus_compl_software) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_encoded_traits.md b/mixs6/MIGS_virus_encoded_traits.md new file mode 100644 index 00000000..abea9dd2 --- /dev/null +++ b/mixs6/MIGS_virus_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_encoded_traits + + + + +URI: [mixs.vocab:MIGS_virus_encoded_traits](https://w3id.org/mixs/vocab/MIGS_virus_encoded_traits) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_env_broad_scale.md b/mixs6/MIGS_virus_env_broad_scale.md new file mode 100644 index 00000000..2f82307a --- /dev/null +++ b/mixs6/MIGS_virus_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_virus_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_virus_env_broad_scale) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_local_scale.md b/mixs6/MIGS_virus_env_local_scale.md new file mode 100644 index 00000000..6161f73f --- /dev/null +++ b/mixs6/MIGS_virus_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_local_scale + + + + +URI: [mixs.vocab:MIGS_virus_env_local_scale](https://w3id.org/mixs/vocab/MIGS_virus_env_local_scale) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_medium.md b/mixs6/MIGS_virus_env_medium.md new file mode 100644 index 00000000..04d6c460 --- /dev/null +++ b/mixs6/MIGS_virus_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_env_medium + + + + +URI: [mixs.vocab:MIGS_virus_env_medium](https://w3id.org/mixs/vocab/MIGS_virus_env_medium) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_env_package.md b/mixs6/MIGS_virus_env_package.md new file mode 100644 index 00000000..821760f5 --- /dev/null +++ b/mixs6/MIGS_virus_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_env_package + + + + +URI: [mixs.vocab:MIGS_virus_env_package](https://w3id.org/mixs/vocab/MIGS_virus_env_package) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_estimated_size.md b/mixs6/MIGS_virus_estimated_size.md new file mode 100644 index 00000000..a1dbdbe5 --- /dev/null +++ b/mixs6/MIGS_virus_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_estimated_size + + + + +URI: [mixs.vocab:MIGS_virus_estimated_size](https://w3id.org/mixs/vocab/MIGS_virus_estimated_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_experimental_factor.md b/mixs6/MIGS_virus_experimental_factor.md new file mode 100644 index 00000000..e4fe55c9 --- /dev/null +++ b/mixs6/MIGS_virus_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_experimental_factor + + + + +URI: [mixs.vocab:MIGS_virus_experimental_factor](https://w3id.org/mixs/vocab/MIGS_virus_experimental_factor) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_feat_pred.md b/mixs6/MIGS_virus_feat_pred.md new file mode 100644 index 00000000..efe080e6 --- /dev/null +++ b/mixs6/MIGS_virus_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_feat_pred + + + + +URI: [mixs.vocab:MIGS_virus_feat_pred](https://w3id.org/mixs/vocab/MIGS_virus_feat_pred) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_geo_loc_name.md b/mixs6/MIGS_virus_geo_loc_name.md new file mode 100644 index 00000000..1a2b6e8e --- /dev/null +++ b/mixs6/MIGS_virus_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_virus_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_virus_geo_loc_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_health_disease_stat.md b/mixs6/MIGS_virus_health_disease_stat.md new file mode 100644 index 00000000..bb108f40 --- /dev/null +++ b/mixs6/MIGS_virus_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_health_disease_stat + + + + +URI: [mixs.vocab:MIGS_virus_health_disease_stat](https://w3id.org/mixs/vocab/MIGS_virus_health_disease_stat) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_host_spec_range.md b/mixs6/MIGS_virus_host_spec_range.md new file mode 100644 index 00000000..937559d3 --- /dev/null +++ b/mixs6/MIGS_virus_host_spec_range.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_host_spec_range + + + + +URI: [mixs.vocab:MIGS_virus_host_spec_range](https://w3id.org/mixs/vocab/MIGS_virus_host_spec_range) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_investigation_type.md b/mixs6/MIGS_virus_investigation_type.md new file mode 100644 index 00000000..d3b016f3 --- /dev/null +++ b/mixs6/MIGS_virus_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_investigation_type + + + + +URI: [mixs.vocab:MIGS_virus_investigation_type](https://w3id.org/mixs/vocab/MIGS_virus_investigation_type) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_isol_growth_condt.md b/mixs6/MIGS_virus_isol_growth_condt.md new file mode 100644 index 00000000..03339b2a --- /dev/null +++ b/mixs6/MIGS_virus_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_virus_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_virus_isol_growth_condt) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lat_lon.md b/mixs6/MIGS_virus_lat_lon.md new file mode 100644 index 00000000..b365a499 --- /dev/null +++ b/mixs6/MIGS_virus_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_virus_lat_lon + + + + +URI: [mixs.vocab:MIGS_virus_lat_lon](https://w3id.org/mixs/vocab/MIGS_virus_lat_lon) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_layout.md b/mixs6/MIGS_virus_lib_layout.md new file mode 100644 index 00000000..1a5dacdd --- /dev/null +++ b/mixs6/MIGS_virus_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_layout + + + + +URI: [mixs.vocab:MIGS_virus_lib_layout](https://w3id.org/mixs/vocab/MIGS_virus_lib_layout) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_reads_seqd.md b/mixs6/MIGS_virus_lib_reads_seqd.md new file mode 100644 index 00000000..c8d802d5 --- /dev/null +++ b/mixs6/MIGS_virus_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_virus_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_virus_lib_reads_seqd) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_screen.md b/mixs6/MIGS_virus_lib_screen.md new file mode 100644 index 00000000..124909fa --- /dev/null +++ b/mixs6/MIGS_virus_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_screen + + + + +URI: [mixs.vocab:MIGS_virus_lib_screen](https://w3id.org/mixs/vocab/MIGS_virus_lib_screen) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_size.md b/mixs6/MIGS_virus_lib_size.md new file mode 100644 index 00000000..bf19fdce --- /dev/null +++ b/mixs6/MIGS_virus_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_size + + + + +URI: [mixs.vocab:MIGS_virus_lib_size](https://w3id.org/mixs/vocab/MIGS_virus_lib_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_lib_vector.md b/mixs6/MIGS_virus_lib_vector.md new file mode 100644 index 00000000..3b23e00e --- /dev/null +++ b/mixs6/MIGS_virus_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_lib_vector + + + + +URI: [mixs.vocab:MIGS_virus_lib_vector](https://w3id.org/mixs/vocab/MIGS_virus_lib_vector) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_nucl_acid_amp.md b/mixs6/MIGS_virus_nucl_acid_amp.md new file mode 100644 index 00000000..efee8686 --- /dev/null +++ b/mixs6/MIGS_virus_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_virus_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_virus_nucl_acid_amp) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_nucl_acid_ext.md b/mixs6/MIGS_virus_nucl_acid_ext.md new file mode 100644 index 00000000..e47ef973 --- /dev/null +++ b/mixs6/MIGS_virus_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_virus_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_virus_nucl_acid_ext) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_num_replicons.md b/mixs6/MIGS_virus_num_replicons.md new file mode 100644 index 00000000..36003fc3 --- /dev/null +++ b/mixs6/MIGS_virus_num_replicons.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_num_replicons + + + + +URI: [mixs.vocab:MIGS_virus_num_replicons](https://w3id.org/mixs/vocab/MIGS_virus_num_replicons) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_number_contig.md b/mixs6/MIGS_virus_number_contig.md new file mode 100644 index 00000000..5b343998 --- /dev/null +++ b/mixs6/MIGS_virus_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_number_contig + + + + +URI: [mixs.vocab:MIGS_virus_number_contig](https://w3id.org/mixs/vocab/MIGS_virus_number_contig) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_pathogenicity.md b/mixs6/MIGS_virus_pathogenicity.md new file mode 100644 index 00000000..c030db33 --- /dev/null +++ b/mixs6/MIGS_virus_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_pathogenicity + + + + +URI: [mixs.vocab:MIGS_virus_pathogenicity](https://w3id.org/mixs/vocab/MIGS_virus_pathogenicity) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_project_name.md b/mixs6/MIGS_virus_project_name.md new file mode 100644 index 00000000..b09e6204 --- /dev/null +++ b/mixs6/MIGS_virus_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_project_name + + + + +URI: [mixs.vocab:MIGS_virus_project_name](https://w3id.org/mixs/vocab/MIGS_virus_project_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_propagation.md b/mixs6/MIGS_virus_propagation.md new file mode 100644 index 00000000..feb5d620 --- /dev/null +++ b/mixs6/MIGS_virus_propagation.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_propagation + + + + +URI: [mixs.vocab:MIGS_virus_propagation](https://w3id.org/mixs/vocab/MIGS_virus_propagation) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_ref_biomaterial.md b/mixs6/MIGS_virus_ref_biomaterial.md new file mode 100644 index 00000000..e9923aa7 --- /dev/null +++ b/mixs6/MIGS_virus_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_virus_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_virus_ref_biomaterial) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_ref_db.md b/mixs6/MIGS_virus_ref_db.md new file mode 100644 index 00000000..294be230 --- /dev/null +++ b/mixs6/MIGS_virus_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_ref_db + + + + +URI: [mixs.vocab:MIGS_virus_ref_db](https://w3id.org/mixs/vocab/MIGS_virus_ref_db) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_samp_collect_device.md b/mixs6/MIGS_virus_samp_collect_device.md new file mode 100644 index 00000000..2cd087b8 --- /dev/null +++ b/mixs6/MIGS_virus_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_samp_collect_device + + + + +URI: [mixs.vocab:MIGS_virus_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_virus_samp_collect_device) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_samp_mat_process.md b/mixs6/MIGS_virus_samp_mat_process.md new file mode 100644 index 00000000..824b26cd --- /dev/null +++ b/mixs6/MIGS_virus_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_virus_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_virus_samp_mat_process) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_samp_size.md b/mixs6/MIGS_virus_samp_size.md new file mode 100644 index 00000000..063c0a84 --- /dev/null +++ b/mixs6/MIGS_virus_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_samp_size + + + + +URI: [mixs.vocab:MIGS_virus_samp_size](https://w3id.org/mixs/vocab/MIGS_virus_samp_size) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sample_name.md b/mixs6/MIGS_virus_sample_name.md new file mode 100644 index 00000000..2072300e --- /dev/null +++ b/mixs6/MIGS_virus_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sample_name + + + + +URI: [mixs.vocab:MIGS_virus_sample_name](https://w3id.org/mixs/vocab/MIGS_virus_sample_name) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_seq_meth.md b/mixs6/MIGS_virus_seq_meth.md new file mode 100644 index 00000000..12a54f20 --- /dev/null +++ b/mixs6/MIGS_virus_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_seq_meth + + + + +URI: [mixs.vocab:MIGS_virus_seq_meth](https://w3id.org/mixs/vocab/MIGS_virus_seq_meth) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sim_search_meth.md b/mixs6/MIGS_virus_sim_search_meth.md new file mode 100644 index 00000000..7cedab79 --- /dev/null +++ b/mixs6/MIGS_virus_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_virus_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_virus_sim_search_meth) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sop.md b/mixs6/MIGS_virus_sop.md new file mode 100644 index 00000000..b2833d26 --- /dev/null +++ b/mixs6/MIGS_virus_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_sop + + + + +URI: [mixs.vocab:MIGS_virus_sop](https://w3id.org/mixs/vocab/MIGS_virus_sop) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_source_mat_id.md b/mixs6/MIGS_virus_source_mat_id.md new file mode 100644 index 00000000..1c6ae3e1 --- /dev/null +++ b/mixs6/MIGS_virus_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_source_mat_id + + + + +URI: [mixs.vocab:MIGS_virus_source_mat_id](https://w3id.org/mixs/vocab/MIGS_virus_source_mat_id) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_specific_host.md b/mixs6/MIGS_virus_specific_host.md new file mode 100644 index 00000000..a6f23215 --- /dev/null +++ b/mixs6/MIGS_virus_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_specific_host + + + + +URI: [mixs.vocab:MIGS_virus_specific_host](https://w3id.org/mixs/vocab/MIGS_virus_specific_host) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_submitted_to_insdc.md b/mixs6/MIGS_virus_submitted_to_insdc.md new file mode 100644 index 00000000..a7018b35 --- /dev/null +++ b/mixs6/MIGS_virus_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_virus_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_virus_submitted_to_insdc) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_subspecf_gen_lin.md b/mixs6/MIGS_virus_subspecf_gen_lin.md new file mode 100644 index 00000000..c31ace14 --- /dev/null +++ b/mixs6/MIGS_virus_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_virus_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_virus_subspecf_gen_lin) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_tax_class.md b/mixs6/MIGS_virus_tax_class.md new file mode 100644 index 00000000..acbdd246 --- /dev/null +++ b/mixs6/MIGS_virus_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_tax_class + + + + +URI: [mixs.vocab:MIGS_virus_tax_class](https://w3id.org/mixs/vocab/MIGS_virus_tax_class) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_tax_ident.md b/mixs6/MIGS_virus_tax_ident.md new file mode 100644 index 00000000..b7e9d7cb --- /dev/null +++ b/mixs6/MIGS_virus_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_tax_ident + + + + +URI: [mixs.vocab:MIGS_virus_tax_ident](https://w3id.org/mixs/vocab/MIGS_virus_tax_ident) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_url.md b/mixs6/MIGS_virus_url.md new file mode 100644 index 00000000..8eacf6b3 --- /dev/null +++ b/mixs6/MIGS_virus_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_url + + + + +URI: [mixs.vocab:MIGS_virus_url](https://w3id.org/mixs/vocab/MIGS_virus_url) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGS_virus_virus_enrich_appr.md b/mixs6/MIGS_virus_virus_enrich_appr.md new file mode 100644 index 00000000..2452475a --- /dev/null +++ b/mixs6/MIGS_virus_virus_enrich_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_virus_virus_enrich_appr + + + + +URI: [mixs.vocab:MIGS_virus_virus_enrich_appr](https://w3id.org/mixs/vocab/MIGS_virus_virus_enrich_appr) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT + +## Parents + + * is_a: [virus_enrich_appr](virus_enrich_appr.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKSSpecimen.md b/mixs6/MIMARKSSpecimen.md new file mode 100644 index 00000000..c8beab73 --- /dev/null +++ b/mixs6/MIMARKSSpecimen.md @@ -0,0 +1,120 @@ + +# Class: MIMARKSSpecimen + + +Minimal Information about a Marker Specimen: specimen + +URI: [mixs.vocab:MIMARKSSpecimen](https://w3id.org/mixs/vocab/MIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SoilMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SedimentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-skinMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-oralMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-gutMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Host-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[AirMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[WaterMIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen],[SoilMIMARKSSpecimen],[SedimentMIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen],[Human-skinMIMARKSSpecimen],[Human-oralMIMARKSSpecimen],[Human-gutMIMARKSSpecimen],[Human-associatedMIMARKSSpecimen],[Host-associatedMIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen],[AirMIMARKSSpecimen]) + +## Mixin for + + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMARKS.specimen | + diff --git a/mixs6/MIMARKSSurvey.md b/mixs6/MIMARKSSurvey.md new file mode 100644 index 00000000..d751e522 --- /dev/null +++ b/mixs6/MIMARKSSurvey.md @@ -0,0 +1,112 @@ + +# Class: MIMARKSSurvey + + +Minimal Information about a Marker Specimen: survey + +URI: [mixs.vocab:MIMARKSSurvey](https://w3id.org/mixs/vocab/MIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SoilMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SedimentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Plant-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-vaginalMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-skinMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-oralMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-gutMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Host-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[AirMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[WaterMIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey],[SoilMIMARKSSurvey],[SedimentMIMARKSSurvey],[Plant-associatedMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey],[Human-vaginalMIMARKSSurvey],[Human-skinMIMARKSSurvey],[Human-oralMIMARKSSurvey],[Human-gutMIMARKSSurvey],[Human-associatedMIMARKSSurvey],[Host-associatedMIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey],[AirMIMARKSSurvey]) + +## Mixin for + + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) (mixin) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + +## Referenced by class + + +## Attributes + + +### Own + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMARKS.survey | + diff --git a/mixs6/MIMARKS_specimen_adapters.md b/mixs6/MIMARKS_specimen_adapters.md new file mode 100644 index 00000000..a713e106 --- /dev/null +++ b/mixs6/MIMARKS_specimen_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_adapters + + + + +URI: [mixs.vocab:MIMARKS_specimen_adapters](https://w3id.org/mixs/vocab/MIMARKS_specimen_adapters) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_assembly_software.md b/mixs6/MIMARKS_specimen_assembly_software.md new file mode 100644 index 00000000..88896b68 --- /dev/null +++ b/mixs6/MIMARKS_specimen_assembly_software.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_assembly_software + + + + +URI: [mixs.vocab:MIMARKS_specimen_assembly_software](https://w3id.org/mixs/vocab/MIMARKS_specimen_assembly_software) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_chimera_check.md b/mixs6/MIMARKS_specimen_chimera_check.md new file mode 100644 index 00000000..26915f53 --- /dev/null +++ b/mixs6/MIMARKS_specimen_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_chimera_check + + + + +URI: [mixs.vocab:MIMARKS_specimen_chimera_check](https://w3id.org/mixs/vocab/MIMARKS_specimen_chimera_check) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_collection_date.md b/mixs6/MIMARKS_specimen_collection_date.md new file mode 100644 index 00000000..a56c3488 --- /dev/null +++ b/mixs6/MIMARKS_specimen_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_collection_date + + + + +URI: [mixs.vocab:MIMARKS_specimen_collection_date](https://w3id.org/mixs/vocab/MIMARKS_specimen_collection_date) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_broad_scale.md b/mixs6/MIMARKS_specimen_env_broad_scale.md new file mode 100644 index 00000000..b7c81d27 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_broad_scale + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_broad_scale](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_broad_scale) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_local_scale.md b/mixs6/MIMARKS_specimen_env_local_scale.md new file mode 100644 index 00000000..523f9db4 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_local_scale + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_local_scale](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_local_scale) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_medium.md b/mixs6/MIMARKS_specimen_env_medium.md new file mode 100644 index 00000000..c54c5057 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_env_medium + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_medium](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_medium) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_env_package.md b/mixs6/MIMARKS_specimen_env_package.md new file mode 100644 index 00000000..c101ddb9 --- /dev/null +++ b/mixs6/MIMARKS_specimen_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_env_package + + + + +URI: [mixs.vocab:MIMARKS_specimen_env_package](https://w3id.org/mixs/vocab/MIMARKS_specimen_env_package) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_experimental_factor.md b/mixs6/MIMARKS_specimen_experimental_factor.md new file mode 100644 index 00000000..300e708e --- /dev/null +++ b/mixs6/MIMARKS_specimen_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_experimental_factor + + + + +URI: [mixs.vocab:MIMARKS_specimen_experimental_factor](https://w3id.org/mixs/vocab/MIMARKS_specimen_experimental_factor) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_geo_loc_name.md b/mixs6/MIMARKS_specimen_geo_loc_name.md new file mode 100644 index 00000000..950adeef --- /dev/null +++ b/mixs6/MIMARKS_specimen_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_geo_loc_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_geo_loc_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_geo_loc_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_investigation_type.md b/mixs6/MIMARKS_specimen_investigation_type.md new file mode 100644 index 00000000..5a407c8c --- /dev/null +++ b/mixs6/MIMARKS_specimen_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_investigation_type + + + + +URI: [mixs.vocab:MIMARKS_specimen_investigation_type](https://w3id.org/mixs/vocab/MIMARKS_specimen_investigation_type) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_lat_lon.md b/mixs6/MIMARKS_specimen_lat_lon.md new file mode 100644 index 00000000..f764eb41 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_specimen_lat_lon + + + + +URI: [mixs.vocab:MIMARKS_specimen_lat_lon](https://w3id.org/mixs/vocab/MIMARKS_specimen_lat_lon) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_lib_layout.md b/mixs6/MIMARKS_specimen_lib_layout.md new file mode 100644 index 00000000..060caaf4 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_layout + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_layout](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_layout) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_reads_seqd.md b/mixs6/MIMARKS_specimen_lib_reads_seqd.md new file mode 100644 index 00000000..2ddfc09e --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_reads_seqd + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_reads_seqd](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_reads_seqd) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_screen.md b/mixs6/MIMARKS_specimen_lib_screen.md new file mode 100644 index 00000000..97827fa7 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_screen + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_screen](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_screen) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_size.md b/mixs6/MIMARKS_specimen_lib_size.md new file mode 100644 index 00000000..69a117c9 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_size + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_size](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_size) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_lib_vector.md b/mixs6/MIMARKS_specimen_lib_vector.md new file mode 100644 index 00000000..a021f543 --- /dev/null +++ b/mixs6/MIMARKS_specimen_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_lib_vector + + + + +URI: [mixs.vocab:MIMARKS_specimen_lib_vector](https://w3id.org/mixs/vocab/MIMARKS_specimen_lib_vector) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_mid.md b/mixs6/MIMARKS_specimen_mid.md new file mode 100644 index 00000000..8f3305fe --- /dev/null +++ b/mixs6/MIMARKS_specimen_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_mid + + + + +URI: [mixs.vocab:MIMARKS_specimen_mid](https://w3id.org/mixs/vocab/MIMARKS_specimen_mid) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_nucl_acid_amp.md b/mixs6/MIMARKS_specimen_nucl_acid_amp.md new file mode 100644 index 00000000..6e4c13c6 --- /dev/null +++ b/mixs6/MIMARKS_specimen_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMARKS_specimen_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMARKS_specimen_nucl_acid_amp) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_nucl_acid_ext.md b/mixs6/MIMARKS_specimen_nucl_acid_ext.md new file mode 100644 index 00000000..071bc984 --- /dev/null +++ b/mixs6/MIMARKS_specimen_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMARKS_specimen_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMARKS_specimen_nucl_acid_ext) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_pcr_cond.md b/mixs6/MIMARKS_specimen_pcr_cond.md new file mode 100644 index 00000000..cb5665e0 --- /dev/null +++ b/mixs6/MIMARKS_specimen_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_pcr_cond + + + + +URI: [mixs.vocab:MIMARKS_specimen_pcr_cond](https://w3id.org/mixs/vocab/MIMARKS_specimen_pcr_cond) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_pcr_primers.md b/mixs6/MIMARKS_specimen_pcr_primers.md new file mode 100644 index 00000000..5d380eac --- /dev/null +++ b/mixs6/MIMARKS_specimen_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_pcr_primers + + + + +URI: [mixs.vocab:MIMARKS_specimen_pcr_primers](https://w3id.org/mixs/vocab/MIMARKS_specimen_pcr_primers) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_project_name.md b/mixs6/MIMARKS_specimen_project_name.md new file mode 100644 index 00000000..51f918f2 --- /dev/null +++ b/mixs6/MIMARKS_specimen_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_project_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_project_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_project_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_rel_to_oxygen.md b/mixs6/MIMARKS_specimen_rel_to_oxygen.md new file mode 100644 index 00000000..2a820aa3 --- /dev/null +++ b/mixs6/MIMARKS_specimen_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMARKS_specimen_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMARKS_specimen_rel_to_oxygen) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_samp_collect_device.md b/mixs6/MIMARKS_specimen_samp_collect_device.md new file mode 100644 index 00000000..27485d9b --- /dev/null +++ b/mixs6/MIMARKS_specimen_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_samp_collect_device + + + + +URI: [mixs.vocab:MIMARKS_specimen_samp_collect_device](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_collect_device) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_samp_mat_process.md b/mixs6/MIMARKS_specimen_samp_mat_process.md new file mode 100644 index 00000000..54438c74 --- /dev/null +++ b/mixs6/MIMARKS_specimen_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_samp_mat_process + + + + +URI: [mixs.vocab:MIMARKS_specimen_samp_mat_process](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_mat_process) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_samp_size.md b/mixs6/MIMARKS_specimen_samp_size.md new file mode 100644 index 00000000..6f0635fe --- /dev/null +++ b/mixs6/MIMARKS_specimen_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_samp_size + + + + +URI: [mixs.vocab:MIMARKS_specimen_samp_size](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_size) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_sample_name.md b/mixs6/MIMARKS_specimen_sample_name.md new file mode 100644 index 00000000..f6c48943 --- /dev/null +++ b/mixs6/MIMARKS_specimen_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_sample_name + + + + +URI: [mixs.vocab:MIMARKS_specimen_sample_name](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_name) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_seq_meth.md b/mixs6/MIMARKS_specimen_seq_meth.md new file mode 100644 index 00000000..9dea6c77 --- /dev/null +++ b/mixs6/MIMARKS_specimen_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_seq_meth + + + + +URI: [mixs.vocab:MIMARKS_specimen_seq_meth](https://w3id.org/mixs/vocab/MIMARKS_specimen_seq_meth) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_seq_quality_check.md b/mixs6/MIMARKS_specimen_seq_quality_check.md new file mode 100644 index 00000000..7858d202 --- /dev/null +++ b/mixs6/MIMARKS_specimen_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_seq_quality_check + + + + +URI: [mixs.vocab:MIMARKS_specimen_seq_quality_check](https://w3id.org/mixs/vocab/MIMARKS_specimen_seq_quality_check) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_size_frac.md b/mixs6/MIMARKS_specimen_size_frac.md new file mode 100644 index 00000000..08816f8c --- /dev/null +++ b/mixs6/MIMARKS_specimen_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_size_frac + + + + +URI: [mixs.vocab:MIMARKS_specimen_size_frac](https://w3id.org/mixs/vocab/MIMARKS_specimen_size_frac) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_sop.md b/mixs6/MIMARKS_specimen_sop.md new file mode 100644 index 00000000..a0a924d0 --- /dev/null +++ b/mixs6/MIMARKS_specimen_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_sop + + + + +URI: [mixs.vocab:MIMARKS_specimen_sop](https://w3id.org/mixs/vocab/MIMARKS_specimen_sop) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_source_mat_id.md b/mixs6/MIMARKS_specimen_source_mat_id.md new file mode 100644 index 00000000..db142343 --- /dev/null +++ b/mixs6/MIMARKS_specimen_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_source_mat_id + + + + +URI: [mixs.vocab:MIMARKS_specimen_source_mat_id](https://w3id.org/mixs/vocab/MIMARKS_specimen_source_mat_id) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_submitted_to_insdc.md b/mixs6/MIMARKS_specimen_submitted_to_insdc.md new file mode 100644 index 00000000..563e452f --- /dev/null +++ b/mixs6/MIMARKS_specimen_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMARKS_specimen_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMARKS_specimen_submitted_to_insdc) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_target_gene.md b/mixs6/MIMARKS_specimen_target_gene.md new file mode 100644 index 00000000..b016be2f --- /dev/null +++ b/mixs6/MIMARKS_specimen_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_specimen_target_gene + + + + +URI: [mixs.vocab:MIMARKS_specimen_target_gene](https://w3id.org/mixs/vocab/MIMARKS_specimen_target_gene) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) diff --git a/mixs6/MIMARKS_specimen_target_subfragment.md b/mixs6/MIMARKS_specimen_target_subfragment.md new file mode 100644 index 00000000..e11cc820 --- /dev/null +++ b/mixs6/MIMARKS_specimen_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_target_subfragment + + + + +URI: [mixs.vocab:MIMARKS_specimen_target_subfragment](https://w3id.org/mixs/vocab/MIMARKS_specimen_target_subfragment) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_url.md b/mixs6/MIMARKS_specimen_url.md new file mode 100644 index 00000000..dbe54533 --- /dev/null +++ b/mixs6/MIMARKS_specimen_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_url + + + + +URI: [mixs.vocab:MIMARKS_specimen_url](https://w3id.org/mixs/vocab/MIMARKS_specimen_url) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_biotic_relationship.md b/mixs6/MIMARKS_survey_biotic_relationship.md new file mode 100644 index 00000000..0febaad8 --- /dev/null +++ b/mixs6/MIMARKS_survey_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_biotic_relationship + + + + +URI: [mixs.vocab:MIMARKS_survey_biotic_relationship](https://w3id.org/mixs/vocab/MIMARKS_survey_biotic_relationship) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_chimera_check.md b/mixs6/MIMARKS_survey_chimera_check.md new file mode 100644 index 00000000..f6092ed8 --- /dev/null +++ b/mixs6/MIMARKS_survey_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_chimera_check + + + + +URI: [mixs.vocab:MIMARKS_survey_chimera_check](https://w3id.org/mixs/vocab/MIMARKS_survey_chimera_check) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_collection_date.md b/mixs6/MIMARKS_survey_collection_date.md new file mode 100644 index 00000000..ec191cac --- /dev/null +++ b/mixs6/MIMARKS_survey_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_collection_date + + + + +URI: [mixs.vocab:MIMARKS_survey_collection_date](https://w3id.org/mixs/vocab/MIMARKS_survey_collection_date) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_broad_scale.md b/mixs6/MIMARKS_survey_env_broad_scale.md new file mode 100644 index 00000000..ed5abfe3 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_broad_scale + + + + +URI: [mixs.vocab:MIMARKS_survey_env_broad_scale](https://w3id.org/mixs/vocab/MIMARKS_survey_env_broad_scale) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_local_scale.md b/mixs6/MIMARKS_survey_env_local_scale.md new file mode 100644 index 00000000..39d14057 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_local_scale + + + + +URI: [mixs.vocab:MIMARKS_survey_env_local_scale](https://w3id.org/mixs/vocab/MIMARKS_survey_env_local_scale) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_medium.md b/mixs6/MIMARKS_survey_env_medium.md new file mode 100644 index 00000000..ccf19d8f --- /dev/null +++ b/mixs6/MIMARKS_survey_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_env_medium + + + + +URI: [mixs.vocab:MIMARKS_survey_env_medium](https://w3id.org/mixs/vocab/MIMARKS_survey_env_medium) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_env_package.md b/mixs6/MIMARKS_survey_env_package.md new file mode 100644 index 00000000..8a4f6994 --- /dev/null +++ b/mixs6/MIMARKS_survey_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_env_package + + + + +URI: [mixs.vocab:MIMARKS_survey_env_package](https://w3id.org/mixs/vocab/MIMARKS_survey_env_package) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_experimental_factor.md b/mixs6/MIMARKS_survey_experimental_factor.md new file mode 100644 index 00000000..bab276a7 --- /dev/null +++ b/mixs6/MIMARKS_survey_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_experimental_factor + + + + +URI: [mixs.vocab:MIMARKS_survey_experimental_factor](https://w3id.org/mixs/vocab/MIMARKS_survey_experimental_factor) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_extrachrom_elements.md b/mixs6/MIMARKS_survey_extrachrom_elements.md new file mode 100644 index 00000000..838655ef --- /dev/null +++ b/mixs6/MIMARKS_survey_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_extrachrom_elements + + + + +URI: [mixs.vocab:MIMARKS_survey_extrachrom_elements](https://w3id.org/mixs/vocab/MIMARKS_survey_extrachrom_elements) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_geo_loc_name.md b/mixs6/MIMARKS_survey_geo_loc_name.md new file mode 100644 index 00000000..7b1527c4 --- /dev/null +++ b/mixs6/MIMARKS_survey_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_geo_loc_name + + + + +URI: [mixs.vocab:MIMARKS_survey_geo_loc_name](https://w3id.org/mixs/vocab/MIMARKS_survey_geo_loc_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_investigation_type.md b/mixs6/MIMARKS_survey_investigation_type.md new file mode 100644 index 00000000..1d7bfd38 --- /dev/null +++ b/mixs6/MIMARKS_survey_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_investigation_type + + + + +URI: [mixs.vocab:MIMARKS_survey_investigation_type](https://w3id.org/mixs/vocab/MIMARKS_survey_investigation_type) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_isol_growth_condt.md b/mixs6/MIMARKS_survey_isol_growth_condt.md new file mode 100644 index 00000000..49b2df15 --- /dev/null +++ b/mixs6/MIMARKS_survey_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_isol_growth_condt + + + + +URI: [mixs.vocab:MIMARKS_survey_isol_growth_condt](https://w3id.org/mixs/vocab/MIMARKS_survey_isol_growth_condt) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_lat_lon.md b/mixs6/MIMARKS_survey_lat_lon.md new file mode 100644 index 00000000..46d28048 --- /dev/null +++ b/mixs6/MIMARKS_survey_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMARKS_survey_lat_lon + + + + +URI: [mixs.vocab:MIMARKS_survey_lat_lon](https://w3id.org/mixs/vocab/MIMARKS_survey_lat_lon) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_nucl_acid_amp.md b/mixs6/MIMARKS_survey_nucl_acid_amp.md new file mode 100644 index 00000000..1caecc81 --- /dev/null +++ b/mixs6/MIMARKS_survey_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMARKS_survey_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMARKS_survey_nucl_acid_amp) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_nucl_acid_ext.md b/mixs6/MIMARKS_survey_nucl_acid_ext.md new file mode 100644 index 00000000..fae56842 --- /dev/null +++ b/mixs6/MIMARKS_survey_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMARKS_survey_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMARKS_survey_nucl_acid_ext) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_pcr_cond.md b/mixs6/MIMARKS_survey_pcr_cond.md new file mode 100644 index 00000000..7bb15154 --- /dev/null +++ b/mixs6/MIMARKS_survey_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_pcr_cond + + + + +URI: [mixs.vocab:MIMARKS_survey_pcr_cond](https://w3id.org/mixs/vocab/MIMARKS_survey_pcr_cond) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_pcr_primers.md b/mixs6/MIMARKS_survey_pcr_primers.md new file mode 100644 index 00000000..be85620d --- /dev/null +++ b/mixs6/MIMARKS_survey_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_pcr_primers + + + + +URI: [mixs.vocab:MIMARKS_survey_pcr_primers](https://w3id.org/mixs/vocab/MIMARKS_survey_pcr_primers) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_project_name.md b/mixs6/MIMARKS_survey_project_name.md new file mode 100644 index 00000000..9b59e331 --- /dev/null +++ b/mixs6/MIMARKS_survey_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_project_name + + + + +URI: [mixs.vocab:MIMARKS_survey_project_name](https://w3id.org/mixs/vocab/MIMARKS_survey_project_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_rel_to_oxygen.md b/mixs6/MIMARKS_survey_rel_to_oxygen.md new file mode 100644 index 00000000..d0aa8549 --- /dev/null +++ b/mixs6/MIMARKS_survey_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMARKS_survey_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMARKS_survey_rel_to_oxygen) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_samp_collect_device.md b/mixs6/MIMARKS_survey_samp_collect_device.md new file mode 100644 index 00000000..d4bae0c1 --- /dev/null +++ b/mixs6/MIMARKS_survey_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_samp_collect_device + + + + +URI: [mixs.vocab:MIMARKS_survey_samp_collect_device](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_collect_device) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_samp_mat_process.md b/mixs6/MIMARKS_survey_samp_mat_process.md new file mode 100644 index 00000000..858b9b0c --- /dev/null +++ b/mixs6/MIMARKS_survey_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_samp_mat_process + + + + +URI: [mixs.vocab:MIMARKS_survey_samp_mat_process](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_mat_process) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_samp_size.md b/mixs6/MIMARKS_survey_samp_size.md new file mode 100644 index 00000000..de41696a --- /dev/null +++ b/mixs6/MIMARKS_survey_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_samp_size + + + + +URI: [mixs.vocab:MIMARKS_survey_samp_size](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_size) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_sample_name.md b/mixs6/MIMARKS_survey_sample_name.md new file mode 100644 index 00000000..35a0b888 --- /dev/null +++ b/mixs6/MIMARKS_survey_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_sample_name + + + + +URI: [mixs.vocab:MIMARKS_survey_sample_name](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_name) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_seq_meth.md b/mixs6/MIMARKS_survey_seq_meth.md new file mode 100644 index 00000000..659551ad --- /dev/null +++ b/mixs6/MIMARKS_survey_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_seq_meth + + + + +URI: [mixs.vocab:MIMARKS_survey_seq_meth](https://w3id.org/mixs/vocab/MIMARKS_survey_seq_meth) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_seq_quality_check.md b/mixs6/MIMARKS_survey_seq_quality_check.md new file mode 100644 index 00000000..542b5528 --- /dev/null +++ b/mixs6/MIMARKS_survey_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_seq_quality_check + + + + +URI: [mixs.vocab:MIMARKS_survey_seq_quality_check](https://w3id.org/mixs/vocab/MIMARKS_survey_seq_quality_check) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_sop.md b/mixs6/MIMARKS_survey_sop.md new file mode 100644 index 00000000..b2f4940b --- /dev/null +++ b/mixs6/MIMARKS_survey_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_sop + + + + +URI: [mixs.vocab:MIMARKS_survey_sop](https://w3id.org/mixs/vocab/MIMARKS_survey_sop) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_source_mat_id.md b/mixs6/MIMARKS_survey_source_mat_id.md new file mode 100644 index 00000000..1834bf59 --- /dev/null +++ b/mixs6/MIMARKS_survey_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_source_mat_id + + + + +URI: [mixs.vocab:MIMARKS_survey_source_mat_id](https://w3id.org/mixs/vocab/MIMARKS_survey_source_mat_id) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_submitted_to_insdc.md b/mixs6/MIMARKS_survey_submitted_to_insdc.md new file mode 100644 index 00000000..0055ba23 --- /dev/null +++ b/mixs6/MIMARKS_survey_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMARKS_survey_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMARKS_survey_submitted_to_insdc) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_subspecf_gen_lin.md b/mixs6/MIMARKS_survey_subspecf_gen_lin.md new file mode 100644 index 00000000..9dc0f40b --- /dev/null +++ b/mixs6/MIMARKS_survey_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIMARKS_survey_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIMARKS_survey_subspecf_gen_lin) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_target_gene.md b/mixs6/MIMARKS_survey_target_gene.md new file mode 100644 index 00000000..f860e4f6 --- /dev/null +++ b/mixs6/MIMARKS_survey_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_target_gene + + + + +URI: [mixs.vocab:MIMARKS_survey_target_gene](https://w3id.org/mixs/vocab/MIMARKS_survey_target_gene) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_target_subfragment.md b/mixs6/MIMARKS_survey_target_subfragment.md new file mode 100644 index 00000000..47519379 --- /dev/null +++ b/mixs6/MIMARKS_survey_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_target_subfragment + + + + +URI: [mixs.vocab:MIMARKS_survey_target_subfragment](https://w3id.org/mixs/vocab/MIMARKS_survey_target_subfragment) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_trophic_level.md b/mixs6/MIMARKS_survey_trophic_level.md new file mode 100644 index 00000000..36471f6f --- /dev/null +++ b/mixs6/MIMARKS_survey_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_trophic_level + + + + +URI: [mixs.vocab:MIMARKS_survey_trophic_level](https://w3id.org/mixs/vocab/MIMARKS_survey_trophic_level) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_survey_url.md b/mixs6/MIMARKS_survey_url.md new file mode 100644 index 00000000..09130744 --- /dev/null +++ b/mixs6/MIMARKS_survey_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_survey_url + + + + +URI: [mixs.vocab:MIMARKS_survey_url](https://w3id.org/mixs/vocab/MIMARKS_survey_url) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/Me.md b/mixs6/Me.md index 71316e7a..44c25296 100644 --- a/mixs6/Me.md +++ b/mixs6/Me.md @@ -1,33 +1,33 @@ -# Class: Me +# Class: ME -me Checklist +Metagenome or Environmental -URI: [mixs.vocab:Me](https://w3id.org/mixs/vocab/Me) +URI: [mixs.vocab:ME](https://w3id.org/mixs/vocab/ME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Me],[WastewaterSludgeMe]uses%20-.->[Me],[SoilMe]uses%20-.->[Me],[SedimentMe]uses%20-.->[Me],[Plant-associatedMe]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironmentMe]uses%20-.->[Me],[MicrobialMatBiofilmMe]uses%20-.->[Me],[HydrocarbonResources-fluidsSwabsMe]uses%20-.->[Me],[HydrocarbonResources-coresMe]uses%20-.->[Me],[Human-vaginalMe]uses%20-.->[Me],[Human-skinMe]uses%20-.->[Me],[Human-oralMe]uses%20-.->[Me],[Human-gutMe]uses%20-.->[Me],[Human-associatedMe]uses%20-.->[Me],[Host-associatedMe]uses%20-.->[Me],[BuiltEnvironmentMe]uses%20-.->[Me],[AirMe]uses%20-.->[Me],[WaterMe],[WastewaterSludgeMe],[SoilMe],[SedimentMe],[Plant-associatedMe],[MiscellaneousNaturalOrArtificialEnvironmentMe],[MicrobialMatBiofilmMe],[HydrocarbonResources-fluidsSwabsMe],[HydrocarbonResources-coresMe],[Human-vaginalMe],[Human-skinMe],[Human-oralMe],[Human-gutMe],[Human-associatedMe],[Host-associatedMe],[BuiltEnvironmentMe],[AirMe]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][ME],[WastewaterSludgeME]uses%20-.->[ME],[SoilME]uses%20-.->[ME],[SedimentME]uses%20-.->[ME],[Plant-associatedME]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironmentME]uses%20-.->[ME],[MicrobialMatBiofilmME]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabsME]uses%20-.->[ME],[HydrocarbonResources-coresME]uses%20-.->[ME],[Human-vaginalME]uses%20-.->[ME],[Human-skinME]uses%20-.->[ME],[Human-oralME]uses%20-.->[ME],[Human-gutME]uses%20-.->[ME],[Human-associatedME]uses%20-.->[ME],[Host-associatedME]uses%20-.->[ME],[BuiltEnvironmentME]uses%20-.->[ME],[AirME]uses%20-.->[ME],[WaterME],[WastewaterSludgeME],[SoilME],[SedimentME],[Plant-associatedME],[MiscellaneousNaturalOrArtificialEnvironmentME],[MicrobialMatBiofilmME],[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-coresME],[Human-vaginalME],[Human-skinME],[Human-oralME],[Human-gutME],[Human-associatedME],[Host-associatedME],[BuiltEnvironmentME],[AirME]) ## Mixin for - * [AirMe](AirMe.md) (mixin) - Combinatorial checklist for air with me - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) (mixin) - Combinatorial checklist for built environment with me - * [Host-associatedMe](Host-associatedMe.md) (mixin) - Combinatorial checklist for host-associated with me - * [Human-associatedMe](Human-associatedMe.md) (mixin) - Combinatorial checklist for human-associated with me - * [Human-gutMe](Human-gutMe.md) (mixin) - Combinatorial checklist for human-gut with me - * [Human-oralMe](Human-oralMe.md) (mixin) - Combinatorial checklist for human-oral with me - * [Human-skinMe](Human-skinMe.md) (mixin) - Combinatorial checklist for human-skin with me - * [Human-vaginalMe](Human-vaginalMe.md) (mixin) - Combinatorial checklist for human-vaginal with me - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with me - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with me - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with me - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with me - * [Plant-associatedMe](Plant-associatedMe.md) (mixin) - Combinatorial checklist for plant-associated with me - * [SedimentMe](SedimentMe.md) (mixin) - Combinatorial checklist for sediment with me - * [SoilMe](SoilMe.md) (mixin) - Combinatorial checklist for soil with me - * [WastewaterSludgeMe](WastewaterSludgeMe.md) (mixin) - Combinatorial checklist for wastewater_sludge with me - * [WaterMe](WaterMe.md) (mixin) - Combinatorial checklist for water with me + * [AirME](AirME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package air + * [BuiltEnvironmentME](BuiltEnvironmentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package built environment + * [Host-associatedME](Host-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package host-associated + * [Human-associatedME](Human-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-associated + * [Human-gutME](Human-gutME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-gut + * [Human-oralME](Human-oralME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-oral + * [Human-skinME](Human-skinME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-skin + * [Human-vaginalME](Human-vaginalME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment + * [Plant-associatedME](Plant-associatedME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package plant-associated + * [SedimentME](SedimentME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package sediment + * [SoilME](SoilME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package soil + * [WastewaterSludgeME](WastewaterSludgeME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge + * [WaterME](WaterME.md) (mixin) - Combinatorial checklist Metagenome or Environmental with environmental package water ## Referenced by class @@ -37,83 +37,90 @@ URI: [mixs.vocab:Me](https://w3id.org/mixs/vocab/Me) ### Own - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) - * [me➞collection_date](me_collection_date.md) REQ + * [ME➞collection_date](ME_collection_date.md) REQ * range: [String](types/String.md) - * [me➞env_broad_scale](me_env_broad_scale.md) REQ + * [ME➞env_broad_scale](ME_env_broad_scale.md) REQ * range: [String](types/String.md) - * [me➞env_local_scale](me_env_local_scale.md) REQ + * [ME➞env_local_scale](ME_env_local_scale.md) REQ * range: [String](types/String.md) - * [me➞env_medium](me_env_medium.md) REQ + * [ME➞env_medium](ME_env_medium.md) REQ * range: [String](types/String.md) - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) - * [me➞geo_loc_name](me_geo_loc_name.md) REQ + * [ME➞geo_loc_name](ME_geo_loc_name.md) REQ * range: [String](types/String.md) - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: - * [me➞lat_lon](me_lat_lon.md) REQ + * [ME➞lat_lon](ME_lat_lon.md) REQ * range: [String](types/String.md) - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | ME | + diff --git a/mixs6/MicrobialMatBiofilm.md b/mixs6/MicrobialMatBiofilm.md index 31e94fdf..090b4aee 100644 --- a/mixs6/MicrobialMatBiofilm.md +++ b/mixs6/MicrobialMatBiofilm.md @@ -7,21 +7,21 @@ microbial mat/biofilm URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBiofilm) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilmMisag],[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilmMimag],[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilmMe],[QuantityValue][MIGSBacteria],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilm],[MIGSBacteria]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSEukaryote.md b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md new file mode 100644 index 00000000..30c7a098 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md @@ -0,0 +1,535 @@ + +# Class: MicrobialMatBiofilmMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilm],[MIGSEukaryote]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSPlant.md b/mixs6/MicrobialMatBiofilmMIGSPlant.md new file mode 100644 index 00000000..d2abc406 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSPlant.md @@ -0,0 +1,505 @@ + +# Class: MicrobialMatBiofilmMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilm],[MIGSPlant]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIGSVirus.md b/mixs6/MicrobialMatBiofilmMIGSVirus.md new file mode 100644 index 00000000..28c9b27e --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIGSVirus.md @@ -0,0 +1,530 @@ + +# Class: MicrobialMatBiofilmMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilm],[MIGSVirus]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md new file mode 100644 index 00000000..542bc844 --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md @@ -0,0 +1,455 @@ + +# Class: MicrobialMatBiofilmMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilm],[MIMARKSSpecimen]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md new file mode 100644 index 00000000..ba7a937e --- /dev/null +++ b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md @@ -0,0 +1,435 @@ + +# Class: MicrobialMatBiofilmMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + +URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilm],[MIMARKSSurvey]) + +## Parents + + * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from microbial mat_biofilm: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMe.md b/mixs6/MicrobialMatBiofilmMe.md index 8d247317..e0309f5a 100644 --- a/mixs6/MicrobialMatBiofilmMe.md +++ b/mixs6/MicrobialMatBiofilmMe.md @@ -1,13 +1,13 @@ -# Class: MicrobialMatBiofilmMe +# Class: MicrobialMatBiofilmME -Combinatorial checklist for microbial mat_biofilm with me +Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm -URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMe) +URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMatBiofilmME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Me],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMe],[MicrobialMatBiofilm],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmME],[MicrobialMatBiofilm],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -299,172 +299,172 @@ URI: [mixs.vocab:MicrobialMatBiofilmMe](https://w3id.org/mixs/vocab/MicrobialMat * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsOrg.md b/mixs6/MicrobialMatBiofilmMigsOrg.md index 592bf61a..717d86c4 100644 --- a/mixs6/MicrobialMatBiofilmMigsOrg.md +++ b/mixs6/MicrobialMatBiofilmMigsOrg.md @@ -1,13 +1,13 @@ -# Class: MicrobialMatBiofilmMigsOrg +# Class: MicrobialMatBiofilmMIGSOrg -Combinatorial checklist for microbial mat_biofilm with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm -URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsOrg) +URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsOrg],[MicrobialMatBiofilmMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsOrg],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilm],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -299,192 +299,192 @@ URI: [mixs.vocab:MicrobialMatBiofilmMigsOrg](https://w3id.org/mixs/vocab/Microbi * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimag.md b/mixs6/MicrobialMatBiofilmMimag.md index b1667bb7..6934ef85 100644 --- a/mixs6/MicrobialMatBiofilmMimag.md +++ b/mixs6/MicrobialMatBiofilmMimag.md @@ -1,13 +1,13 @@ -# Class: MicrobialMatBiofilmMimag +# Class: MicrobialMatBiofilmMIMAG -Combinatorial checklist for microbial mat_biofilm with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm -URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimag) +URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Mimag],[MicrobialMatBiofilmMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Mimag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimag],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilm],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -299,252 +299,252 @@ URI: [mixs.vocab:MicrobialMatBiofilmMimag](https://w3id.org/mixs/vocab/Microbial * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMisag.md b/mixs6/MicrobialMatBiofilmMisag.md index f331a4cc..3f34e8e1 100644 --- a/mixs6/MicrobialMatBiofilmMisag.md +++ b/mixs6/MicrobialMatBiofilmMisag.md @@ -1,13 +1,13 @@ -# Class: MicrobialMatBiofilmMisag +# Class: MicrobialMatBiofilmMISAG -Combinatorial checklist for microbial mat_biofilm with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm -URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMisag) +URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Misag],[MicrobialMatBiofilmMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Misag],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMisag],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilm],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -299,257 +299,257 @@ URI: [mixs.vocab:MicrobialMatBiofilmMisag](https://w3id.org/mixs/vocab/Microbial * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMiuvig.md b/mixs6/MicrobialMatBiofilmMiuvig.md index c90aad19..45a9dab4 100644 --- a/mixs6/MicrobialMatBiofilmMiuvig.md +++ b/mixs6/MicrobialMatBiofilmMiuvig.md @@ -1,13 +1,13 @@ -# Class: MicrobialMatBiofilmMiuvig +# Class: MicrobialMatBiofilmMIUVIG -Combinatorial checklist for microbial mat_biofilm with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm -URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMiuvig) +URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[MicrobialMatBiofilmMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Miuvig],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMiuvig],[MicrobialMatBiofilm]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilm],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -299,322 +299,322 @@ URI: [mixs.vocab:MicrobialMatBiofilmMiuvig](https://w3id.org/mixs/vocab/Microbia * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MigsOrg.md b/mixs6/MigsOrg.md index 74eee03c..0db6b760 100644 --- a/mixs6/MigsOrg.md +++ b/mixs6/MigsOrg.md @@ -1,33 +1,33 @@ -# Class: MigsOrg +# Class: MIGSOrg -migs_org Checklist +Minimal Information about a Genome Sequence: org -URI: [mixs.vocab:MigsOrg](https://w3id.org/mixs/vocab/MigsOrg) +URI: [mixs.vocab:MIGSOrg](https://w3id.org/mixs/vocab/MIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsOrg],[WastewaterSludgeMigsOrg]uses%20-.->[MigsOrg],[SoilMigsOrg]uses%20-.->[MigsOrg],[SedimentMigsOrg]uses%20-.->[MigsOrg],[Plant-associatedMigsOrg]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg]uses%20-.->[MigsOrg],[MicrobialMatBiofilmMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg]uses%20-.->[MigsOrg],[HydrocarbonResources-coresMigsOrg]uses%20-.->[MigsOrg],[Human-vaginalMigsOrg]uses%20-.->[MigsOrg],[Human-skinMigsOrg]uses%20-.->[MigsOrg],[Human-oralMigsOrg]uses%20-.->[MigsOrg],[Human-gutMigsOrg]uses%20-.->[MigsOrg],[Human-associatedMigsOrg]uses%20-.->[MigsOrg],[Host-associatedMigsOrg]uses%20-.->[MigsOrg],[BuiltEnvironmentMigsOrg]uses%20-.->[MigsOrg],[AirMigsOrg]uses%20-.->[MigsOrg],[WaterMigsOrg],[WastewaterSludgeMigsOrg],[SoilMigsOrg],[SedimentMigsOrg],[Plant-associatedMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MicrobialMatBiofilmMigsOrg],[HydrocarbonResources-fluidsSwabsMigsOrg],[HydrocarbonResources-coresMigsOrg],[Human-vaginalMigsOrg],[Human-skinMigsOrg],[Human-oralMigsOrg],[Human-gutMigsOrg],[Human-associatedMigsOrg],[Host-associatedMigsOrg],[BuiltEnvironmentMigsOrg],[AirMigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSOrg],[WastewaterSludgeMIGSOrg]uses%20-.->[MIGSOrg],[SoilMIGSOrg]uses%20-.->[MIGSOrg],[SedimentMIGSOrg]uses%20-.->[MIGSOrg],[Plant-associatedMIGSOrg]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[MicrobialMatBiofilmMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-coresMIGSOrg]uses%20-.->[MIGSOrg],[Human-vaginalMIGSOrg]uses%20-.->[MIGSOrg],[Human-skinMIGSOrg]uses%20-.->[MIGSOrg],[Human-oralMIGSOrg]uses%20-.->[MIGSOrg],[Human-gutMIGSOrg]uses%20-.->[MIGSOrg],[Human-associatedMIGSOrg]uses%20-.->[MIGSOrg],[Host-associatedMIGSOrg]uses%20-.->[MIGSOrg],[BuiltEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[AirMIGSOrg]uses%20-.->[MIGSOrg],[WaterMIGSOrg],[WastewaterSludgeMIGSOrg],[SoilMIGSOrg],[SedimentMIGSOrg],[Plant-associatedMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MicrobialMatBiofilmMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-coresMIGSOrg],[Human-vaginalMIGSOrg],[Human-skinMIGSOrg],[Human-oralMIGSOrg],[Human-gutMIGSOrg],[Human-associatedMIGSOrg],[Host-associatedMIGSOrg],[BuiltEnvironmentMIGSOrg],[AirMIGSOrg]) ## Mixin for - * [AirMigsOrg](AirMigsOrg.md) (mixin) - Combinatorial checklist for air with migs_org - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) (mixin) - Combinatorial checklist for built environment with migs_org - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) (mixin) - Combinatorial checklist for host-associated with migs_org - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) (mixin) - Combinatorial checklist for human-associated with migs_org - * [Human-gutMigsOrg](Human-gutMigsOrg.md) (mixin) - Combinatorial checklist for human-gut with migs_org - * [Human-oralMigsOrg](Human-oralMigsOrg.md) (mixin) - Combinatorial checklist for human-oral with migs_org - * [Human-skinMigsOrg](Human-skinMigsOrg.md) (mixin) - Combinatorial checklist for human-skin with migs_org - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) (mixin) - Combinatorial checklist for human-vaginal with migs_org - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_org - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_org - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_org - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) (mixin) - Combinatorial checklist for plant-associated with migs_org - * [SedimentMigsOrg](SedimentMigsOrg.md) (mixin) - Combinatorial checklist for sediment with migs_org - * [SoilMigsOrg](SoilMigsOrg.md) (mixin) - Combinatorial checklist for soil with migs_org - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_org - * [WaterMigsOrg](WaterMigsOrg.md) (mixin) - Combinatorial checklist for water with migs_org + * [AirMIGSOrg](AirMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated + * [SedimentMIGSOrg](SedimentMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment + * [SoilMIGSOrg](SoilMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge + * [WaterMIGSOrg](WaterMIGSOrg.md) (mixin) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water ## Referenced by class @@ -37,91 +37,98 @@ URI: [mixs.vocab:MigsOrg](https://w3id.org/mixs/vocab/MigsOrg) ### Own - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) - * [migs_org➞collection_date](migs_org_collection_date.md) REQ + * [MIGS org➞collection_date](MIGS_org_collection_date.md) REQ * range: [String](types/String.md) - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) - * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) REQ + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) REQ * range: [String](types/String.md) - * [migs_org➞env_local_scale](migs_org_env_local_scale.md) REQ + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) REQ * range: [String](types/String.md) - * [migs_org➞env_medium](migs_org_env_medium.md) REQ + * [MIGS org➞env_medium](MIGS_org_env_medium.md) REQ * range: [String](types/String.md) - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) - * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) REQ + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) REQ * range: [String](types/String.md) - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) - * [migs_org➞lat_lon](migs_org_lat_lon.md) REQ + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) REQ * range: [String](types/String.md) - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIGS.org | + diff --git a/mixs6/Mimag.md b/mixs6/Mimag.md index 7f0d0072..477feccd 100644 --- a/mixs6/Mimag.md +++ b/mixs6/Mimag.md @@ -1,33 +1,33 @@ -# Class: Mimag +# Class: MIMAG -mimag Checklist +Minimum Information About a Metagenome-Assembled Genome -URI: [mixs.vocab:Mimag](https://w3id.org/mixs/vocab/Mimag) +URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Mimag],[WastewaterSludgeMimag]uses%20-.->[Mimag],[SoilMimag]uses%20-.->[Mimag],[SedimentMimag]uses%20-.->[Mimag],[Plant-associatedMimag]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag]uses%20-.->[Mimag],[MicrobialMatBiofilmMimag]uses%20-.->[Mimag],[HydrocarbonResources-fluidsSwabsMimag]uses%20-.->[Mimag],[HydrocarbonResources-coresMimag]uses%20-.->[Mimag],[Human-vaginalMimag]uses%20-.->[Mimag],[Human-skinMimag]uses%20-.->[Mimag],[Human-oralMimag]uses%20-.->[Mimag],[Human-gutMimag]uses%20-.->[Mimag],[Human-associatedMimag]uses%20-.->[Mimag],[Host-associatedMimag]uses%20-.->[Mimag],[BuiltEnvironmentMimag]uses%20-.->[Mimag],[AirMimag]uses%20-.->[Mimag],[WaterMimag],[WastewaterSludgeMimag],[SoilMimag],[SedimentMimag],[Plant-associatedMimag],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MicrobialMatBiofilmMimag],[HydrocarbonResources-fluidsSwabsMimag],[HydrocarbonResources-coresMimag],[Human-vaginalMimag],[Human-skinMimag],[Human-oralMimag],[Human-gutMimag],[Human-associatedMimag],[Host-associatedMimag],[BuiltEnvironmentMimag],[AirMimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMAG],[WastewaterSludgeMIMAG]uses%20-.->[MIMAG],[SoilMIMAG]uses%20-.->[MIMAG],[SedimentMIMAG]uses%20-.->[MIMAG],[Plant-associatedMIMAG]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG]uses%20-.->[MIMAG],[MicrobialMatBiofilmMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabsMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-coresMIMAG]uses%20-.->[MIMAG],[Human-vaginalMIMAG]uses%20-.->[MIMAG],[Human-skinMIMAG]uses%20-.->[MIMAG],[Human-oralMIMAG]uses%20-.->[MIMAG],[Human-gutMIMAG]uses%20-.->[MIMAG],[Human-associatedMIMAG]uses%20-.->[MIMAG],[Host-associatedMIMAG]uses%20-.->[MIMAG],[BuiltEnvironmentMIMAG]uses%20-.->[MIMAG],[AirMIMAG]uses%20-.->[MIMAG],[WaterMIMAG],[WastewaterSludgeMIMAG],[SoilMIMAG],[SedimentMIMAG],[Plant-associatedMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MicrobialMatBiofilmMIMAG],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-coresMIMAG],[Human-vaginalMIMAG],[Human-skinMIMAG],[Human-oralMIMAG],[Human-gutMIMAG],[Human-associatedMIMAG],[Host-associatedMIMAG],[BuiltEnvironmentMIMAG],[AirMIMAG]) ## Mixin for - * [AirMimag](AirMimag.md) (mixin) - Combinatorial checklist for air with mimag - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) (mixin) - Combinatorial checklist for built environment with mimag - * [Host-associatedMimag](Host-associatedMimag.md) (mixin) - Combinatorial checklist for host-associated with mimag - * [Human-associatedMimag](Human-associatedMimag.md) (mixin) - Combinatorial checklist for human-associated with mimag - * [Human-gutMimag](Human-gutMimag.md) (mixin) - Combinatorial checklist for human-gut with mimag - * [Human-oralMimag](Human-oralMimag.md) (mixin) - Combinatorial checklist for human-oral with mimag - * [Human-skinMimag](Human-skinMimag.md) (mixin) - Combinatorial checklist for human-skin with mimag - * [Human-vaginalMimag](Human-vaginalMimag.md) (mixin) - Combinatorial checklist for human-vaginal with mimag - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimag - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimag - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimag - * [Plant-associatedMimag](Plant-associatedMimag.md) (mixin) - Combinatorial checklist for plant-associated with mimag - * [SedimentMimag](SedimentMimag.md) (mixin) - Combinatorial checklist for sediment with mimag - * [SoilMimag](SoilMimag.md) (mixin) - Combinatorial checklist for soil with mimag - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimag - * [WaterMimag](WaterMimag.md) (mixin) - Combinatorial checklist for water with mimag + * [AirMIMAG](AirMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment + * [Host-associatedMIMAG](Host-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated + * [Human-associatedMIMAG](Human-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated + * [Human-gutMIMAG](Human-gutMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut + * [Human-oralMIMAG](Human-oralMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral + * [Human-skinMIMAG](Human-skinMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated + * [SedimentMIMAG](SedimentMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment + * [SoilMIMAG](SoilMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge + * [WaterMIMAG](WaterMIMAG.md) (mixin) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water ## Referenced by class @@ -37,115 +37,122 @@ URI: [mixs.vocab:Mimag](https://w3id.org/mixs/vocab/Mimag) ### Own - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: - * [mimag➞collection_date](mimag_collection_date.md) REQ + * [MIMAG➞collection_date](MIMAG_collection_date.md) REQ * range: [String](types/String.md) - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: - * [mimag➞env_broad_scale](mimag_env_broad_scale.md) REQ + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) REQ * range: [String](types/String.md) - * [mimag➞env_local_scale](mimag_env_local_scale.md) REQ + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) REQ * range: [String](types/String.md) - * [mimag➞env_medium](mimag_env_medium.md) REQ + * [MIMAG➞env_medium](MIMAG_env_medium.md) REQ * range: [String](types/String.md) - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) - * [mimag➞geo_loc_name](mimag_geo_loc_name.md) REQ + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) REQ * range: [String](types/String.md) - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: - * [mimag➞lat_lon](mimag_lat_lon.md) REQ + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) REQ * range: [String](types/String.md) - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIMAG | + diff --git a/mixs6/Misag.md b/mixs6/Misag.md index 697d9fb3..8dafcb1e 100644 --- a/mixs6/Misag.md +++ b/mixs6/Misag.md @@ -1,33 +1,33 @@ -# Class: Misag +# Class: MISAG -misag Checklist +Minimum Information About a Single Amplified Genome -URI: [mixs.vocab:Misag](https://w3id.org/mixs/vocab/Misag) +URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Misag],[WastewaterSludgeMisag]uses%20-.->[Misag],[SoilMisag]uses%20-.->[Misag],[SedimentMisag]uses%20-.->[Misag],[Plant-associatedMisag]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironmentMisag]uses%20-.->[Misag],[MicrobialMatBiofilmMisag]uses%20-.->[Misag],[HydrocarbonResources-fluidsSwabsMisag]uses%20-.->[Misag],[HydrocarbonResources-coresMisag]uses%20-.->[Misag],[Human-vaginalMisag]uses%20-.->[Misag],[Human-skinMisag]uses%20-.->[Misag],[Human-oralMisag]uses%20-.->[Misag],[Human-gutMisag]uses%20-.->[Misag],[Human-associatedMisag]uses%20-.->[Misag],[Host-associatedMisag]uses%20-.->[Misag],[BuiltEnvironmentMisag]uses%20-.->[Misag],[AirMisag]uses%20-.->[Misag],[WaterMisag],[WastewaterSludgeMisag],[SoilMisag],[SedimentMisag],[Plant-associatedMisag],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MicrobialMatBiofilmMisag],[HydrocarbonResources-fluidsSwabsMisag],[HydrocarbonResources-coresMisag],[Human-vaginalMisag],[Human-skinMisag],[Human-oralMisag],[Human-gutMisag],[Human-associatedMisag],[Host-associatedMisag],[BuiltEnvironmentMisag],[AirMisag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MISAG],[WastewaterSludgeMISAG]uses%20-.->[MISAG],[SoilMISAG]uses%20-.->[MISAG],[SedimentMISAG]uses%20-.->[MISAG],[Plant-associatedMISAG]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG]uses%20-.->[MISAG],[MicrobialMatBiofilmMISAG]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabsMISAG]uses%20-.->[MISAG],[HydrocarbonResources-coresMISAG]uses%20-.->[MISAG],[Human-vaginalMISAG]uses%20-.->[MISAG],[Human-skinMISAG]uses%20-.->[MISAG],[Human-oralMISAG]uses%20-.->[MISAG],[Human-gutMISAG]uses%20-.->[MISAG],[Human-associatedMISAG]uses%20-.->[MISAG],[Host-associatedMISAG]uses%20-.->[MISAG],[BuiltEnvironmentMISAG]uses%20-.->[MISAG],[AirMISAG]uses%20-.->[MISAG],[WaterMISAG],[WastewaterSludgeMISAG],[SoilMISAG],[SedimentMISAG],[Plant-associatedMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MicrobialMatBiofilmMISAG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-coresMISAG],[Human-vaginalMISAG],[Human-skinMISAG],[Human-oralMISAG],[Human-gutMISAG],[Human-associatedMISAG],[Host-associatedMISAG],[BuiltEnvironmentMISAG],[AirMISAG]) ## Mixin for - * [AirMisag](AirMisag.md) (mixin) - Combinatorial checklist for air with misag - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) (mixin) - Combinatorial checklist for built environment with misag - * [Host-associatedMisag](Host-associatedMisag.md) (mixin) - Combinatorial checklist for host-associated with misag - * [Human-associatedMisag](Human-associatedMisag.md) (mixin) - Combinatorial checklist for human-associated with misag - * [Human-gutMisag](Human-gutMisag.md) (mixin) - Combinatorial checklist for human-gut with misag - * [Human-oralMisag](Human-oralMisag.md) (mixin) - Combinatorial checklist for human-oral with misag - * [Human-skinMisag](Human-skinMisag.md) (mixin) - Combinatorial checklist for human-skin with misag - * [Human-vaginalMisag](Human-vaginalMisag.md) (mixin) - Combinatorial checklist for human-vaginal with misag - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with misag - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with misag - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with misag - * [Plant-associatedMisag](Plant-associatedMisag.md) (mixin) - Combinatorial checklist for plant-associated with misag - * [SedimentMisag](SedimentMisag.md) (mixin) - Combinatorial checklist for sediment with misag - * [SoilMisag](SoilMisag.md) (mixin) - Combinatorial checklist for soil with misag - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) (mixin) - Combinatorial checklist for wastewater_sludge with misag - * [WaterMisag](WaterMisag.md) (mixin) - Combinatorial checklist for water with misag + * [AirMISAG](AirMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment + * [Host-associatedMISAG](Host-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated + * [Human-associatedMISAG](Human-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated + * [Human-gutMISAG](Human-gutMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut + * [Human-oralMISAG](Human-oralMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral + * [Human-skinMISAG](Human-skinMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin + * [Human-vaginalMISAG](Human-vaginalMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMISAG](Plant-associatedMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated + * [SedimentMISAG](SedimentMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment + * [SoilMISAG](SoilMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge + * [WaterMISAG](WaterMISAG.md) (mixin) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water ## Referenced by class @@ -37,117 +37,124 @@ URI: [mixs.vocab:Misag](https://w3id.org/mixs/vocab/Misag) ### Own - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) - * [misag➞collection_date](misag_collection_date.md) REQ + * [MISAG➞collection_date](MISAG_collection_date.md) REQ * range: [String](types/String.md) - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: - * [misag➞env_broad_scale](misag_env_broad_scale.md) REQ + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) REQ * range: [String](types/String.md) - * [misag➞env_local_scale](misag_env_local_scale.md) REQ + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) REQ * range: [String](types/String.md) - * [misag➞env_medium](misag_env_medium.md) REQ + * [MISAG➞env_medium](MISAG_env_medium.md) REQ * range: [String](types/String.md) - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) - * [misag➞geo_loc_name](misag_geo_loc_name.md) REQ + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) REQ * range: [String](types/String.md) - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: - * [misag➞lat_lon](misag_lat_lon.md) REQ + * [MISAG➞lat_lon](MISAG_lat_lon.md) REQ * range: [String](types/String.md) - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MISAG | + diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md index c3229252..527bc0d4 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md @@ -7,21 +7,21 @@ miscellaneous natural or artificial environment URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMe],[QuantityValue][MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSBacteria]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md new file mode 100644 index 00000000..f962fb99 --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md @@ -0,0 +1,459 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSEukaryote]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md new file mode 100644 index 00000000..bb6b145e --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md @@ -0,0 +1,429 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSPlant]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md new file mode 100644 index 00000000..2e0d175d --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md @@ -0,0 +1,454 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSVirus]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md new file mode 100644 index 00000000..24c0eded --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md @@ -0,0 +1,379 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSpecimen]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md new file mode 100644 index 00000000..c90ede6c --- /dev/null +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md @@ -0,0 +1,359 @@ + +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSurvey]) + +## Parents + + * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from miscellaneous natural or artificial environment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md index bc5cd283..501fec88 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md @@ -1,13 +1,13 @@ -# Class: MiscellaneousNaturalOrArtificialEnvironmentMe +# Class: MiscellaneousNaturalOrArtificialEnvironmentME -Combinatorial checklist for miscellaneous natural or artificial environment with me +Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMe) +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Me],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMe],[MiscellaneousNaturalOrArtificialEnvironment],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentME],[MiscellaneousNaturalOrArtificialEnvironment],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -223,172 +223,172 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMe](https://w3id.org * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md index 3daecfa1..e2d40c62 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md @@ -1,13 +1,13 @@ -# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsOrg +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg -Combinatorial checklist for miscellaneous natural or artificial environment with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg) +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -223,192 +223,192 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](https://w3i * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md index afe96989..e06f2529 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md @@ -1,13 +1,13 @@ -# Class: MiscellaneousNaturalOrArtificialEnvironmentMimag +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIMAG -Combinatorial checklist for miscellaneous natural or artificial environment with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimag) +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Mimag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimag],[MiscellaneousNaturalOrArtificialEnvironment],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironment],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -223,252 +223,252 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimag](https://w3id. * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md index 995098e2..527980f7 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md @@ -1,13 +1,13 @@ -# Class: MiscellaneousNaturalOrArtificialEnvironmentMisag +# Class: MiscellaneousNaturalOrArtificialEnvironmentMISAG -Combinatorial checklist for miscellaneous natural or artificial environment with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMisag) +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Misag],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMisag],[MiscellaneousNaturalOrArtificialEnvironment],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironment],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -223,257 +223,257 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMisag](https://w3id. * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md index 90cacc5a..897ead64 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md @@ -1,13 +1,13 @@ -# Class: MiscellaneousNaturalOrArtificialEnvironmentMiuvig +# Class: MiscellaneousNaturalOrArtificialEnvironmentMIUVIG -Combinatorial checklist for miscellaneous natural or artificial environment with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMiuvig) +URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MiscellaneousNaturalOrArtificialEnvironment]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironment],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -223,322 +223,322 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMiuvig](https://w3id * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Miuvig.md b/mixs6/Miuvig.md index 37d1902f..2fc63fcb 100644 --- a/mixs6/Miuvig.md +++ b/mixs6/Miuvig.md @@ -1,33 +1,33 @@ -# Class: Miuvig +# Class: MIUVIG -miuvig Checklist +Minimum Information About an Uncultivated Virus Genome -URI: [mixs.vocab:Miuvig](https://w3id.org/mixs/vocab/Miuvig) +URI: [mixs.vocab:MIUVIG](https://w3id.org/mixs/vocab/MIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][Miuvig],[WastewaterSludgeMiuvig]uses%20-.->[Miuvig],[SoilMiuvig]uses%20-.->[Miuvig],[SedimentMiuvig]uses%20-.->[Miuvig],[Plant-associatedMiuvig]uses%20-.->[Miuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig]uses%20-.->[Miuvig],[MicrobialMatBiofilmMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-fluidsSwabsMiuvig]uses%20-.->[Miuvig],[HydrocarbonResources-coresMiuvig]uses%20-.->[Miuvig],[Human-vaginalMiuvig]uses%20-.->[Miuvig],[Human-skinMiuvig]uses%20-.->[Miuvig],[Human-oralMiuvig]uses%20-.->[Miuvig],[Human-gutMiuvig]uses%20-.->[Miuvig],[Human-associatedMiuvig]uses%20-.->[Miuvig],[Host-associatedMiuvig]uses%20-.->[Miuvig],[BuiltEnvironmentMiuvig]uses%20-.->[Miuvig],[AirMiuvig]uses%20-.->[Miuvig],[WaterMiuvig],[WastewaterSludgeMiuvig],[SoilMiuvig],[SedimentMiuvig],[Plant-associatedMiuvig],[MiscellaneousNaturalOrArtificialEnvironmentMiuvig],[MicrobialMatBiofilmMiuvig],[HydrocarbonResources-fluidsSwabsMiuvig],[HydrocarbonResources-coresMiuvig],[Human-vaginalMiuvig],[Human-skinMiuvig],[Human-oralMiuvig],[Human-gutMiuvig],[Human-associatedMiuvig],[Host-associatedMiuvig],[BuiltEnvironmentMiuvig],[AirMiuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIUVIG],[WastewaterSludgeMIUVIG]uses%20-.->[MIUVIG],[SoilMIUVIG]uses%20-.->[MIUVIG],[SedimentMIUVIG]uses%20-.->[MIUVIG],[Plant-associatedMIUVIG]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG]uses%20-.->[MIUVIG],[MicrobialMatBiofilmMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-coresMIUVIG]uses%20-.->[MIUVIG],[Human-vaginalMIUVIG]uses%20-.->[MIUVIG],[Human-skinMIUVIG]uses%20-.->[MIUVIG],[Human-oralMIUVIG]uses%20-.->[MIUVIG],[Human-gutMIUVIG]uses%20-.->[MIUVIG],[Human-associatedMIUVIG]uses%20-.->[MIUVIG],[Host-associatedMIUVIG]uses%20-.->[MIUVIG],[BuiltEnvironmentMIUVIG]uses%20-.->[MIUVIG],[AirMIUVIG]uses%20-.->[MIUVIG],[WaterMIUVIG],[WastewaterSludgeMIUVIG],[SoilMIUVIG],[SedimentMIUVIG],[Plant-associatedMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MicrobialMatBiofilmMIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-coresMIUVIG],[Human-vaginalMIUVIG],[Human-skinMIUVIG],[Human-oralMIUVIG],[Human-gutMIUVIG],[Human-associatedMIUVIG],[Host-associatedMIUVIG],[BuiltEnvironmentMIUVIG],[AirMIUVIG]) ## Mixin for - * [AirMiuvig](AirMiuvig.md) (mixin) - Combinatorial checklist for air with miuvig - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) (mixin) - Combinatorial checklist for built environment with miuvig - * [Host-associatedMiuvig](Host-associatedMiuvig.md) (mixin) - Combinatorial checklist for host-associated with miuvig - * [Human-associatedMiuvig](Human-associatedMiuvig.md) (mixin) - Combinatorial checklist for human-associated with miuvig - * [Human-gutMiuvig](Human-gutMiuvig.md) (mixin) - Combinatorial checklist for human-gut with miuvig - * [Human-oralMiuvig](Human-oralMiuvig.md) (mixin) - Combinatorial checklist for human-oral with miuvig - * [Human-skinMiuvig](Human-skinMiuvig.md) (mixin) - Combinatorial checklist for human-skin with miuvig - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) (mixin) - Combinatorial checklist for human-vaginal with miuvig - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with miuvig - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with miuvig - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with miuvig - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) (mixin) - Combinatorial checklist for plant-associated with miuvig - * [SedimentMiuvig](SedimentMiuvig.md) (mixin) - Combinatorial checklist for sediment with miuvig - * [SoilMiuvig](SoilMiuvig.md) (mixin) - Combinatorial checklist for soil with miuvig - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) (mixin) - Combinatorial checklist for wastewater_sludge with miuvig - * [WaterMiuvig](WaterMiuvig.md) (mixin) - Combinatorial checklist for water with miuvig + * [AirMIUVIG](AirMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated + * [Human-gutMIUVIG](Human-gutMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut + * [Human-oralMIUVIG](Human-oralMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral + * [Human-skinMIUVIG](Human-skinMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated + * [SedimentMIUVIG](SedimentMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment + * [SoilMIUVIG](SoilMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge + * [WaterMIUVIG](WaterMIUVIG.md) (mixin) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water ## Referenced by class @@ -37,143 +37,150 @@ URI: [mixs.vocab:Miuvig](https://w3id.org/mixs/vocab/Miuvig) ### Own - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: - * [miuvig➞collection_date](miuvig_collection_date.md) REQ + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) REQ * range: [String](types/String.md) - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) - * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) REQ + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) REQ * range: [String](types/String.md) - * [miuvig➞env_local_scale](miuvig_env_local_scale.md) REQ + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) REQ * range: [String](types/String.md) - * [miuvig➞env_medium](miuvig_env_medium.md) REQ + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) REQ * range: [String](types/String.md) - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) - * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) REQ + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) REQ * range: [String](types/String.md) - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: - * [miuvig➞lat_lon](miuvig_lat_lon.md) REQ + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) REQ * range: [String](types/String.md) - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | MIUVIG | + diff --git a/mixs6/Plant-associated.md b/mixs6/Plant-associated.md index 8a310352..b30a2b34 100644 --- a/mixs6/Plant-associated.md +++ b/mixs6/Plant-associated.md @@ -7,21 +7,21 @@ plant-associated URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMiuvig],[Plant-associatedMisag],[Plant-associatedMimarksS],[Plant-associatedMimarksC],[Plant-associatedMimag],[Plant-associatedMigsVi],[Plant-associatedMigsPl],[Plant-associatedMigsOrg],[Plant-associatedMigsEu],[Plant-associatedMigsBa],[Plant-associatedMe],[QuantityValue][MIGSBacteria],[Plant-associated]^-[Plant-associatedMIGSBacteria],[Plant-associated],[MIGSBacteria]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSEukaryote.md b/mixs6/Plant-associatedMIGSEukaryote.md new file mode 100644 index 00000000..3486854b --- /dev/null +++ b/mixs6/Plant-associatedMIGSEukaryote.md @@ -0,0 +1,579 @@ + +# Class: Plant-associatedMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plant-associatedMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Plant-associated]^-[Plant-associatedMIGSEukaryote],[Plant-associated],[MIGSEukaryote]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSPlant.md b/mixs6/Plant-associatedMIGSPlant.md new file mode 100644 index 00000000..aec619ea --- /dev/null +++ b/mixs6/Plant-associatedMIGSPlant.md @@ -0,0 +1,549 @@ + +# Class: Plant-associatedMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-associatedMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSPlant],[Plant-associated]^-[Plant-associatedMIGSPlant],[Plant-associated],[MIGSPlant]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIGSVirus.md b/mixs6/Plant-associatedMIGSVirus.md new file mode 100644 index 00000000..17400154 --- /dev/null +++ b/mixs6/Plant-associatedMIGSVirus.md @@ -0,0 +1,574 @@ + +# Class: Plant-associatedMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-associatedMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSVirus],[Plant-associated]^-[Plant-associatedMIGSVirus],[Plant-associated],[MIGSVirus]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/Plant-associatedMIMARKSSpecimen.md b/mixs6/Plant-associatedMIMARKSSpecimen.md new file mode 100644 index 00000000..9f74e05d --- /dev/null +++ b/mixs6/Plant-associatedMIMARKSSpecimen.md @@ -0,0 +1,499 @@ + +# Class: Plant-associatedMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Plant-associated]^-[Plant-associatedMIMARKSSpecimen],[Plant-associated],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMIMARKSSurvey.md b/mixs6/Plant-associatedMIMARKSSurvey.md new file mode 100644 index 00000000..40d16752 --- /dev/null +++ b/mixs6/Plant-associatedMIMARKSSurvey.md @@ -0,0 +1,479 @@ + +# Class: Plant-associatedMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + +URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Plant-associated]^-[Plant-associatedMIMARKSSurvey],[Plant-associated],[MIMARKSSurvey]) + +## Parents + + * is_a: [Plant-associated](Plant-associated.md) - plant-associated + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from plant-associated: + + * [air_temp_regm](air_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + * range: [String](types/String.md) + * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [ances_data](ances_data.md) OPT + * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + * range: [String](types/String.md) + * Example: A/3*B None + * [antibiotic_regm](antibiotic_regm.md) OPT + * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + * range: [String](types/String.md) + * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [biol_stat](biol_stat.md) OPT + * Description: The level of genome modification + * range: + * Example: natural None + * [biotic_regm](biotic_regm.md) OPT + * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + * range: [String](types/String.md) + * Example: sample inoculated with Rhizobium spp. Culture None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_mutagen](chem_mutagen.md) OPT + * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + * range: [String](types/String.md) + * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [climate_environment](climate_environment.md) OPT + * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + * range: [String](types/String.md) + * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [cult_root_med](cult_root_med.md) OPT + * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fertilizer_regm](fertilizer_regm.md) OPT + * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + * range: [String](types/String.md) + * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [fungicide_regm](fungicide_regm.md) OPT + * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + * range: [String](types/String.md) + * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [gaseous_environment](gaseous_environment.md) OPT + * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + * range: [String](types/String.md) + * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [genetic_mod](genetic_mod.md) OPT + * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + * range: [String](types/String.md) + * Example: aox1A transgenic None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [gravity](gravity.md) OPT + * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + * range: [String](types/String.md) + * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [growth_facil](growth_facil.md) OPT + * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research + * range: [String](types/String.md) + * Example: Growth chamber [CO_715:0000189] None + * [growth_habit](growth_habit.md) OPT + * Description: Characteristic shape, appearance or growth form of a plant species + * range: + * Example: spreading None + * [growth_hormone_regm](growth_hormone_regm.md) OPT + * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + * range: [String](types/String.md) + * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [herbicide_regm](herbicide_regm.md) OPT + * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [host_age](host_age.md) OPT + * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + * range: [QuantityValue](QuantityValue.md) + * Example: 10 days None + * [host_common_name](host_common_name.md) OPT + * Description: Common name of the host, e.g. Human + * range: [String](types/String.md) + * Example: mussel None + * [host_disease_stat](host_disease_stat.md) OPT + * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + * range: [String](types/String.md) + * Example: rabies [DOID:11260] None + * [host_dry_mass](host_dry_mass.md) OPT + * Description: Measurement of dry mass + * range: [QuantityValue](QuantityValue.md) + * Example: 500 gram None + * [host_genotype](host_genotype.md) OPT + * Description: Observed genotype + * range: [String](types/String.md) + * Example: C57BL/6 None + * [host_height](host_height.md) OPT + * Description: The height of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 meter None + * [host_infra_specific_name](host_infra_specific_name.md) OPT + * Description: Taxonomic information about the host below subspecies level + * range: [String](types/String.md) + * Example: borealis None + * [host_infra_specific_rank](host_infra_specific_rank.md) OPT + * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. + * range: [String](types/String.md) + * Example: subspecies None + * [host_length](host_length.md) OPT + * Description: The length of subject + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter None + * [host_life_stage](host_life_stage.md) OPT + * Description: Description of life stage of host + * range: [String](types/String.md) + * Example: adult None + * [host_phenotype](host_phenotype.md) OPT + * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + * range: [String](types/String.md) + * Example: elongated [PATO:0001154] None + * [host_taxid](host_taxid.md) OPT + * Description: NCBI taxon id of the host, e.g. 9606 + * range: [String](types/String.md) + * Example: 7955 None + * [host_tot_mass](host_tot_mass.md) OPT + * Description: Total mass of the host at collection, the unit depends on host + * range: [QuantityValue](QuantityValue.md) + * Example: 2500 gram None + * [host_wet_mass](host_wet_mass.md) OPT + * Description: Measurement of wet mass + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 gram None + * [humidity_regm](humidity_regm.md) OPT + * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_regm](light_regm.md) OPT + * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + * range: [String](types/String.md) + * Example: incandescant light;10 lux;450 nanometer None + * [mechanical_damage](mechanical_damage.md) OPT + * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + * range: [String](types/String.md) + * Example: pruning;bark None + * [mineral_nutr_regm](mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + * range: [String](types/String.md) + * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT + * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + * range: [String](types/String.md) + * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [pesticide_regm](pesticide_regm.md) OPT + * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + * range: [String](types/String.md) + * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [ph_regm](ph_regm.md) OPT + * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + * range: [String](types/String.md) + * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None + * [plant_growth_med](plant_growth_med.md) OPT + * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + * range: + * Example: hydroponic plant culture media [EO:0007067] None + * [plant_product](plant_product.md) OPT + * Description: Substance produced by the plant, where the sample was obtained from + * range: [String](types/String.md) + * Example: xylem sap [PO:0025539] None + * [plant_sex](plant_sex.md) OPT + * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + * range: + * Example: Hermaphroditic None + * [plant_struc](plant_struc.md) OPT + * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + * range: [String](types/String.md) + * Example: epidermis [PO:0005679] None + * [radiation_regm](radiation_regm.md) OPT + * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + * range: [String](types/String.md) + * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [rainfall_regm](rainfall_regm.md) OPT + * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [root_cond](root_cond.md) OPT + * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + * range: [String](types/String.md) + * Example: http://himedialabs.com/TD/PT158.pdf None + * [root_med_carbon](root_med_carbon.md) OPT + * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + * range: [String](types/String.md) + * Example: sucrose None + * [root_med_macronutr](root_med_macronutr.md) OPT + * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + * range: [String](types/String.md) + * Example: KH2PO4;170¬†milligram per liter None + * [root_med_micronutr](root_med_micronutr.md) OPT + * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + * range: [String](types/String.md) + * Example: H3BO3;6.2¬†milligram per liter None + * [root_med_ph](root_med_ph.md) OPT + * Description: pH measurement of the culture rooting medium; e.g. 5.5. + * range: [Double](types/Double.md) + * Example: 7.5 None + * [root_med_regl](root_med_regl.md) OPT + * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + * range: [String](types/String.md) + * Example: abscisic acid;0.75 milligram per liter None + * [root_med_solid](root_med_solid.md) OPT + * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + * range: [String](types/String.md) + * Example: agar None + * [root_med_suppl](root_med_suppl.md) OPT + * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + * range: [String](types/String.md) + * Example: nicotinic acid;0.5 milligram per liter None + * [salt_regm](salt_regm.md) OPT + * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + * range: [String](types/String.md) + * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [samp_capt_status](samp_capt_status.md) OPT + * Description: Reason for the sample + * range: + * Example: farm sample None + * [samp_dis_stage](samp_dis_stage.md) OPT + * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + * range: [String](types/String.md) + * Example: infection None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_environment](season_environment.md) OPT + * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + * range: [String](types/String.md) + * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [standing_water_regm](standing_water_regm.md) OPT + * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT + * Description: Description of plant tissue culture growth media used + * range: [String](types/String.md) + * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None + * [water_temp_regm](water_temp_regm.md) OPT + * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + * [watering_regm](watering_regm.md) OPT + * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + * range: [String](types/String.md) + * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMe.md b/mixs6/Plant-associatedMe.md index 0865f77c..46fb10ed 100644 --- a/mixs6/Plant-associatedMe.md +++ b/mixs6/Plant-associatedMe.md @@ -1,13 +1,13 @@ -# Class: Plant-associatedMe +# Class: Plant-associatedME -Combinatorial checklist for plant-associated with me +Combinatorial checklist Metagenome or Environmental with environmental package plant-associated -URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associatedMe) +URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Me],[Plant-associated]^-[Plant-associatedMe],[Plant-associated],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[ME],[Plant-associated]^-[Plant-associatedME],[Plant-associated],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -343,172 +343,172 @@ URI: [mixs.vocab:Plant-associatedMe](https://w3id.org/mixs/vocab/Plant-associate * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsOrg.md b/mixs6/Plant-associatedMigsOrg.md index 1cb1c6e9..b6b9d055 100644 --- a/mixs6/Plant-associatedMigsOrg.md +++ b/mixs6/Plant-associatedMigsOrg.md @@ -1,13 +1,13 @@ -# Class: Plant-associatedMigsOrg +# Class: Plant-associatedMIGSOrg -Combinatorial checklist for plant-associated with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated -URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-associatedMigsOrg) +URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsOrg],[Plant-associated]^-[Plant-associatedMigsOrg],[Plant-associated],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSOrg],[Plant-associated]^-[Plant-associatedMIGSOrg],[Plant-associated],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -343,192 +343,192 @@ URI: [mixs.vocab:Plant-associatedMigsOrg](https://w3id.org/mixs/vocab/Plant-asso * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimag.md b/mixs6/Plant-associatedMimag.md index a973cc6a..354893e1 100644 --- a/mixs6/Plant-associatedMimag.md +++ b/mixs6/Plant-associatedMimag.md @@ -1,13 +1,13 @@ -# Class: Plant-associatedMimag +# Class: Plant-associatedMIMAG -Combinatorial checklist for plant-associated with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated -URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associatedMimag) +URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Mimag],[Plant-associated]^-[Plant-associatedMimag],[Plant-associated],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMAG],[Plant-associated]^-[Plant-associatedMIMAG],[Plant-associated],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -343,252 +343,252 @@ URI: [mixs.vocab:Plant-associatedMimag](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMisag.md b/mixs6/Plant-associatedMisag.md index 9dacb368..5963f27d 100644 --- a/mixs6/Plant-associatedMisag.md +++ b/mixs6/Plant-associatedMisag.md @@ -1,13 +1,13 @@ -# Class: Plant-associatedMisag +# Class: Plant-associatedMISAG -Combinatorial checklist for plant-associated with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated -URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associatedMisag) +URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Misag],[Plant-associated]^-[Plant-associatedMisag],[Plant-associated],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MISAG],[Plant-associated]^-[Plant-associatedMISAG],[Plant-associated],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -343,257 +343,257 @@ URI: [mixs.vocab:Plant-associatedMisag](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMiuvig.md b/mixs6/Plant-associatedMiuvig.md index 445a1e2e..781df78d 100644 --- a/mixs6/Plant-associatedMiuvig.md +++ b/mixs6/Plant-associatedMiuvig.md @@ -1,13 +1,13 @@ -# Class: Plant-associatedMiuvig +# Class: Plant-associatedMIUVIG -Combinatorial checklist for plant-associated with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated -URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-associatedMiuvig) +URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[Miuvig],[Plant-associated]^-[Plant-associatedMiuvig],[Plant-associated],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIUVIG],[Plant-associated]^-[Plant-associatedMIUVIG],[Plant-associated],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -343,322 +343,322 @@ URI: [mixs.vocab:Plant-associatedMiuvig](https://w3id.org/mixs/vocab/Plant-assoc * range: [String](types/String.md) * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/QuantityValue.md b/mixs6/QuantityValue.md new file mode 100644 index 00000000..5e63b60d --- /dev/null +++ b/mixs6/QuantityValue.md @@ -0,0 +1,196 @@ + +# Class: QuantityValue + + +used to record a measurement + +URI: [mixs.vocab:QuantityValue](https://w3id.org/mixs/vocab/QuantityValue) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[ME]++-%20samp_size%200..1>[QuantityValue|has_unit:string%20%3F;has_numeric_value:double%20%3F;has_raw_value:string%20%3F],[MIGSBacteria]++-%20samp_size%200..1>[QuantityValue],[MIGSEukaryote]++-%20samp_size%200..1>[QuantityValue],[MIGSOrg]++-%20samp_size%200..1>[QuantityValue],[MIGSPlant]++-%20samp_size%200..1>[QuantityValue],[MIGSVirus]++-%20samp_size%200..1>[QuantityValue],[MIMAG]++-%20samp_size%200..1>[QuantityValue],[MIMARKSSpecimen]++-%20samp_size%200..1>[QuantityValue],[MIMARKSSurvey]++-%20samp_size%200..1>[QuantityValue],[MISAG]++-%20samp_size%200..1>[QuantityValue],[MIUVIG]++-%20samp_size%200..1>[QuantityValue],[BuiltEnvironment]++-%20abs_air_humidity%200..1>[QuantityValue],[BuiltEnvironment]++-%20air_temp%200..1>[QuantityValue],[Soil]++-%20al_sat%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20alkalinity%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20alkalinity%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alkalinity%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20alkalinity%200..1>[QuantityValue],[Sediment]++-%20alkalinity%200..1>[QuantityValue],[WastewaterSludge]++-%20alkalinity%200..1>[QuantityValue],[Water]++-%20alkalinity%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alkyl_diethers%200..1>[QuantityValue],[Sediment]++-%20alkyl_diethers%200..1>[QuantityValue],[Water]++-%20alkyl_diethers%200..1>[QuantityValue],[Core]++-%20alt%200..1>[QuantityValue],[Air]++-%20alt%200..1>[QuantityValue],[BuiltEnvironment]++-%20alt%200..1>[QuantityValue],[Host-associated]++-%20alt%200..1>[QuantityValue],[Human-associated]++-%20alt%200..1>[QuantityValue],[Human-gut]++-%20alt%200..1>[QuantityValue],[Human-oral]++-%20alt%200..1>[QuantityValue],[Human-skin]++-%20alt%200..1>[QuantityValue],[Human-vaginal]++-%20alt%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20alt%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20alt%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20alt%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20alt%200..1>[QuantityValue],[Plant-associated]++-%20alt%200..1>[QuantityValue],[Sediment]++-%20alt%200..1>[QuantityValue],[Soil]++-%20alt%200..1>[QuantityValue],[WastewaterSludge]++-%20alt%200..1>[QuantityValue],[Water]++-%20alt%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20aminopept_act%200..1>[QuantityValue],[Sediment]++-%20aminopept_act%200..1>[QuantityValue],[Water]++-%20aminopept_act%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20ammonium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20ammonium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20ammonium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20ammonium%200..1>[QuantityValue],[Sediment]++-%20ammonium%200..1>[QuantityValue],[Water]++-%20ammonium%200..1>[QuantityValue],[BuiltEnvironment]++-%20amount_light%200..1>[QuantityValue],[Soil]++-%20annual_precpt%200..1>[QuantityValue],[Soil]++-%20annual_temp%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20api%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20api%200..1>[QuantityValue],[BuiltEnvironment]++-%20avg_dew_point%200..1>[QuantityValue],[BuiltEnvironment]++-%20avg_temp%200..1>[QuantityValue],[Water]++-%20bac_prod%200..1>[QuantityValue],[Water]++-%20bac_resp%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Sediment]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Water]++-%20bacteria_carb_prod%200..1>[QuantityValue],[Air]++-%20barometric_press%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20benzene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20benzene%200..1>[QuantityValue],[WastewaterSludge]++-%20biochem_oxygen_dem%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bishomohopanol%200..1>[QuantityValue],[Sediment]++-%20bishomohopanol%200..1>[QuantityValue],[Water]++-%20bishomohopanol%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20bromide%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20bromide%200..1>[QuantityValue],[Sediment]++-%20bromide%200..1>[QuantityValue],[Water]++-%20bromide%200..1>[QuantityValue],[BuiltEnvironment]++-%20built_struc_age%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20calcium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20calcium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20calcium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20calcium%200..1>[QuantityValue],[Sediment]++-%20calcium%200..1>[QuantityValue],[Water]++-%20calcium%200..1>[QuantityValue],[Air]++-%20carb_dioxide%200..1>[QuantityValue],[BuiltEnvironment]++-%20carb_dioxide%200..1>[QuantityValue],[Air]++-%20carb_monoxide%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20carb_nitro_ratio%200..1>[QuantityValue],[Sediment]++-%20carb_nitro_ratio%200..1>[QuantityValue],[Water]++-%20carb_nitro_ratio%200..1>[QuantityValue],[BuiltEnvironment]++-%2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itrite%200..1>[QuantityValue],[Water]++-%20nitrite%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20nitro%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20nitro%200..1>[QuantityValue],[Sediment]++-%20nitro%200..1>[QuantityValue],[Water]++-%20nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_carb%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_carb%200..1>[QuantityValue],[Sediment]++-%20org_carb%200..1>[QuantityValue],[Water]++-%20org_carb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_matter%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_matter%200..1>[QuantityValue],[Sediment]++-%20org_matter%200..1>[QuantityValue],[Water]++-%20org_matter%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20org_nitro%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20org_nitro%200..1>[QuantityValue],[Sediment]++-%20org_nitro%200..1>[QuantityValue],[Water]++-%20org_nitro%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20owc_tvdss%200..1>[QuantityValue],[Air]++-%20oxygen%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20part_org_carb%200..1>[QuantityValue],[Sediment]++-%20part_org_carb%200..1>[QuantityValue],[Water]++-%20part_org_carb%200..1>[QuantityValue],[Water]++-%20part_org_nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[Sediment]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[Water]++-%20petroleum_hydrocarb%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20phosphate%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20phosphate%200..1>[QuantityValue],[Sediment]++-%20phosphate%200..1>[QuantityValue],[WastewaterSludge]++-%20phosphate%200..1>[QuantityValue],[Water]++-%20phosphate%200..1>[QuantityValue],[Water]++-%20photon_flux%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20potassium%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20potassium%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20potassium%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20potassium%200..1>[QuantityValue],[Sediment]++-%20potassium%200..1>[QuantityValue],[Water]++-%20potassium%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20pour_point%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20pour_point%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20pressure%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20pressure%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20pressure%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20pressure%200..1>[QuantityValue],[Sediment]++-%20pressure%200..1>[QuantityValue],[Water]++-%20pressure%200..1>[QuantityValue],[Water]++-%20primary_prod%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20prod_rate%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20redox_potential%200..1>[QuantityValue],[Sediment]++-%20redox_potential%200..1>[QuantityValue],[Water]++-%20redox_potential%200..1>[QuantityValue],[BuiltEnvironment]++-%20rel_air_humidity%200..1>[QuantityValue],[BuiltEnvironment]++-%20rel_humidity_out%200..1>[QuantityValue],[BuiltEnvironment]++-%20room_air_exch_rate%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20salinity%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20salinity%200..1>[QuantityValue],[Sediment]++-%20salinity%200..1>[QuantityValue],[Water]++-%20salinity%200..1>[QuantityValue],[Air]++-%20samp_salinity%200..1>[QuantityValue],[Host-associated]++-%20samp_salinity%200..1>[QuantityValue],[Human-associated]++-%20samp_salinity%200..1>[QuantityValue],[Human-gut]++-%20samp_salinity%200..1>[QuantityValue],[Human-oral]++-%20samp_salinity%200..1>[QuantityValue],[Human-skin]++-%20samp_salinity%200..1>[QuantityValue],[Human-vaginal]++-%20samp_salinity%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20samp_salinity%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20samp_salinity%200..1>[QuantityValue],[Plant-associated]++-%20samp_salinity%200..1>[QuantityValue],[WastewaterSludge]++-%20samp_salinity%200..1>[QuantityValue],[MIGSEukaryote]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSBacteria]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSPlant]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSVirus]++-%20samp_size(i)%200..1>[QuantityValue],[MIGSOrg]++-%20samp_size(i)%200..1>[QuantityValue],[ME]++-%20samp_size(i)%200..1>[QuantityValue],[MIMARKSSpecimen]++-%20samp_size(i)%200..1>[QuantityValue],[MIMARKSSurvey]++-%20samp_size(i)%200..1>[QuantityValue],[MISAG]++-%20samp_size(i)%200..1>[QuantityValue],[MIMAG]++-%20samp_size(i)%200..1>[QuantityValue],[MIUVIG]++-%20samp_size(i)%200..1>[QuantityValue],[Core]++-%20samp_size%200..1>[QuantityValue],[Air]++-%20samp_store_temp%200..1>[QuantityValue],[Host-associated]++-%20samp_store_temp%200..1>[QuantityValue],[Human-associated]++-%20samp_store_temp%200..1>[QuantityValue],[Human-gut]++-%20samp_store_temp%200..1>[QuantityVal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+-%20temp_out%200..1>[QuantityValue],[Soil]++-%20texture%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20toluene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20toluene%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_carb%200..1>[QuantityValue],[Sediment]++-%20tot_carb%200..1>[QuantityValue],[Sediment]++-%20tot_depth_water_col%200..1>[QuantityValue],[Water]++-%20tot_depth_water_col%200..1>[QuantityValue],[Water]++-%20tot_diss_nitro%200..1>[QuantityValue],[Water]++-%20tot_inorg_nitro%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_iron%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_iron%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_nitro%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_nitro%200..1>[QuantityValue],[WastewaterSludge]++-%20tot_nitro%200..1>[QuantityValue],[Water]++-%20tot_nitro%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_nitro_content%200..1>[QuantityValue],[Sediment]++-%20tot_nitro_content%200..1>[QuantityValue],[Soil]++-%20tot_nitro_content%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20tot_org_carb%200..1>[QuantityValue],[Sediment]++-%20tot_org_carb%200..1>[QuantityValue],[Soil]++-%20tot_org_carb%200..1>[QuantityValue],[Water]++-%20tot_part_carb%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_phosp%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_phosp%200..1>[QuantityValue],[Water]++-%20tot_phosp%200..1>[QuantityValue],[WastewaterSludge]++-%20tot_phosphate%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tot_sulfur%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tot_sulfur%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20turbidity%200..1>[QuantityValue],[Sediment]++-%20turbidity%200..1>[QuantityValue],[Water]++-%20turbidity%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tvdss_of_hcr_pressure%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tvdss_of_hcr_pressure%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20tvdss_of_hcr_temp%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20tvdss_of_hcr_temp%200..1>[QuantityValue],[Air]++-%20ventilation_rate%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20vfa%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20vfa%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20vfa_fw%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20vfa_fw%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_area%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_height%200..1>[QuantityValue],[BuiltEnvironment]++-%20wall_thermal_mass%200..1>[QuantityValue],[MicrobialMatBiofilm]++-%20water_content%200..1>[QuantityValue],[Sediment]++-%20water_content%200..1>[QuantityValue],[Soil]++-%20water_content%200..1>[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironment]++-%20water_current%200..1>[QuantityValue],[Water]++-%20water_current%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20water_cut%200..1>[QuantityValue],[BuiltEnvironment]++-%20water_feat_size%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20water_production_rate%200..1>[QuantityValue],[Air]++-%20wind_speed%200..1>[QuantityValue],[HydrocarbonResources-cores]++-%20xylene%200..1>[QuantityValue],[HydrocarbonResources-fluidsSwabs]++-%20xylene%200..1>[QuantityValue],[Water],[WastewaterSludge],[Soil],[Sediment],[Plant-associated],[MiscellaneousNaturalOrArtificialEnvironment],[MicrobialMatBiofilm],[HydrocarbonResources-fluidsSwabs],[HydrocarbonResources-cores],[Human-vaginal],[Human-skin],[Human-oral],[Human-gut],[Human-associated],[Host-associated],[Core],[BuiltEnvironment],[Air],[MIUVIG],[MISAG],[MIMARKSSurvey],[MIMARKSSpecimen],[MIMAG],[MIGSVirus],[MIGSPlant],[MIGSOrg],[MIGSEukaryote],[MIGSBacteria],[ME]) + +## Referenced by class + + * **[ME](ME.md)** *[ME➞samp_size](ME_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSBacteria](MIGSBacteria.md)** *[MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSEukaryote](MIGSEukaryote.md)** *[MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSOrg](MIGSOrg.md)** *[MIGS org➞samp_size](MIGS_org_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSPlant](MIGSPlant.md)** *[MIGS plant➞samp_size](MIGS_plant_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIGSVirus](MIGSVirus.md)** *[MIGS virus➞samp_size](MIGS_virus_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMAG](MIMAG.md)** *[MIMAG➞samp_size](MIMAG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMARKSSpecimen](MIMARKSSpecimen.md)** *[MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIMARKSSurvey](MIMARKSSurvey.md)** *[MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MISAG](MISAG.md)** *[MISAG➞samp_size](MISAG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **[MIUVIG](MIUVIG.md)** *[MIUVIG➞samp_size](MIUVIG_samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[abs_air_humidity](abs_air_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[air_temp](air_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[al_sat](al_sat.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alkalinity](alkalinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alkyl_diethers](alkyl_diethers.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[alt](alt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[aminopept_act](aminopept_act.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ammonium](ammonium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[amount_light](amount_light.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[annual_precpt](annual_precpt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[annual_temp](annual_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[api](api.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[avg_dew_point](avg_dew_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[avg_temp](avg_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bac_prod](bac_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bac_resp](bac_resp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bacteria_carb_prod](bacteria_carb_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[barometric_press](barometric_press.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[benzene](benzene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[biochem_oxygen_dem](biochem_oxygen_dem.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bishomohopanol](bishomohopanol.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[bromide](bromide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[built_struc_age](built_struc_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[calcium](calcium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_dioxide](carb_dioxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_monoxide](carb_monoxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[carb_nitro_ratio](carb_nitro_ratio.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ceil_area](ceil_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ceil_thermal_mass](ceil_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chem_oxygen_dem](chem_oxygen_dem.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chloride](chloride.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[chlorophyll](chlorophyll.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[conduc](conduc.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[density](density.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[dew_point](dew_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_carb_dioxide](diss_carb_dioxide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_hydrogen](diss_hydrogen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_carb](diss_inorg_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_nitro](diss_inorg_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_inorg_phosp](diss_inorg_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_iron](diss_iron.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_org_carb](diss_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_org_nitro](diss_org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_oxygen](diss_oxygen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[diss_oxygen_fluid](diss_oxygen_fluid.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[door_size](door_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[down_par](down_par.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[efficiency_percent](efficiency_percent.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[elev](elev.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ethylbenzene](ethylbenzene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[exp_duct](exp_duct.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[extreme_salinity](extreme_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_age](floor_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_area](floor_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[floor_thermal_mass](floor_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[fluor](fluor.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[glucosidase_act](glucosidase_act.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[hcr_fw_salinity](hcr_fw_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[height_carper_fiber](height_carper_fiber.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_age](host_age.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_blood_press_diast](host_blood_press_diast.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_blood_press_syst](host_blood_press_syst.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_body_mass_index](host_body_mass_index.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_body_temp](host_body_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_dry_mass](host_dry_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_height](host_height.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_length](host_length.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_pulse](host_pulse.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_tot_mass](host_tot_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[host_wet_mass](host_wet_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[humidity](humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[indust_eff_percent](indust_eff_percent.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[inside_lux](inside_lux.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[iwf](iwf.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[light_intensity](light_intensity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[magnesium](magnesium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[mean_frict_vel](mean_frict_vel.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[mean_peak_frict_vel](mean_peak_frict_vel.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[methane](methane.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[microbial_biomass](microbial_biomass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitrate](nitrate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitrite](nitrite.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[nitro](nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_carb](org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_matter](org_matter.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[org_nitro](org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[owc_tvdss](owc_tvdss.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[oxygen](oxygen.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[part_org_carb](part_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[part_org_nitro](part_org_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[petroleum_hydrocarb](petroleum_hydrocarb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[phosphate](phosphate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[photon_flux](photon_flux.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[potassium](potassium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[pour_point](pour_point.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[pressure](pressure.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[primary_prod](primary_prod.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[prod_rate](prod_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[redox_potential](redox_potential.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[rel_air_humidity](rel_air_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[rel_humidity_out](rel_humidity_out.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[room_air_exch_rate](room_air_exch_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[salinity](salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_salinity](samp_salinity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_size](samp_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_store_temp](samp_store_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[samp_vol_we_dna_ext](samp_vol_we_dna_ext.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[season_precpt](season_precpt.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[season_temp](season_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[silicate](silicate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[size_frac_low](size_frac_low.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[size_frac_up](size_frac_up.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[slope_aspect](slope_aspect.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[slope_gradient](slope_gradient.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sludge_retent_time](sludge_retent_time.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sodium](sodium.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[solar_irradiance](solar_irradiance.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[soluble_react_phosp](soluble_react_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[specific_humidity](specific_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfate](sulfate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfate_fw](sulfate_fw.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[sulfide](sulfide.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_humidity](surf_humidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_moisture](surf_moisture.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[surf_temp](surf_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[suspend_part_matter](suspend_part_matter.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tan](tan.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[temp](temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[temp_out](temp_out.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[texture](texture.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[toluene](toluene.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_carb](tot_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_depth_water_col](tot_depth_water_col.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_diss_nitro](tot_diss_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_inorg_nitro](tot_inorg_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_iron](tot_iron.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_nitro](tot_nitro.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_nitro_content](tot_nitro_content.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_org_carb](tot_org_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_part_carb](tot_part_carb.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_phosp](tot_phosp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_phosphate](tot_phosphate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tot_sulfur](tot_sulfur.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[turbidity](turbidity.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[tvdss_of_hcr_temp](tvdss_of_hcr_temp.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[ventilation_rate](ventilation_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[vfa](vfa.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[vfa_fw](vfa_fw.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_area](wall_area.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_height](wall_height.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wall_thermal_mass](wall_thermal_mass.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_content](water_content.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_current](water_current.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_cut](water_cut.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_feat_size](water_feat_size.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[water_production_rate](water_production_rate.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[wind_speed](wind_speed.md)* OPT **[QuantityValue](QuantityValue.md)** + * **None** *[xylene](xylene.md)* OPT **[QuantityValue](QuantityValue.md)** + +## Attributes + + +### Own + + * [➞has numeric value](quantityValue__has_numeric_value.md) OPT + * range: [Double](types/Double.md) + * [➞has raw value](quantityValue__has_raw_value.md) OPT + * range: [String](types/String.md) + * [➞has unit](quantityValue__has_unit.md) OPT + * Description: Example "m" + * range: [String](types/String.md) diff --git a/mixs6/Sediment.md b/mixs6/Sediment.md index 28646d9e..3ce7b16d 100644 --- a/mixs6/Sediment.md +++ b/mixs6/Sediment.md @@ -7,21 +7,21 @@ sediment URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig],[SedimentMisag],[SedimentMimarksS],[SedimentMimarksC],[SedimentMimag],[SedimentMigsVi],[SedimentMigsPl],[SedimentMigsOrg],[SedimentMigsEu],[SedimentMigsBa],[SedimentMe],[QuantityValue][MIGSBacteria],[Sediment]^-[SedimentMIGSBacteria],[Sediment],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSEukaryote.md b/mixs6/SedimentMIGSEukaryote.md new file mode 100644 index 00000000..98b47fc9 --- /dev/null +++ b/mixs6/SedimentMIGSEukaryote.md @@ -0,0 +1,559 @@ + +# Class: SedimentMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Sediment]^-[SedimentMIGSEukaryote],[Sediment],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSPlant.md b/mixs6/SedimentMIGSPlant.md new file mode 100644 index 00000000..a372cb36 --- /dev/null +++ b/mixs6/SedimentMIGSPlant.md @@ -0,0 +1,529 @@ + +# Class: SedimentMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Sediment]^-[SedimentMIGSPlant],[Sediment],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIGSVirus.md b/mixs6/SedimentMIGSVirus.md new file mode 100644 index 00000000..a6f2352f --- /dev/null +++ b/mixs6/SedimentMIGSVirus.md @@ -0,0 +1,554 @@ + +# Class: SedimentMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + +URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Sediment]^-[SedimentMIGSVirus],[Sediment],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SedimentMIMARKSSpecimen.md b/mixs6/SedimentMIMARKSSpecimen.md new file mode 100644 index 00000000..84368dae --- /dev/null +++ b/mixs6/SedimentMIMARKSSpecimen.md @@ -0,0 +1,479 @@ + +# Class: SedimentMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + +URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Sediment]^-[SedimentMIMARKSSpecimen],[Sediment],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMIMARKSSurvey.md b/mixs6/SedimentMIMARKSSurvey.md new file mode 100644 index 00000000..23b8e9f5 --- /dev/null +++ b/mixs6/SedimentMIMARKSSurvey.md @@ -0,0 +1,459 @@ + +# Class: SedimentMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + +URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Sediment]^-[SedimentMIMARKSSurvey],[Sediment],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Sediment](Sediment.md) - sediment + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from sediment: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [methane](methane.md) OPT + * Description: Methane (gas) amount or concentration at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 1800 parts per billion None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [particle_class](particle_class.md) OPT + * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + * range: [String](types/String.md) + * Example: None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [porosity](porosity.md) OPT + * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + * range: [String](types/String.md) + * Example: None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [sediment_type](sediment_type.md) OPT + * Description: Information about the sediment type based on major constituents + * range: + * Example: biogenous None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_carb](tot_carb.md) OPT + * Description: Total carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SedimentMe.md b/mixs6/SedimentMe.md index e4d2ee98..e80089a8 100644 --- a/mixs6/SedimentMe.md +++ b/mixs6/SedimentMe.md @@ -1,13 +1,13 @@ -# Class: SedimentMe +# Class: SedimentME -Combinatorial checklist for sediment with me +Combinatorial checklist Metagenome or Environmental with environmental package sediment -URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) +URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Me],[Sediment]^-[SedimentMe],[Sediment],[QuantityValue],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Sediment]^-[SedimentME],[Sediment],[QuantityValue],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -323,172 +323,172 @@ URI: [mixs.vocab:SedimentMe](https://w3id.org/mixs/vocab/SedimentMe) * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsOrg.md b/mixs6/SedimentMigsOrg.md index 98d68cd4..20109f52 100644 --- a/mixs6/SedimentMigsOrg.md +++ b/mixs6/SedimentMigsOrg.md @@ -1,13 +1,13 @@ -# Class: SedimentMigsOrg +# Class: SedimentMIGSOrg -Combinatorial checklist for sediment with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment -URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) +URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsOrg],[Sediment]^-[SedimentMigsOrg],[Sediment],[QuantityValue],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Sediment]^-[SedimentMIGSOrg],[Sediment],[QuantityValue],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -323,192 +323,192 @@ URI: [mixs.vocab:SedimentMigsOrg](https://w3id.org/mixs/vocab/SedimentMigsOrg) * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SedimentMimag.md b/mixs6/SedimentMimag.md index 574e973b..a97b940f 100644 --- a/mixs6/SedimentMimag.md +++ b/mixs6/SedimentMimag.md @@ -1,13 +1,13 @@ -# Class: SedimentMimag +# Class: SedimentMIMAG -Combinatorial checklist for sediment with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment -URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) +URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Mimag],[Sediment]^-[SedimentMimag],[Sediment],[QuantityValue],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Sediment]^-[SedimentMIMAG],[Sediment],[QuantityValue],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -323,252 +323,252 @@ URI: [mixs.vocab:SedimentMimag](https://w3id.org/mixs/vocab/SedimentMimag) * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SedimentMisag.md b/mixs6/SedimentMisag.md index ec72e9bf..40a1b0f2 100644 --- a/mixs6/SedimentMisag.md +++ b/mixs6/SedimentMisag.md @@ -1,13 +1,13 @@ -# Class: SedimentMisag +# Class: SedimentMISAG -Combinatorial checklist for sediment with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment -URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) +URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Misag],[Sediment]^-[SedimentMisag],[Sediment],[QuantityValue],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Sediment]^-[SedimentMISAG],[Sediment],[QuantityValue],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -323,257 +323,257 @@ URI: [mixs.vocab:SedimentMisag](https://w3id.org/mixs/vocab/SedimentMisag) * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SedimentMiuvig.md b/mixs6/SedimentMiuvig.md index 94201cfe..e1137cff 100644 --- a/mixs6/SedimentMiuvig.md +++ b/mixs6/SedimentMiuvig.md @@ -1,13 +1,13 @@ -# Class: SedimentMiuvig +# Class: SedimentMIUVIG -Combinatorial checklist for sediment with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment -URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) +URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Miuvig],[Sediment]^-[SedimentMiuvig],[Sediment],[QuantityValue],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Sediment]^-[SedimentMIUVIG],[Sediment],[QuantityValue],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -323,322 +323,322 @@ URI: [mixs.vocab:SedimentMiuvig](https://w3id.org/mixs/vocab/SedimentMiuvig) * range: [QuantityValue](QuantityValue.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Soil.md b/mixs6/Soil.md index b03f851e..a793f98e 100644 --- a/mixs6/Soil.md +++ b/mixs6/Soil.md @@ -7,21 +7,21 @@ soil URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig],[SoilMisag],[SoilMimarksS],[SoilMimarksC],[SoilMimag],[SoilMigsVi],[SoilMigsPl],[SoilMigsOrg],[SoilMigsEu],[SoilMigsBa],[SoilMe],[QuantityValue][MIGSBacteria],[Soil]^-[SoilMIGSBacteria],[Soil],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSEukaryote.md b/mixs6/SoilMIGSEukaryote.md new file mode 100644 index 00000000..9625d385 --- /dev/null +++ b/mixs6/SoilMIGSEukaryote.md @@ -0,0 +1,503 @@ + +# Class: SoilMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + +URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Soil]^-[SoilMIGSEukaryote],[Soil],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSPlant.md b/mixs6/SoilMIGSPlant.md new file mode 100644 index 00000000..2b70935f --- /dev/null +++ b/mixs6/SoilMIGSPlant.md @@ -0,0 +1,473 @@ + +# Class: SoilMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + +URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Soil]^-[SoilMIGSPlant],[Soil],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIGSVirus.md b/mixs6/SoilMIGSVirus.md new file mode 100644 index 00000000..5b98bb31 --- /dev/null +++ b/mixs6/SoilMIGSVirus.md @@ -0,0 +1,498 @@ + +# Class: SoilMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + +URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Soil]^-[SoilMIGSVirus],[Soil],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/SoilMIMARKSSpecimen.md b/mixs6/SoilMIMARKSSpecimen.md new file mode 100644 index 00000000..e8fb6847 --- /dev/null +++ b/mixs6/SoilMIMARKSSpecimen.md @@ -0,0 +1,423 @@ + +# Class: SoilMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + +URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Soil]^-[SoilMIMARKSSpecimen],[Soil],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMIMARKSSurvey.md b/mixs6/SoilMIMARKSSurvey.md new file mode 100644 index 00000000..f7628dd5 --- /dev/null +++ b/mixs6/SoilMIMARKSSurvey.md @@ -0,0 +1,403 @@ + +# Class: SoilMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + +URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Soil]^-[SoilMIMARKSSurvey],[Soil],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Soil](Soil.md) - soil + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from soil: + + * [agrochem_addition](agrochem_addition.md) OPT + * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications + * range: [String](types/String.md) + * Example: roundup;5 milligram per liter;2018-06-21 None + * [al_sat](al_sat.md) OPT + * Description: Aluminum saturation (esp. For tropical soils) + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [al_sat_meth](al_sat_meth.md) OPT + * Description: Reference or method used in determining Al saturation + * range: [String](types/String.md) + * Example: None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [annual_precpt](annual_precpt.md) OPT + * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [annual_temp](annual_temp.md) OPT + * Description: Mean annual temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 12.5 degree Celsius None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [crop_rotation](crop_rotation.md) OPT + * Description: Whether or not crop is rotated, and if yes, rotation schedule + * range: [String](types/String.md) + * Example: yes;R2/2017-01-01/2018-12-31/P6M None + * [cur_land_use](cur_land_use.md) OPT + * Description: Present state of sample site + * range: + * Example: conifers None + * [cur_vegetation](cur_vegetation.md) OPT + * Description: Vegetation classification from one or more standard classification systems, or agricultural crop + * range: [String](types/String.md) + * Example: None + * [cur_vegetation_meth](cur_vegetation_meth.md) OPT + * Description: Reference or method used in vegetation classification + * range: [String](types/String.md) + * Example: None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [drainage_class](drainage_class.md) OPT + * Description: Drainage classification from a standard system such as the USDA system + * range: + * Example: well None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [extreme_event](extreme_event.md) OPT + * Description: Unusual physical events that may have affected microbial populations + * range: [String](types/String.md) + * Example: None + * [extreme_salinity](extreme_salinity.md) OPT + * Description: Measured salinity + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [fao_class](fao_class.md) OPT + * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + * range: + * Example: Luvisols None + * [fire](fire.md) OPT + * Description: Historical and/or physical evidence of fire + * range: [String](types/String.md) + * Example: None + * [flooding](flooding.md) OPT + * Description: Historical and/or physical evidence of flooding + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [heavy_metals](heavy_metals.md) OPT + * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations + * range: [String](types/String.md) + * Example: None + * [heavy_metals_meth](heavy_metals_meth.md) OPT + * Description: Reference or method used in determining heavy metals + * range: [String](types/String.md) + * Example: None + * [horizon](horizon.md) OPT + * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + * range: + * Example: A horizon None + * [horizon_meth](horizon_meth.md) OPT + * Description: Reference or method used in determining the horizon + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [link_addit_analys](link_addit_analys.md) OPT + * Description: Link to additional analysis results performed on the sample + * range: [String](types/String.md) + * Example: None + * [link_class_info](link_class_info.md) OPT + * Description: Link to digitized soil maps or other soil classification information + * range: [String](types/String.md) + * Example: None + * [link_climate_info](link_climate_info.md) OPT + * Description: Link to climate resource + * range: [String](types/String.md) + * Example: None + * [local_class](local_class.md) OPT + * Description: Soil classification based on local soil classification system + * range: [String](types/String.md) + * Example: None + * [local_class_meth](local_class_meth.md) OPT + * Description: Reference or method used in determining the local soil classification + * range: [String](types/String.md) + * Example: None + * [microbial_biomass](microbial_biomass.md) OPT + * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [microbial_biomass_meth](microbial_biomass_meth.md) OPT + * Description: Reference or method used in determining microbial biomass + * range: [String](types/String.md) + * Example: None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [ph_meth](ph_meth.md) OPT + * Description: Reference or method used in determining ph + * range: [String](types/String.md) + * Example: None + * [pool_dna_extracts](pool_dna_extracts.md) OPT + * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + * range: [String](types/String.md) + * Example: yes;5 None + * [previous_land_use](previous_land_use.md) OPT + * Description: Previous land use and dates + * range: [String](types/String.md) + * Example: None + * [previous_land_use_meth](previous_land_use_meth.md) OPT + * Description: Reference or method used in determining previous land use and dates + * range: [String](types/String.md) + * Example: None + * [profile_position](profile_position.md) OPT + * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + * range: + * Example: summit None + * [salinity_meth](salinity_meth.md) OPT + * Description: Reference or method used in determining salinity + * range: [String](types/String.md) + * Example: None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [season_precpt](season_precpt.md) OPT + * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [season_temp](season_temp.md) OPT + * Description: Mean seasonal temperature + * range: [QuantityValue](QuantityValue.md) + * Example: 18 degree Celsius None + * [sieving](sieving.md) OPT + * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved + * range: [String](types/String.md) + * Example: None + * [slope_aspect](slope_aspect.md) OPT + * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [slope_gradient](slope_gradient.md) OPT + * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [soil_type](soil_type.md) OPT + * Description: Soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [soil_type_meth](soil_type_meth.md) OPT + * Description: Reference or method used in determining soil series name or other lower-level classification + * range: [String](types/String.md) + * Example: None + * [store_cond](store_cond.md) OPT + * Description: Explain how and for how long the soil sample was stored before DNA extraction + * range: [String](types/String.md) + * Example: -20 degree Celsius freezer;P2Y10D None + * [texture](texture.md) OPT + * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [texture_meth](texture_meth.md) OPT + * Description: Reference or method used in determining soil texture + * range: [String](types/String.md) + * Example: None + * [tillage](tillage.md) OPT + * Description: Note method(s) used for tilling + * range: + * Example: chisel None + * [tot_nitro_content](tot_nitro_content.md) OPT + * Description: Total nitrogen content of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT + * Description: Reference or method used in determining the total nitrogen + * range: [String](types/String.md) + * Example: None + * [tot_org_c_meth](tot_org_c_meth.md) OPT + * Description: Reference or method used in determining total organic carbon + * range: [String](types/String.md) + * Example: None + * [tot_org_carb](tot_org_carb.md) OPT + * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content](water_content.md) OPT + * Description: Water content measurement + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [water_content_soil_meth](water_content_soil_meth.md) OPT + * Description: Reference or method used in determining the water content of soil + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/SoilMe.md b/mixs6/SoilMe.md index 3dae9c38..c48b99d7 100644 --- a/mixs6/SoilMe.md +++ b/mixs6/SoilMe.md @@ -1,13 +1,13 @@ -# Class: SoilMe +# Class: SoilME -Combinatorial checklist for soil with me +Combinatorial checklist Metagenome or Environmental with environmental package soil -URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) +URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Me],[Soil]^-[SoilMe],[Soil],[QuantityValue],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Soil]^-[SoilME],[Soil],[QuantityValue],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -267,172 +267,172 @@ URI: [mixs.vocab:SoilMe](https://w3id.org/mixs/vocab/SoilMe) * range: [String](types/String.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SoilMigsOrg.md b/mixs6/SoilMigsOrg.md index 313b1796..ea63bc82 100644 --- a/mixs6/SoilMigsOrg.md +++ b/mixs6/SoilMigsOrg.md @@ -1,13 +1,13 @@ -# Class: SoilMigsOrg +# Class: SoilMIGSOrg -Combinatorial checklist for soil with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil -URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) +URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsOrg],[Soil]^-[SoilMigsOrg],[Soil],[QuantityValue],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Soil]^-[SoilMIGSOrg],[Soil],[QuantityValue],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -267,192 +267,192 @@ URI: [mixs.vocab:SoilMigsOrg](https://w3id.org/mixs/vocab/SoilMigsOrg) * range: [String](types/String.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SoilMimag.md b/mixs6/SoilMimag.md index 8f609c07..f4cda22c 100644 --- a/mixs6/SoilMimag.md +++ b/mixs6/SoilMimag.md @@ -1,13 +1,13 @@ -# Class: SoilMimag +# Class: SoilMIMAG -Combinatorial checklist for soil with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil -URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) +URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Mimag],[Soil]^-[SoilMimag],[Soil],[QuantityValue],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Soil]^-[SoilMIMAG],[Soil],[QuantityValue],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -267,252 +267,252 @@ URI: [mixs.vocab:SoilMimag](https://w3id.org/mixs/vocab/SoilMimag) * range: [String](types/String.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SoilMisag.md b/mixs6/SoilMisag.md index 7bbdebf7..03788bf3 100644 --- a/mixs6/SoilMisag.md +++ b/mixs6/SoilMisag.md @@ -1,13 +1,13 @@ -# Class: SoilMisag +# Class: SoilMISAG -Combinatorial checklist for soil with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil -URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) +URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Misag],[Soil]^-[SoilMisag],[Soil],[QuantityValue],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Soil]^-[SoilMISAG],[Soil],[QuantityValue],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -267,257 +267,257 @@ URI: [mixs.vocab:SoilMisag](https://w3id.org/mixs/vocab/SoilMisag) * range: [String](types/String.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/SoilMiuvig.md b/mixs6/SoilMiuvig.md index 51d4ec13..8941ac26 100644 --- a/mixs6/SoilMiuvig.md +++ b/mixs6/SoilMiuvig.md @@ -1,13 +1,13 @@ -# Class: SoilMiuvig +# Class: SoilMIUVIG -Combinatorial checklist for soil with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil -URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) +URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[Miuvig],[Soil]^-[SoilMiuvig],[Soil],[QuantityValue],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Soil]^-[SoilMIUVIG],[Soil],[QuantityValue],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -267,322 +267,322 @@ URI: [mixs.vocab:SoilMiuvig](https://w3id.org/mixs/vocab/SoilMiuvig) * range: [String](types/String.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludge.md b/mixs6/WastewaterSludge.md index c169a3de..e79f569a 100644 --- a/mixs6/WastewaterSludge.md +++ b/mixs6/WastewaterSludge.md @@ -7,21 +7,21 @@ wastewater/sludge URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig],[WastewaterSludgeMisag],[WastewaterSludgeMimarksS],[WastewaterSludgeMimarksC],[WastewaterSludgeMimag],[WastewaterSludgeMigsVi],[WastewaterSludgeMigsPl],[WastewaterSludgeMigsOrg],[WastewaterSludgeMigsEu],[WastewaterSludgeMigsBa],[WastewaterSludgeMe],[QuantityValue][MIGSBacteria],[WastewaterSludge]^-[WastewaterSludgeMIGSBacteria],[WastewaterSludge],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSEukaryote.md b/mixs6/WastewaterSludgeMIGSEukaryote.md new file mode 100644 index 00000000..689b2143 --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSEukaryote.md @@ -0,0 +1,443 @@ + +# Class: WastewaterSludgeMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSEukaryote],[WastewaterSludge]^-[WastewaterSludgeMIGSEukaryote],[WastewaterSludge],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSPlant.md b/mixs6/WastewaterSludgeMIGSPlant.md new file mode 100644 index 00000000..b1101bab --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSPlant.md @@ -0,0 +1,413 @@ + +# Class: WastewaterSludgeMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSPlant],[WastewaterSludge]^-[WastewaterSludgeMIGSPlant],[WastewaterSludge],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIGSVirus.md b/mixs6/WastewaterSludgeMIGSVirus.md new file mode 100644 index 00000000..a011b650 --- /dev/null +++ b/mixs6/WastewaterSludgeMIGSVirus.md @@ -0,0 +1,438 @@ + +# Class: WastewaterSludgeMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSVirus],[WastewaterSludge]^-[WastewaterSludgeMIGSVirus],[WastewaterSludge],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WastewaterSludgeMIMARKSSpecimen.md b/mixs6/WastewaterSludgeMIMARKSSpecimen.md new file mode 100644 index 00000000..d05256a9 --- /dev/null +++ b/mixs6/WastewaterSludgeMIMARKSSpecimen.md @@ -0,0 +1,363 @@ + +# Class: WastewaterSludgeMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludge],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMIMARKSSurvey.md b/mixs6/WastewaterSludgeMIMARKSSurvey.md new file mode 100644 index 00000000..d7ff24dd --- /dev/null +++ b/mixs6/WastewaterSludgeMIMARKSSurvey.md @@ -0,0 +1,343 @@ + +# Class: WastewaterSludgeMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + +URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSurvey],[WastewaterSludge],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from wastewater_sludge: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT + * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chem_oxygen_dem](chem_oxygen_dem.md) OPT + * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [efficiency_percent](efficiency_percent.md) OPT + * Description: Percentage of volatile solids removed from the anaerobic digestor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [emulsions](emulsions.md) OPT + * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + * range: [String](types/String.md) + * Example: None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [gaseous_substances](gaseous_substances.md) OPT + * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [indust_eff_percent](indust_eff_percent.md) OPT + * Description: Percentage of industrial effluents received by wastewater treatment plant + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [inorg_particles](inorg_particles.md) OPT + * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + * range: [String](types/String.md) + * Example: None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [org_particles](org_particles.md) OPT + * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + * range: [String](types/String.md) + * Example: None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [pre_treatment](pre_treatment.md) OPT + * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + * range: [String](types/String.md) + * Example: None + * [primary_treatment](primary_treatment.md) OPT + * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + * range: [String](types/String.md) + * Example: None + * [reactor_type](reactor_type.md) OPT + * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + * range: [String](types/String.md) + * Example: None + * [samp_salinity](samp_salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 1 milligram per liter None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [secondary_treatment](secondary_treatment.md) OPT + * Description: The process for substantially degrading the biological content of the sewage + * range: [String](types/String.md) + * Example: None + * [sewage_type](sewage_type.md) OPT + * Description: Type of wastewater treatment plant as municipial or industrial + * range: [String](types/String.md) + * Example: None + * [sludge_retent_time](sludge_retent_time.md) OPT + * Description: The time activated sludge remains in reactor + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_inorg_mat](soluble_inorg_mat.md) OPT + * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + * range: [String](types/String.md) + * Example: None + * [soluble_org_mat](soluble_org_mat.md) OPT + * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + * range: [String](types/String.md) + * Example: None + * [suspend_solids](suspend_solids.md) OPT + * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + * range: [String](types/String.md) + * Example: None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tertiary_treatment](tertiary_treatment.md) OPT + * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + * range: [String](types/String.md) + * Example: None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_phosphate](tot_phosphate.md) OPT + * Description: Total amount or concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: None + * [wastewater_type](wastewater_type.md) OPT + * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + * range: [String](types/String.md) + * Example: None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMe.md b/mixs6/WastewaterSludgeMe.md index 991d6ee4..105f9315 100644 --- a/mixs6/WastewaterSludgeMe.md +++ b/mixs6/WastewaterSludgeMe.md @@ -1,13 +1,13 @@ -# Class: WastewaterSludgeMe +# Class: WastewaterSludgeME -Combinatorial checklist for wastewater_sludge with me +Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge -URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludgeMe) +URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludgeME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Me],[WastewaterSludge]^-[WastewaterSludgeMe],[WastewaterSludge],[QuantityValue],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[ME],[WastewaterSludge]^-[WastewaterSludgeME],[WastewaterSludge],[QuantityValue],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -207,172 +207,172 @@ URI: [mixs.vocab:WastewaterSludgeMe](https://w3id.org/mixs/vocab/WastewaterSludg * range: [String](types/String.md) * Example: None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsOrg.md b/mixs6/WastewaterSludgeMigsOrg.md index 674f8c01..391e1d6c 100644 --- a/mixs6/WastewaterSludgeMigsOrg.md +++ b/mixs6/WastewaterSludgeMigsOrg.md @@ -1,13 +1,13 @@ -# Class: WastewaterSludgeMigsOrg +# Class: WastewaterSludgeMIGSOrg -Combinatorial checklist for wastewater_sludge with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge -URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMigsOrg) +URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsOrg],[WastewaterSludge]^-[WastewaterSludgeMigsOrg],[WastewaterSludge],[QuantityValue],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSOrg],[WastewaterSludge]^-[WastewaterSludgeMIGSOrg],[WastewaterSludge],[QuantityValue],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -207,192 +207,192 @@ URI: [mixs.vocab:WastewaterSludgeMigsOrg](https://w3id.org/mixs/vocab/Wastewater * range: [String](types/String.md) * Example: None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimag.md b/mixs6/WastewaterSludgeMimag.md index 45af03c6..26c6dc62 100644 --- a/mixs6/WastewaterSludgeMimag.md +++ b/mixs6/WastewaterSludgeMimag.md @@ -1,13 +1,13 @@ -# Class: WastewaterSludgeMimag +# Class: WastewaterSludgeMIMAG -Combinatorial checklist for wastewater_sludge with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge -URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSludgeMimag) +URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSludgeMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Mimag],[WastewaterSludge]^-[WastewaterSludgeMimag],[WastewaterSludge],[QuantityValue],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMAG],[WastewaterSludge]^-[WastewaterSludgeMIMAG],[WastewaterSludge],[QuantityValue],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -207,252 +207,252 @@ URI: [mixs.vocab:WastewaterSludgeMimag](https://w3id.org/mixs/vocab/WastewaterSl * range: [String](types/String.md) * Example: None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMisag.md b/mixs6/WastewaterSludgeMisag.md index e852dd0f..53d84cc7 100644 --- a/mixs6/WastewaterSludgeMisag.md +++ b/mixs6/WastewaterSludgeMisag.md @@ -1,13 +1,13 @@ -# Class: WastewaterSludgeMisag +# Class: WastewaterSludgeMISAG -Combinatorial checklist for wastewater_sludge with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge -URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSludgeMisag) +URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSludgeMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Misag],[WastewaterSludge]^-[WastewaterSludgeMisag],[WastewaterSludge],[QuantityValue],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MISAG],[WastewaterSludge]^-[WastewaterSludgeMISAG],[WastewaterSludge],[QuantityValue],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -207,257 +207,257 @@ URI: [mixs.vocab:WastewaterSludgeMisag](https://w3id.org/mixs/vocab/WastewaterSl * range: [String](types/String.md) * Example: None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMiuvig.md b/mixs6/WastewaterSludgeMiuvig.md index 1ed5690c..9c418938 100644 --- a/mixs6/WastewaterSludgeMiuvig.md +++ b/mixs6/WastewaterSludgeMiuvig.md @@ -1,13 +1,13 @@ -# Class: WastewaterSludgeMiuvig +# Class: WastewaterSludgeMIUVIG -Combinatorial checklist for wastewater_sludge with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge -URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterSludgeMiuvig) +URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterSludgeMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[Miuvig],[WastewaterSludge]^-[WastewaterSludgeMiuvig],[WastewaterSludge],[QuantityValue],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIUVIG],[WastewaterSludge]^-[WastewaterSludgeMIUVIG],[WastewaterSludge],[QuantityValue],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -207,322 +207,322 @@ URI: [mixs.vocab:WastewaterSludgeMiuvig](https://w3id.org/mixs/vocab/WastewaterS * range: [String](types/String.md) * Example: None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/Water.md b/mixs6/Water.md index 13f03f4b..9a69b7dc 100644 --- a/mixs6/Water.md +++ b/mixs6/Water.md @@ -7,21 +7,21 @@ water URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig],[WaterMisag],[WaterMimarksS],[WaterMimarksC],[WaterMimag],[WaterMigsVi],[WaterMigsPl],[WaterMigsOrg],[WaterMigsEu],[WaterMigsBa],[WaterMe],[QuantityValue][MIGSBacteria],[Water]^-[WaterMIGSBacteria],[Water],[QuantityValue],[MIGSBacteria]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) OPT + * range: + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞url](MIGS_bacteria_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSEukaryote.md b/mixs6/WaterMIGSEukaryote.md new file mode 100644 index 00000000..b3c47be3 --- /dev/null +++ b/mixs6/WaterMIGSEukaryote.md @@ -0,0 +1,619 @@ + +# Class: WaterMIGSEukaryote + + +Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + +URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukaryote) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Water]^-[WaterMIGSEukaryote],[Water],[QuantityValue],[MIGSEukaryote]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) OPT + * range: + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSPlant.md b/mixs6/WaterMIGSPlant.md new file mode 100644 index 00000000..ce6ec339 --- /dev/null +++ b/mixs6/WaterMIGSPlant.md @@ -0,0 +1,589 @@ + +# Class: WaterMIGSPlant + + +Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + +URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Water]^-[WaterMIGSPlant],[Water],[QuantityValue],[MIGSPlant]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS plant: + + * [MIGS plant➞adapters](MIGS_plant_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞annot](MIGS_plant_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞env_package](MIGS_plant_env_package.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞project_name](MIGS_plant_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞propagation](MIGS_plant_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sop](MIGS_plant_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) OPT + * range: + +### Mixed in from MIGS plant: + + * [MIGS plant➞url](MIGS_plant_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIGSVirus.md b/mixs6/WaterMIGSVirus.md new file mode 100644 index 00000000..aaead86a --- /dev/null +++ b/mixs6/WaterMIGSVirus.md @@ -0,0 +1,614 @@ + +# Class: WaterMIGSVirus + + +Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + +URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Water]^-[WaterMIGSVirus],[Water],[QuantityValue],[MIGSVirus]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIGS virus: + + * [MIGS virus➞adapters](MIGS_virus_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞annot](MIGS_virus_annot.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞env_package](MIGS_virus_env_package.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞project_name](MIGS_virus_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞propagation](MIGS_virus_propagation.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sop](MIGS_virus_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) OPT + * range: + +### Mixed in from MIGS virus: + + * [MIGS virus➞url](MIGS_virus_url.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) OPT + * range: diff --git a/mixs6/WaterMIMARKSSpecimen.md b/mixs6/WaterMIMARKSSpecimen.md new file mode 100644 index 00000000..90772ab7 --- /dev/null +++ b/mixs6/WaterMIMARKSSpecimen.md @@ -0,0 +1,539 @@ + +# Class: WaterMIMARKSSpecimen + + +Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + +URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSSpecimen) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Water]^-[WaterMIMARKSSpecimen],[Water],[QuantityValue],[MIMARKSSpecimen]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMIMARKSSurvey.md b/mixs6/WaterMIMARKSSurvey.md new file mode 100644 index 00000000..150f3d46 --- /dev/null +++ b/mixs6/WaterMIMARKSSurvey.md @@ -0,0 +1,519 @@ + +# Class: WaterMIMARKSSurvey + + +Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + +URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSurvey) + + +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Water]^-[WaterMIMARKSSurvey],[Water],[QuantityValue],[MIMARKSSurvey]) + +## Parents + + * is_a: [Water](Water.md) - water + +## Uses Mixins + + * mixin: [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + +## Attributes + + +### Inherited from water: + + * [alkalinity](alkalinity.md) OPT + * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + * range: [QuantityValue](QuantityValue.md) + * Example: 50 milligram per liter None + * [alkalinity_method](alkalinity_method.md) OPT + * Description: Method used for alkalinity measurement + * range: [String](types/String.md) + * Example: titration None + * [alkyl_diethers](alkyl_diethers.md) OPT + * Description: Concentration of alkyl diethers + * range: [QuantityValue](QuantityValue.md) + * Example: 0.005 mole per liter None + * [alt](alt.md) OPT + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [aminopept_act](aminopept_act.md) OPT + * Description: Measurement of aminopeptidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.269 mole per liter per hour None + * [ammonium](ammonium.md) OPT + * Description: Concentration of ammonium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 milligram per liter None + * [atmospheric_data](atmospheric_data.md) OPT + * Description: Measurement of atmospheric data; can include multiple data + * range: [String](types/String.md) + * Example: wind speed;9 knots None + * [bac_prod](bac_prod.md) OPT + * Description: Bacterial production in the water column measured by isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter per day None + * [bac_resp](bac_resp.md) OPT + * Description: Measurement of bacterial respiration in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 300 micromole oxygen per liter per hour None + * [bacteria_carb_prod](bacteria_carb_prod.md) OPT + * Description: Measurement of bacterial carbon production + * range: [QuantityValue](QuantityValue.md) + * Example: 2.53 microgram per liter per hour None + * [biomass](biomass.md) OPT + * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + * range: [String](types/String.md) + * Example: total;20 gram None + * [bishomohopanol](bishomohopanol.md) OPT + * Description: Concentration of bishomohopanol + * range: [QuantityValue](QuantityValue.md) + * Example: 14 microgram per liter None + * [bromide](bromide.md) OPT + * Description: Concentration of bromide + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 parts per million None + * [calcium](calcium.md) OPT + * Description: Concentration of calcium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micromole per liter None + * [carb_nitro_ratio](carb_nitro_ratio.md) OPT + * Description: Ratio of amount or concentrations of carbon to nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.417361111 None + * [chem_administration](chem_administration.md) OPT + * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + * range: [String](types/String.md) + * Example: agar [CHEBI:2509];2018-05-11T20:00Z None + * [chloride](chloride.md) OPT + * Description: Concentration of chloride in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5000 milligram per liter None + * [chlorophyll](chlorophyll.md) OPT + * Description: Concentration of chlorophyll + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per cubic meter None + * [collection_date](collection_date.md) OPT + * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant + * range: [String](types/String.md) + * Example: 2018-05-11T10:00:00+01:00 None + * [conduc](conduc.md) OPT + * Description: Electrical conductivity of water + * range: [QuantityValue](QuantityValue.md) + * Example: 10 milliSiemens per centimeter None + * [density](density.md) OPT + * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + * range: [QuantityValue](QuantityValue.md) + * Example: 1000 kilogram per cubic meter None + * [depth](depth.md) OPT + * Description: Please refer to the definitions of depth in the environmental packages + * range: [String](types/String.md) + * Example: None + * [diether_lipids](diether_lipids.md) OPT + * Description: Concentration of diether lipids; can include multiple types of diether lipids + * range: [String](types/String.md) + * Example: 0.2 nanogram per liter None + * [diss_carb_dioxide](diss_carb_dioxide.md) OPT + * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 milligram per liter None + * [diss_hydrogen](diss_hydrogen.md) OPT + * Description: Concentration of dissolved hydrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [diss_inorg_carb](diss_inorg_carb.md) OPT + * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + * range: [QuantityValue](QuantityValue.md) + * Example: 2059 micromole per kilogram None + * [diss_inorg_nitro](diss_inorg_nitro.md) OPT + * Description: Concentration of dissolved inorganic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 761 micromole per liter None + * [diss_inorg_phosp](diss_inorg_phosp.md) OPT + * Description: Concentration of dissolved inorganic phosphorus in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 56.5 micromole per liter None + * [diss_org_carb](diss_org_carb.md) OPT + * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 197 micromole per liter None + * [diss_org_nitro](diss_org_nitro.md) OPT + * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [diss_oxygen](diss_oxygen.md) OPT + * Description: Concentration of dissolved oxygen + * range: [QuantityValue](QuantityValue.md) + * Example: 175 micromole per kilogram None + * [down_par](down_par.md) OPT + * Description: Visible waveband radiance and irradiance measurements in the water column + * range: [QuantityValue](QuantityValue.md) + * Example: 28.71 microEinstein per square meter per second None + * [elev](elev.md) OPT + * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + * range: [QuantityValue](QuantityValue.md) + * Example: 100 meter None + * [env_broad_scale](env_broad_scale.md) OPT + * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: forest biome [ENVO:01000174] None + * [env_local_scale](env_local_scale.md) OPT + * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: litter layer [ENVO:01000338] None + * [env_medium](env_medium.md) OPT + * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html + * range: [String](types/String.md) + * Example: soil [ENVO:00001998] None + * [fluor](fluor.md) OPT + * Description: Raw or converted fluorescence of water + * range: [QuantityValue](QuantityValue.md) + * Example: 2.5 volts None + * [geo_loc_name](geo_loc_name.md) OPT + * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) + * range: [String](types/String.md) + * Example: Germany;North Rhine-Westphalia;Eifel National Park None + * [glucosidase_act](glucosidase_act.md) OPT + * Description: Measurement of glucosidase activity + * range: [QuantityValue](QuantityValue.md) + * Example: 5 mol per liter per hour None + * [lat_lon](lat_lon.md) OPT + * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system + * range: [String](types/String.md) + * Example: 50.586825 6.408977 None + * [light_intensity](light_intensity.md) OPT + * Description: Measurement of light intensity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 lux None + * [magnesium](magnesium.md) OPT + * Description: Concentration of magnesium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 52.8 micromole per kilogram None + * [mean_frict_vel](mean_frict_vel.md) OPT + * Description: Measurement of mean friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 meter per second None + * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT + * Description: Measurement of mean peak friction velocity + * range: [QuantityValue](QuantityValue.md) + * Example: 1 meter per second None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [n_alkanes](n_alkanes.md) OPT + * Description: Concentration of n-alkanes; can include multiple n-alkanes + * range: [String](types/String.md) + * Example: n-hexadecane;100 milligram per liter None + * [nitrate](nitrate.md) OPT + * Description: Concentration of nitrate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 65 micromole per liter None + * [nitrite](nitrite.md) OPT + * Description: Concentration of nitrite in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 micromole per liter None + * [nitro](nitro.md) OPT + * Description: Concentration of nitrogen (total) + * range: [QuantityValue](QuantityValue.md) + * Example: 4.2 micromole per liter None + * [org_carb](org_carb.md) OPT + * Description: Concentration of organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.5 microgram per liter None + * [org_matter](org_matter.md) OPT + * Description: Concentration of organic matter + * range: [QuantityValue](QuantityValue.md) + * Example: 1.75 milligram per cubic meter None + * [org_nitro](org_nitro.md) OPT + * Description: Concentration of organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 4 micromole per liter None + * [organism_count](organism_count.md) OPT + * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) + * range: + * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None + * [oxy_stat_samp](oxy_stat_samp.md) OPT + * Description: Oxygenation status of sample + * range: + * Example: aerobic None + * [part_org_carb](part_org_carb.md) OPT + * Description: Concentration of particulate organic carbon + * range: [QuantityValue](QuantityValue.md) + * Example: 1.92 micromole per liter None + * [part_org_nitro](part_org_nitro.md) OPT + * Description: Concentration of particulate organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 micromole per liter None + * [perturbation](perturbation.md) OPT + * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + * range: [String](types/String.md) + * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None + * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT + * Description: Concentration of petroleum hydrocarbon + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [ph](ph.md) OPT + * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + * range: [Double](types/Double.md) + * Example: 7.2 None + * [phaeopigments](phaeopigments.md) OPT + * Description: Concentration of phaeopigments; can include multiple phaeopigments + * range: [String](types/String.md) + * Example: 2.5 milligram per cubic meter None + * [phosphate](phosphate.md) OPT + * Description: Concentration of phosphate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.7 micromole per liter None + * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT + * Description: Concentration of phospholipid fatty acids; can include multiple values + * range: [String](types/String.md) + * Example: 2.98 milligram per liter None + * [photon_flux](photon_flux.md) OPT + * Description: Measurement of photon flux + * range: [QuantityValue](QuantityValue.md) + * Example: 3.926 micromole photons per second per square meter None + * [potassium](potassium.md) OPT + * Description: Concentration of potassium in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 463 milligram per liter None + * [pressure](pressure.md) OPT + * Description: Pressure to which the sample is subject to, in atmospheres + * range: [QuantityValue](QuantityValue.md) + * Example: 50 atmosphere None + * [primary_prod](primary_prod.md) OPT + * Description: Measurement of primary production, generally measured as isotope uptake + * range: [QuantityValue](QuantityValue.md) + * Example: 100 milligram per cubic meter per day None + * [redox_potential](redox_potential.md) OPT + * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + * range: [QuantityValue](QuantityValue.md) + * Example: 300 millivolt None + * [salinity](salinity.md) OPT + * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + * range: [QuantityValue](QuantityValue.md) + * Example: 25 practical salinity unit None + * [samp_store_dur](samp_store_dur.md) OPT + * Description: Duration for which the sample was stored + * range: [String](types/String.md) + * Example: P1Y6M None + * [samp_store_loc](samp_store_loc.md) OPT + * Description: Location at which sample was stored, usually name of a specific freezer/room + * range: [String](types/String.md) + * Example: Freezer no:5 None + * [samp_store_temp](samp_store_temp.md) OPT + * Description: Temperature at which sample was stored, e.g. -80 degree Celsius + * range: [QuantityValue](QuantityValue.md) + * Example: -80 degree Celsius None + * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT + * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction + * range: [QuantityValue](QuantityValue.md) + * Example: 1500 milliliter None + * [silicate](silicate.md) OPT + * Description: Concentration of silicate + * range: [QuantityValue](QuantityValue.md) + * Example: 0.05 micromole per liter None + * [size_frac_low](size_frac_low.md) OPT + * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 0.2 micrometer None + * [size_frac_up](size_frac_up.md) OPT + * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 20 micrometer None + * [sodium](sodium.md) OPT + * Description: Sodium concentration in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 10.5 milligram per liter None + * [soluble_react_phosp](soluble_react_phosp.md) OPT + * Description: Concentration of soluble reactive phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.1 milligram per liter None + * [sulfate](sulfate.md) OPT + * Description: Concentration of sulfate in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 5 micromole per liter None + * [sulfide](sulfide.md) OPT + * Description: Concentration of sulfide in the sample + * range: [QuantityValue](QuantityValue.md) + * Example: 2 micromole per liter None + * [suspend_part_matter](suspend_part_matter.md) OPT + * Description: Concentration of suspended particulate matter + * range: [QuantityValue](QuantityValue.md) + * Example: 0.5 milligram per liter None + * [temp](temp.md) OPT + * Description: Temperature of the sample at the time of sampling + * range: [QuantityValue](QuantityValue.md) + * Example: 25 degree Celsius None + * [tidal_stage](tidal_stage.md) OPT + * Description: Stage of tide + * range: + * Example: high tide None + * [tot_depth_water_col](tot_depth_water_col.md) OPT + * Description: Measurement of total depth of water column + * range: [QuantityValue](QuantityValue.md) + * Example: 500 meter None + * [tot_diss_nitro](tot_diss_nitro.md) OPT + * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_inorg_nitro](tot_inorg_nitro.md) OPT + * Description: Total inorganic nitrogen content + * range: [QuantityValue](QuantityValue.md) + * Example: 40 microgram per liter None + * [tot_nitro](tot_nitro.md) OPT + * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen + * range: [QuantityValue](QuantityValue.md) + * Example: 50 micromole per liter None + * [tot_part_carb](tot_part_carb.md) OPT + * Description: Total particulate carbon content + * range: [QuantityValue](QuantityValue.md) + * Example: 35 micromole per liter None + * [tot_phosp](tot_phosp.md) OPT + * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus + * range: [QuantityValue](QuantityValue.md) + * Example: 0.03 milligram per liter None + * [turbidity](turbidity.md) OPT + * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles + * range: [QuantityValue](QuantityValue.md) + * Example: 0.3 nephelometric turbidity units None + * [water_current](water_current.md) OPT + * Description: Measurement of magnitude and direction of flow within a fluid + * range: [QuantityValue](QuantityValue.md) + * Example: 10 cubic meter per second None + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) REQ + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) OPT + * range: [String](types/String.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) OPT + * range: + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞url](MIMARKS_survey_url.md) OPT + * range: [String](types/String.md) diff --git a/mixs6/WaterMe.md b/mixs6/WaterMe.md index 6262db6c..7223710b 100644 --- a/mixs6/WaterMe.md +++ b/mixs6/WaterMe.md @@ -1,13 +1,13 @@ -# Class: WaterMe +# Class: WaterME -Combinatorial checklist for water with me +Combinatorial checklist Metagenome or Environmental with environmental package water -URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) +URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMe|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Me],[Water]^-[WaterMe],[Water],[QuantityValue],[Me]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Water]^-[WaterME],[Water],[QuantityValue],[ME]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) ## Uses Mixins - * mixin: [Me](Me.md) - me Checklist + * mixin: [ME](ME.md) - Metagenome or Environmental ## Attributes @@ -383,172 +383,172 @@ URI: [mixs.vocab:WaterMe](https://w3id.org/mixs/vocab/WaterMe) * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from me: +### Mixed in from ME: - * [me➞adapters](me_adapters.md) OPT + * [ME➞adapters](ME_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞annot](me_annot.md) OPT + * [ME➞annot](ME_annot.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_name](me_assembly_name.md) OPT + * [ME➞assembly_name](ME_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_qual](me_assembly_qual.md) OPT + * [ME➞assembly_qual](ME_assembly_qual.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞assembly_software](me_assembly_software.md) OPT + * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞env_package](me_env_package.md) OPT + * [ME➞env_package](ME_env_package.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞experimental_factor](me_experimental_factor.md) OPT + * [ME➞experimental_factor](ME_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞feat_pred](me_feat_pred.md) OPT + * [ME➞feat_pred](ME_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞investigation_type](me_investigation_type.md) REQ + * [ME➞investigation_type](ME_investigation_type.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_layout](me_lib_layout.md) OPT + * [ME➞lib_layout](ME_lib_layout.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) OPT + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_screen](me_lib_screen.md) OPT + * [ME➞lib_screen](ME_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_size](me_lib_size.md) OPT + * [ME➞lib_size](ME_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞lib_vector](me_lib_vector.md) OPT + * [ME➞lib_vector](ME_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞mid](me_mid.md) OPT + * [ME➞mid](ME_mid.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) OPT + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) OPT + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞number_contig](me_number_contig.md) OPT + * [ME➞number_contig](ME_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞project_name](me_project_name.md) REQ + * [ME➞project_name](ME_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_biomaterial](me_ref_biomaterial.md) OPT + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞ref_db](me_ref_db.md) OPT + * [ME➞ref_db](ME_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) OPT + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_collect_device](me_samp_collect_device.md) OPT + * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_mat_process](me_samp_mat_process.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞samp_size](me_samp_size.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sample_name](me_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞seq_meth](me_seq_meth.md) REQ + * [ME➞seq_meth](ME_seq_meth.md) REQ * range: -### Mixed in from me: +### Mixed in from ME: - * [me➞sim_search_meth](me_sim_search_meth.md) OPT + * [ME➞sim_search_meth](ME_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞size_frac](me_size_frac.md) OPT + * [ME➞size_frac](ME_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞sop](me_sop.md) OPT + * [ME➞sop](ME_sop.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞source_mat_id](me_source_mat_id.md) OPT + * [ME➞source_mat_id](ME_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) REQ + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞tax_class](me_tax_class.md) OPT + * [ME➞tax_class](ME_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from me: +### Mixed in from ME: - * [me➞url](me_url.md) OPT + * [ME➞url](ME_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WaterMigsOrg.md b/mixs6/WaterMigsOrg.md index edb74005..00716a11 100644 --- a/mixs6/WaterMigsOrg.md +++ b/mixs6/WaterMigsOrg.md @@ -1,13 +1,13 @@ -# Class: WaterMigsOrg +# Class: WaterMIGSOrg -Combinatorial checklist for water with migs_org +Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water -URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) +URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsOrg],[Water]^-[WaterMigsOrg],[Water],[QuantityValue],[MigsOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Water]^-[WaterMIGSOrg],[Water],[QuantityValue],[MIGSOrg]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) ## Uses Mixins - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist + * mixin: [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org ## Attributes @@ -383,192 +383,192 @@ URI: [mixs.vocab:WaterMigsOrg](https://w3id.org/mixs/vocab/WaterMigsOrg) * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞adapters](migs_org_adapters.md) OPT + * [MIGS org➞adapters](MIGS_org_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞annot](migs_org_annot.md) OPT + * [MIGS org➞annot](MIGS_org_annot.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_name](migs_org_assembly_name.md) OPT + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) OPT + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞assembly_software](migs_org_assembly_software.md) REQ + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_score](migs_org_compl_score.md) OPT + * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞compl_software](migs_org_compl_software.md) OPT + * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞env_package](migs_org_env_package.md) OPT + * [MIGS org➞env_package](MIGS_org_env_package.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞estimated_size](migs_org_estimated_size.md) OPT + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) OPT + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) OPT + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞feat_pred](migs_org_feat_pred.md) OPT + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞investigation_type](migs_org_investigation_type.md) REQ + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) REQ + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_layout](migs_org_lib_layout.md) OPT + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) OPT + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_screen](migs_org_lib_screen.md) OPT + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_size](migs_org_lib_size.md) OPT + * [MIGS org➞lib_size](MIGS_org_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞lib_vector](migs_org_lib_vector.md) OPT + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) OPT + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) OPT + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞number_contig](migs_org_number_contig.md) OPT + * [MIGS org➞number_contig](MIGS_org_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞project_name](migs_org_project_name.md) REQ + * [MIGS org➞project_name](MIGS_org_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) OPT + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞ref_db](migs_org_ref_db.md) OPT + * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) OPT + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞samp_size](migs_org_samp_size.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sample_name](migs_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞seq_meth](migs_org_seq_meth.md) REQ + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) OPT + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞sop](migs_org_sop.md) OPT + * [MIGS org➞sop](MIGS_org_sop.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) OPT + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) REQ + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) OPT + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_class](migs_org_tax_class.md) OPT + * [MIGS org➞tax_class](MIGS_org_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞tax_ident](migs_org_tax_ident.md) OPT + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) OPT * range: -### Mixed in from migs_org: +### Mixed in from MIGS org: - * [migs_org➞url](migs_org_url.md) OPT + * [MIGS org➞url](MIGS_org_url.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WaterMimag.md b/mixs6/WaterMimag.md index 351a322d..d1e8bcb4 100644 --- a/mixs6/WaterMimag.md +++ b/mixs6/WaterMimag.md @@ -1,13 +1,13 @@ -# Class: WaterMimag +# Class: WaterMIMAG -Combinatorial checklist for water with mimag +Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water -URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) +URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Mimag],[Water]^-[WaterMimag],[Water],[QuantityValue],[Mimag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Water]^-[WaterMIMAG],[Water],[QuantityValue],[MIMAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) ## Uses Mixins - * mixin: [Mimag](Mimag.md) - mimag Checklist + * mixin: [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome ## Attributes @@ -383,252 +383,252 @@ URI: [mixs.vocab:WaterMimag](https://w3id.org/mixs/vocab/WaterMimag) * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞adapters](mimag_adapters.md) OPT + * [MIMAG➞adapters](MIMAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞annot](mimag_annot.md) OPT + * [MIMAG➞annot](MIMAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_name](mimag_assembly_name.md) OPT + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_qual](mimag_assembly_qual.md) REQ + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞assembly_software](mimag_assembly_software.md) REQ + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_param](mimag_bin_param.md) REQ + * [MIMAG➞bin_param](MIMAG_bin_param.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞bin_software](mimag_bin_software.md) REQ + * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_appr](mimag_compl_appr.md) OPT + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_score](mimag_compl_score.md) REQ + * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞compl_software](mimag_compl_software.md) REQ + * [MIMAG➞compl_software](MIMAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_score](mimag_contam_score.md) REQ + * [MIMAG➞contam_score](MIMAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) OPT + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) OPT + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞decontam_software](mimag_decontam_software.md) OPT + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞env_package](mimag_env_package.md) OPT + * [MIMAG➞env_package](MIMAG_env_package.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞experimental_factor](mimag_experimental_factor.md) OPT + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞feat_pred](mimag_feat_pred.md) OPT + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞investigation_type](mimag_investigation_type.md) REQ + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_layout](mimag_lib_layout.md) OPT + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) OPT + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_screen](mimag_lib_screen.md) OPT + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_size](mimag_lib_size.md) OPT + * [MIMAG➞lib_size](MIMAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞lib_vector](mimag_lib_vector.md) OPT + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) OPT + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞mid](mimag_mid.md) OPT + * [MIMAG➞mid](MIMAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) OPT + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) OPT + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞number_contig](mimag_number_contig.md) OPT + * [MIMAG➞number_contig](MIMAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞project_name](mimag_project_name.md) REQ + * [MIMAG➞project_name](MIMAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) OPT + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) OPT + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞ref_db](mimag_ref_db.md) OPT + * [MIMAG➞ref_db](MIMAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) OPT + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) OPT + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞samp_size](mimag_samp_size.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sample_name](mimag_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞seq_meth](mimag_seq_meth.md) REQ + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) OPT + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞size_frac](mimag_size_frac.md) OPT + * [MIMAG➞size_frac](MIMAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞sop](mimag_sop.md) OPT + * [MIMAG➞sop](MIMAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞source_mat_id](mimag_source_mat_id.md) OPT + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) REQ + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_class](mimag_tax_class.md) OPT + * [MIMAG➞tax_class](MIMAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞tax_ident](mimag_tax_ident.md) REQ + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) REQ * range: -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) OPT + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞trnas](mimag_trnas.md) OPT + * [MIMAG➞trnas](MIMAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞url](mimag_url.md) OPT + * [MIMAG➞url](MIMAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) OPT + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from mimag: +### Mixed in from MIMAG: - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) OPT + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WaterMisag.md b/mixs6/WaterMisag.md index daf6f06c..725e677a 100644 --- a/mixs6/WaterMisag.md +++ b/mixs6/WaterMisag.md @@ -1,13 +1,13 @@ -# Class: WaterMisag +# Class: WaterMISAG -Combinatorial checklist for water with misag +Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water -URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) +URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMisag|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Misag],[Water]^-[WaterMisag],[Water],[QuantityValue],[Misag]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Water]^-[WaterMISAG],[Water],[QuantityValue],[MISAG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) ## Uses Mixins - * mixin: [Misag](Misag.md) - misag Checklist + * mixin: [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome ## Attributes @@ -383,257 +383,257 @@ URI: [mixs.vocab:WaterMisag](https://w3id.org/mixs/vocab/WaterMisag) * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞adapters](misag_adapters.md) OPT + * [MISAG➞adapters](MISAG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞annot](misag_annot.md) OPT + * [MISAG➞annot](MISAG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_name](misag_assembly_name.md) OPT + * [MISAG➞assembly_name](MISAG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_qual](misag_assembly_qual.md) REQ + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞assembly_software](misag_assembly_software.md) REQ + * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_appr](misag_compl_appr.md) OPT + * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_score](misag_compl_score.md) REQ + * [MISAG➞compl_score](MISAG_compl_score.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞compl_software](misag_compl_software.md) REQ + * [MISAG➞compl_software](MISAG_compl_software.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_score](misag_contam_score.md) REQ + * [MISAG➞contam_score](MISAG_contam_score.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_input](misag_contam_screen_input.md) OPT + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞contam_screen_param](misag_contam_screen_param.md) OPT + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞decontam_software](misag_decontam_software.md) OPT + * [MISAG➞decontam_software](MISAG_decontam_software.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞env_package](misag_env_package.md) OPT + * [MISAG➞env_package](MISAG_env_package.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞experimental_factor](misag_experimental_factor.md) OPT + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞feat_pred](misag_feat_pred.md) OPT + * [MISAG➞feat_pred](MISAG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞investigation_type](misag_investigation_type.md) REQ + * [MISAG➞investigation_type](MISAG_investigation_type.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_layout](misag_lib_layout.md) OPT + * [MISAG➞lib_layout](MISAG_lib_layout.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) OPT + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_screen](misag_lib_screen.md) OPT + * [MISAG➞lib_screen](MISAG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_size](misag_lib_size.md) OPT + * [MISAG➞lib_size](MISAG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞lib_vector](misag_lib_vector.md) OPT + * [MISAG➞lib_vector](MISAG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞mid](misag_mid.md) OPT + * [MISAG➞mid](MISAG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) OPT + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) OPT + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞number_contig](misag_number_contig.md) OPT + * [MISAG➞number_contig](MISAG_number_contig.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞project_name](misag_project_name.md) REQ + * [MISAG➞project_name](MISAG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) OPT + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞ref_db](misag_ref_db.md) OPT + * [MISAG➞ref_db](MISAG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) OPT + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_collect_device](misag_samp_collect_device.md) OPT + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_mat_process](misag_samp_mat_process.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞samp_size](misag_samp_size.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sample_name](misag_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞seq_meth](misag_seq_meth.md) REQ + * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sim_search_meth](misag_sim_search_meth.md) OPT + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) REQ + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) OPT + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞size_frac](misag_size_frac.md) OPT + * [MISAG➞size_frac](MISAG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sop](misag_sop.md) OPT + * [MISAG➞sop](MISAG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞sort_tech](misag_sort_tech.md) REQ + * [MISAG➞sort_tech](MISAG_sort_tech.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞source_mat_id](misag_source_mat_id.md) OPT + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) REQ + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_class](misag_tax_class.md) OPT + * [MISAG➞tax_class](MISAG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞tax_ident](misag_tax_ident.md) REQ + * [MISAG➞tax_ident](MISAG_tax_ident.md) REQ * range: -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trna_ext_software](misag_trna_ext_software.md) OPT + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞trnas](misag_trnas.md) OPT + * [MISAG➞trnas](MISAG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞url](misag_url.md) OPT + * [MISAG➞url](MISAG_url.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) REQ + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) REQ * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) OPT + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover](misag_x_16s_recover.md) OPT + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) -### Mixed in from misag: +### Mixed in from MISAG: - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) OPT + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT * range: [String](types/String.md) diff --git a/mixs6/WaterMiuvig.md b/mixs6/WaterMiuvig.md index cfa11a1f..f7bb7fcb 100644 --- a/mixs6/WaterMiuvig.md +++ b/mixs6/WaterMiuvig.md @@ -1,13 +1,13 @@ -# Class: WaterMiuvig +# Class: WaterMIUVIG -Combinatorial checklist for water with miuvig +Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water -URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) +URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMiuvig|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[Miuvig],[Water]^-[WaterMiuvig],[Water],[QuantityValue],[Miuvig]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Water]^-[WaterMIUVIG],[Water],[QuantityValue],[MIUVIG]) ## Parents @@ -15,7 +15,7 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) ## Uses Mixins - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist + * mixin: [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ## Attributes @@ -383,322 +383,322 @@ URI: [mixs.vocab:WaterMiuvig](https://w3id.org/mixs/vocab/WaterMiuvig) * range: [QuantityValue](QuantityValue.md) * Example: 10 cubic meter per second None -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞adapters](miuvig_adapters.md) OPT + * [MIUVIG➞adapters](MIUVIG_adapters.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞annot](miuvig_annot.md) OPT + * [MIUVIG➞annot](MIUVIG_annot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_name](miuvig_assembly_name.md) OPT + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) REQ + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞assembly_software](miuvig_assembly_software.md) REQ + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_param](miuvig_bin_param.md) OPT + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞bin_software](miuvig_bin_software.md) OPT + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) OPT + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_appr](miuvig_compl_appr.md) OPT + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_score](miuvig_compl_score.md) OPT + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞compl_software](miuvig_compl_software.md) OPT + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞detec_type](miuvig_detec_type.md) REQ + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞env_package](miuvig_env_package.md) OPT + * [MIUVIG➞env_package](MIUVIG_env_package.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞estimated_size](miuvig_estimated_size.md) OPT + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) OPT + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞feat_pred](miuvig_feat_pred.md) OPT + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) OPT + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) OPT + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) OPT + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞investigation_type](miuvig_investigation_type.md) REQ + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_layout](miuvig_lib_layout.md) OPT + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) OPT + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_screen](miuvig_lib_screen.md) OPT + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_size](miuvig_lib_size.md) OPT + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞lib_vector](miuvig_lib_vector.md) OPT + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) OPT + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞mid](miuvig_mid.md) OPT + * [MIUVIG➞mid](MIUVIG_mid.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) OPT + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) OPT + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞number_contig](miuvig_number_contig.md) REQ + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) OPT + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) REQ + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) REQ + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞project_name](miuvig_project_name.md) REQ + * [MIUVIG➞project_name](MIUVIG_project_name.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) OPT + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) OPT + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞ref_db](miuvig_ref_db.md) OPT + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) OPT + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞samp_size](miuvig_samp_size.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sample_name](miuvig_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞seq_meth](miuvig_seq_meth.md) REQ + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) OPT + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) OPT + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) OPT + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞size_frac](miuvig_size_frac.md) OPT + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sop](miuvig_sop.md) OPT + * [MIUVIG➞sop](MIUVIG_sop.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞sort_tech](miuvig_sort_tech.md) OPT + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) OPT + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞source_uvig](miuvig_source_uvig.md) REQ + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞specific_host](miuvig_specific_host.md) OPT + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) REQ + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_class](miuvig_tax_class.md) OPT + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞tax_ident](miuvig_tax_ident.md) OPT + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) OPT * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) OPT + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞trnas](miuvig_trnas.md) OPT + * [MIUVIG➞trnas](MIUVIG_trnas.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞url](miuvig_url.md) OPT + * [MIUVIG➞url](MIUVIG_url.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) REQ + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) REQ * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) REQ + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) REQ * range: -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) OPT + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_db](miuvig_votu_db.md) OPT + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) OPT + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) OPT + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) OPT * range: [String](types/String.md) -### Mixed in from miuvig: +### Mixed in from MIUVIG: - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) OPT + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) OPT * range: [String](types/String.md) diff --git a/mixs6/abs_air_humidity.md b/mixs6/abs_air_humidity.md index 1c714c79..52486c9e 100644 --- a/mixs6/abs_air_humidity.md +++ b/mixs6/abs_air_humidity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/adapters.md b/mixs6/adapters.md index 58fa9e3f..35017538 100644 --- a/mixs6/adapters.md +++ b/mixs6/adapters.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞adapters](me_adapters.md) - * [migs_ba➞adapters](migs_ba_adapters.md) - * [migs_eu➞adapters](migs_eu_adapters.md) - * [migs_org➞adapters](migs_org_adapters.md) - * [migs_pl➞adapters](migs_pl_adapters.md) - * [migs_vi➞adapters](migs_vi_adapters.md) - * [mimag➞adapters](mimag_adapters.md) - * [mimarks_s➞adapters](mimarks_s_adapters.md) - * [misag➞adapters](misag_adapters.md) - * [miuvig➞adapters](miuvig_adapters.md) + * [ME➞adapters](ME_adapters.md) + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) + * [MIGS org➞adapters](MIGS_org_adapters.md) + * [MIGS plant➞adapters](MIGS_plant_adapters.md) + * [MIGS virus➞adapters](MIGS_virus_adapters.md) + * [MIMAG➞adapters](MIMAG_adapters.md) + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) + * [MISAG➞adapters](MISAG_adapters.md) + * [MIUVIG➞adapters](MIUVIG_adapters.md) ## Used by diff --git a/mixs6/add_recov_method.md b/mixs6/add_recov_method.md index da1de359..8b9f14d7 100644 --- a/mixs6/add_recov_method.md +++ b/mixs6/add_recov_method.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/additional_info.md b/mixs6/additional_info.md index 6fbb55ac..4f35a316 100644 --- a/mixs6/additional_info.md +++ b/mixs6/additional_info.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/address.md b/mixs6/address.md index 8291231f..9331d40d 100644 --- a/mixs6/address.md +++ b/mixs6/address.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/adj_room.md b/mixs6/adj_room.md index 6de39287..1e4e6da6 100644 --- a/mixs6/adj_room.md +++ b/mixs6/adj_room.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/aero_struc.md b/mixs6/aero_struc.md index e3ce786f..08cd9b01 100644 --- a/mixs6/aero_struc.md +++ b/mixs6/aero_struc.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/agrochem_addition.md b/mixs6/agrochem_addition.md index afb0af15..7a611b8a 100644 --- a/mixs6/agrochem_addition.md +++ b/mixs6/agrochem_addition.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/air_temp.md b/mixs6/air_temp.md index 027f9a90..03e92a96 100644 --- a/mixs6/air_temp.md +++ b/mixs6/air_temp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/air_temp_regm.md b/mixs6/air_temp_regm.md index 46b24fde..a1b41176 100644 --- a/mixs6/air_temp_regm.md +++ b/mixs6/air_temp_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/al_sat.md b/mixs6/al_sat.md index ba7afe92..a7b1fed3 100644 --- a/mixs6/al_sat.md +++ b/mixs6/al_sat.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/al_sat_meth.md b/mixs6/al_sat_meth.md index 2bf95412..34aaed58 100644 --- a/mixs6/al_sat_meth.md +++ b/mixs6/al_sat_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/alkalinity.md b/mixs6/alkalinity.md index 33c0158a..b40c67e7 100644 --- a/mixs6/alkalinity.md +++ b/mixs6/alkalinity.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/alkalinity_method.md b/mixs6/alkalinity_method.md index 879fdf80..cd94bfa5 100644 --- a/mixs6/alkalinity_method.md +++ b/mixs6/alkalinity_method.md @@ -21,41 +21,41 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/alkyl_diethers.md b/mixs6/alkyl_diethers.md index 7de16fae..81358d6d 100644 --- a/mixs6/alkyl_diethers.md +++ b/mixs6/alkyl_diethers.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/alt.md b/mixs6/alt.md index ed96c90c..8feed6ad 100644 --- a/mixs6/alt.md +++ b/mixs6/alt.md @@ -21,210 +21,210 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/aminopept_act.md b/mixs6/aminopept_act.md index bf87d253..c9fdfca1 100644 --- a/mixs6/aminopept_act.md +++ b/mixs6/aminopept_act.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/ammonium.md b/mixs6/ammonium.md index 6964d32d..2d1c6e91 100644 --- a/mixs6/ammonium.md +++ b/mixs6/ammonium.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/amniotic_fluid_color.md b/mixs6/amniotic_fluid_color.md index acd8387c..2de32e94 100644 --- a/mixs6/amniotic_fluid_color.md +++ b/mixs6/amniotic_fluid_color.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/amount_light.md b/mixs6/amount_light.md index c5600065..4b6adda1 100644 --- a/mixs6/amount_light.md +++ b/mixs6/amount_light.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ances_data.md b/mixs6/ances_data.md index 0ec8ed6b..287183ce 100644 --- a/mixs6/ances_data.md +++ b/mixs6/ances_data.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/annot.md b/mixs6/annot.md index c973f9ea..bbfc7741 100644 --- a/mixs6/annot.md +++ b/mixs6/annot.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞annot](me_annot.md) - * [migs_ba➞annot](migs_ba_annot.md) - * [migs_eu➞annot](migs_eu_annot.md) - * [migs_org➞annot](migs_org_annot.md) - * [migs_pl➞annot](migs_pl_annot.md) - * [migs_vi➞annot](migs_vi_annot.md) - * [mimag➞annot](mimag_annot.md) - * [misag➞annot](misag_annot.md) - * [miuvig➞annot](miuvig_annot.md) + * [ME➞annot](ME_annot.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) + * [MIGS org➞annot](MIGS_org_annot.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) + * [MIMAG➞annot](MIMAG_annot.md) + * [MISAG➞annot](MISAG_annot.md) + * [MIUVIG➞annot](MIUVIG_annot.md) ## Used by diff --git a/mixs6/annual_precpt.md b/mixs6/annual_precpt.md index 6f10b51f..b08b6538 100644 --- a/mixs6/annual_precpt.md +++ b/mixs6/annual_precpt.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/annual_temp.md b/mixs6/annual_temp.md index 0da57680..d5c13234 100644 --- a/mixs6/annual_temp.md +++ b/mixs6/annual_temp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/antibiotic_regm.md b/mixs6/antibiotic_regm.md index 8eb661ad..4f1beafb 100644 --- a/mixs6/antibiotic_regm.md +++ b/mixs6/antibiotic_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/api.md b/mixs6/api.md index c5bd057a..752d1c42 100644 --- a/mixs6/api.md +++ b/mixs6/api.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/arch_struc.md b/mixs6/arch_struc.md index 3c887bb6..83de3d0f 100644 --- a/mixs6/arch_struc.md +++ b/mixs6/arch_struc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/aromatics_pc.md b/mixs6/aromatics_pc.md index 0d1e1017..ec591f0b 100644 --- a/mixs6/aromatics_pc.md +++ b/mixs6/aromatics_pc.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/asphaltenes_pc.md b/mixs6/asphaltenes_pc.md index e1fd8307..a565766a 100644 --- a/mixs6/asphaltenes_pc.md +++ b/mixs6/asphaltenes_pc.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/assembly_name.md b/mixs6/assembly_name.md index eabd813f..35e9b919 100644 --- a/mixs6/assembly_name.md +++ b/mixs6/assembly_name.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞assembly_name](me_assembly_name.md) - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) - * [migs_org➞assembly_name](migs_org_assembly_name.md) - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) - * [mimag➞assembly_name](mimag_assembly_name.md) - * [misag➞assembly_name](misag_assembly_name.md) - * [miuvig➞assembly_name](miuvig_assembly_name.md) + * [ME➞assembly_name](ME_assembly_name.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) + * [MISAG➞assembly_name](MISAG_assembly_name.md) + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) ## Used by diff --git a/mixs6/assembly_qual.md b/mixs6/assembly_qual.md index d74a6e44..bc33715d 100644 --- a/mixs6/assembly_qual.md +++ b/mixs6/assembly_qual.md @@ -17,15 +17,15 @@ None -> OPT ## Children - * [me➞assembly_qual](me_assembly_qual.md) - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) - * [mimag➞assembly_qual](mimag_assembly_qual.md) - * [misag➞assembly_qual](misag_assembly_qual.md) - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) + * [ME➞assembly_qual](ME_assembly_qual.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) ## Used by diff --git a/mixs6/assembly_software.md b/mixs6/assembly_software.md index 475c7ade..d1febe3b 100644 --- a/mixs6/assembly_software.md +++ b/mixs6/assembly_software.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞assembly_software](me_assembly_software.md) - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) - * [migs_org➞assembly_software](migs_org_assembly_software.md) - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) - * [mimag➞assembly_software](mimag_assembly_software.md) - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) - * [misag➞assembly_software](misag_assembly_software.md) - * [miuvig➞assembly_software](miuvig_assembly_software.md) + * [ME➞assembly_software](ME_assembly_software.md) + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) + * [MISAG➞assembly_software](MISAG_assembly_software.md) + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) ## Used by diff --git a/mixs6/atmospheric_data.md b/mixs6/atmospheric_data.md index ea1ab1fc..c6fcc0ea 100644 --- a/mixs6/atmospheric_data.md +++ b/mixs6/atmospheric_data.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/avg_dew_point.md b/mixs6/avg_dew_point.md index 97359bdd..5eeef9fd 100644 --- a/mixs6/avg_dew_point.md +++ b/mixs6/avg_dew_point.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/avg_occup.md b/mixs6/avg_occup.md index 1c51c4cf..c8264297 100644 --- a/mixs6/avg_occup.md +++ b/mixs6/avg_occup.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/avg_temp.md b/mixs6/avg_temp.md index 14ae4ab9..f9a2bcbb 100644 --- a/mixs6/avg_temp.md +++ b/mixs6/avg_temp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/bac_prod.md b/mixs6/bac_prod.md index 208216cd..0bf8ba45 100644 --- a/mixs6/bac_prod.md +++ b/mixs6/bac_prod.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/bac_resp.md b/mixs6/bac_resp.md index 1786e84b..86bfb147 100644 --- a/mixs6/bac_resp.md +++ b/mixs6/bac_resp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/bacteria_carb_prod.md b/mixs6/bacteria_carb_prod.md index fa04aa19..2eb8662c 100644 --- a/mixs6/bacteria_carb_prod.md +++ b/mixs6/bacteria_carb_prod.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/barometric_press.md b/mixs6/barometric_press.md index 39fb5431..e49fb0a2 100644 --- a/mixs6/barometric_press.md +++ b/mixs6/barometric_press.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/basin.md b/mixs6/basin.md index f4740e3c..1230a7f8 100644 --- a/mixs6/basin.md +++ b/mixs6/basin.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/bathroom_count.md b/mixs6/bathroom_count.md index 357867db..4e4fc5de 100644 --- a/mixs6/bathroom_count.md +++ b/mixs6/bathroom_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/bedroom_count.md b/mixs6/bedroom_count.md index c25ad009..7d582a91 100644 --- a/mixs6/bedroom_count.md +++ b/mixs6/bedroom_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/benzene.md b/mixs6/benzene.md index 4006a265..4a7ff31d 100644 --- a/mixs6/benzene.md +++ b/mixs6/benzene.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/bin_param.md b/mixs6/bin_param.md index 53209920..7d4875c0 100644 --- a/mixs6/bin_param.md +++ b/mixs6/bin_param.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [mimag➞bin_param](mimag_bin_param.md) - * [miuvig➞bin_param](miuvig_bin_param.md) + * [MIMAG➞bin_param](MIMAG_bin_param.md) + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) ## Used by diff --git a/mixs6/bin_software.md b/mixs6/bin_software.md index 0b3e1643..caad1712 100644 --- a/mixs6/bin_software.md +++ b/mixs6/bin_software.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [mimag➞bin_software](mimag_bin_software.md) - * [miuvig➞bin_software](miuvig_bin_software.md) + * [MIMAG➞bin_software](MIMAG_bin_software.md) + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) ## Used by diff --git a/mixs6/biochem_oxygen_dem.md b/mixs6/biochem_oxygen_dem.md index c8c380cb..e317baa5 100644 --- a/mixs6/biochem_oxygen_dem.md +++ b/mixs6/biochem_oxygen_dem.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/biocide.md b/mixs6/biocide.md index 5caff76b..0bf76430 100644 --- a/mixs6/biocide.md +++ b/mixs6/biocide.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/biocide_admin_method.md b/mixs6/biocide_admin_method.md index 9df099b2..c7abc3e9 100644 --- a/mixs6/biocide_admin_method.md +++ b/mixs6/biocide_admin_method.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/biol_stat.md b/mixs6/biol_stat.md index c2319266..a968623e 100644 --- a/mixs6/biol_stat.md +++ b/mixs6/biol_stat.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/biomass.md b/mixs6/biomass.md index c0a44fe2..ff37aeee 100644 --- a/mixs6/biomass.md +++ b/mixs6/biomass.md @@ -21,53 +21,53 @@ None -> OPT [String](types/String.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/biotic_regm.md b/mixs6/biotic_regm.md index 9b823c5a..784834a4 100644 --- a/mixs6/biotic_regm.md +++ b/mixs6/biotic_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/biotic_relationship.md b/mixs6/biotic_relationship.md index 0afbbafe..ae0b19b9 100644 --- a/mixs6/biotic_relationship.md +++ b/mixs6/biotic_relationship.md @@ -17,11 +17,11 @@ None -> OPT ## Children - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) ## Used by diff --git a/mixs6/birth_control.md b/mixs6/birth_control.md index 44c30127..047812ff 100644 --- a/mixs6/birth_control.md +++ b/mixs6/birth_control.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/bishomohopanol.md b/mixs6/bishomohopanol.md index 62c8bb95..66b5b3c9 100644 --- a/mixs6/bishomohopanol.md +++ b/mixs6/bishomohopanol.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/blood_blood_disord.md b/mixs6/blood_blood_disord.md index 601100e5..eaf58810 100644 --- a/mixs6/blood_blood_disord.md +++ b/mixs6/blood_blood_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/bromide.md b/mixs6/bromide.md index c386f9d6..5f24579c 100644 --- a/mixs6/bromide.md +++ b/mixs6/bromide.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/build_docs.md b/mixs6/build_docs.md index 82ca5bbf..f66e7f31 100644 --- a/mixs6/build_docs.md +++ b/mixs6/build_docs.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/build_occup_type.md b/mixs6/build_occup_type.md index 9174bc08..bf41605a 100644 --- a/mixs6/build_occup_type.md +++ b/mixs6/build_occup_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/building_setting.md b/mixs6/building_setting.md index fa98b086..80eaeb9c 100644 --- a/mixs6/building_setting.md +++ b/mixs6/building_setting.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/built_struc_age.md b/mixs6/built_struc_age.md index fb1d0e15..0d3d55a1 100644 --- a/mixs6/built_struc_age.md +++ b/mixs6/built_struc_age.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/built_struc_set.md b/mixs6/built_struc_set.md index 9afab716..fcacbd5b 100644 --- a/mixs6/built_struc_set.md +++ b/mixs6/built_struc_set.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/built_struc_type.md b/mixs6/built_struc_type.md index 78313c3a..3a74ad3a 100644 --- a/mixs6/built_struc_type.md +++ b/mixs6/built_struc_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/calcium.md b/mixs6/calcium.md index 6d1230be..7e4a5246 100644 --- a/mixs6/calcium.md +++ b/mixs6/calcium.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/carb_dioxide.md b/mixs6/carb_dioxide.md index 4641ab3d..9afc31b7 100644 --- a/mixs6/carb_dioxide.md +++ b/mixs6/carb_dioxide.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/carb_monoxide.md b/mixs6/carb_monoxide.md index a5a2cab9..f2844b44 100644 --- a/mixs6/carb_monoxide.md +++ b/mixs6/carb_monoxide.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/carb_nitro_ratio.md b/mixs6/carb_nitro_ratio.md index 9a61abe1..c9933b2a 100644 --- a/mixs6/carb_nitro_ratio.md +++ b/mixs6/carb_nitro_ratio.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_area.md b/mixs6/ceil_area.md index d8e2e2de..1e7ba20b 100644 --- a/mixs6/ceil_area.md +++ b/mixs6/ceil_area.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_cond.md b/mixs6/ceil_cond.md index 39fe60d0..649cecd0 100644 --- a/mixs6/ceil_cond.md +++ b/mixs6/ceil_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_finish_mat.md b/mixs6/ceil_finish_mat.md index 336aaa09..6243ac32 100644 --- a/mixs6/ceil_finish_mat.md +++ b/mixs6/ceil_finish_mat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_struc.md b/mixs6/ceil_struc.md index 2102334c..fa4e149e 100644 --- a/mixs6/ceil_struc.md +++ b/mixs6/ceil_struc.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_texture.md b/mixs6/ceil_texture.md index 9fe49b7f..41364d8d 100644 --- a/mixs6/ceil_texture.md +++ b/mixs6/ceil_texture.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_thermal_mass.md b/mixs6/ceil_thermal_mass.md index 2c612407..f8cc24e5 100644 --- a/mixs6/ceil_thermal_mass.md +++ b/mixs6/ceil_thermal_mass.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_type.md b/mixs6/ceil_type.md index c1b3d071..08ae6bdc 100644 --- a/mixs6/ceil_type.md +++ b/mixs6/ceil_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ceil_water_mold.md b/mixs6/ceil_water_mold.md index 575979d1..5703c98a 100644 --- a/mixs6/ceil_water_mold.md +++ b/mixs6/ceil_water_mold.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/chem_administration.md b/mixs6/chem_administration.md index db90ce62..29d42a47 100644 --- a/mixs6/chem_administration.md +++ b/mixs6/chem_administration.md @@ -21,161 +21,161 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/chem_mutagen.md b/mixs6/chem_mutagen.md index 6384e2af..9ff2e8ae 100644 --- a/mixs6/chem_mutagen.md +++ b/mixs6/chem_mutagen.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/chem_oxygen_dem.md b/mixs6/chem_oxygen_dem.md index b1d77d33..284e26df 100644 --- a/mixs6/chem_oxygen_dem.md +++ b/mixs6/chem_oxygen_dem.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/chem_treatment.md b/mixs6/chem_treatment.md index 7138c847..d35f644d 100644 --- a/mixs6/chem_treatment.md +++ b/mixs6/chem_treatment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/chem_treatment_method.md b/mixs6/chem_treatment_method.md index 00bfcec1..ac48e98a 100644 --- a/mixs6/chem_treatment_method.md +++ b/mixs6/chem_treatment_method.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/chimera_check.md b/mixs6/chimera_check.md index c882dfa8..db70e55b 100644 --- a/mixs6/chimera_check.md +++ b/mixs6/chimera_check.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) ## Used by diff --git a/mixs6/chloride.md b/mixs6/chloride.md index 699804b1..784b812d 100644 --- a/mixs6/chloride.md +++ b/mixs6/chloride.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/chlorophyll.md b/mixs6/chlorophyll.md index 5a7854c5..5daab2a2 100644 --- a/mixs6/chlorophyll.md +++ b/mixs6/chlorophyll.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/climate_environment.md b/mixs6/climate_environment.md index 42fa1709..c4977a1a 100644 --- a/mixs6/climate_environment.md +++ b/mixs6/climate_environment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/collection_date.md b/mixs6/collection_date.md index 8f76f286..06ce45aa 100644 --- a/mixs6/collection_date.md +++ b/mixs6/collection_date.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞collection_date](me_collection_date.md) - * [migs_ba➞collection_date](migs_ba_collection_date.md) - * [migs_eu➞collection_date](migs_eu_collection_date.md) - * [migs_org➞collection_date](migs_org_collection_date.md) - * [migs_pl➞collection_date](migs_pl_collection_date.md) - * [migs_vi➞collection_date](migs_vi_collection_date.md) - * [mimag➞collection_date](mimag_collection_date.md) - * [mimarks_c➞collection_date](mimarks_c_collection_date.md) - * [mimarks_s➞collection_date](mimarks_s_collection_date.md) - * [misag➞collection_date](misag_collection_date.md) - * [miuvig➞collection_date](miuvig_collection_date.md) + * [ME➞collection_date](ME_collection_date.md) + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) + * [MIGS org➞collection_date](MIGS_org_collection_date.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) + * [MIMAG➞collection_date](MIMAG_collection_date.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) + * [MISAG➞collection_date](MISAG_collection_date.md) + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/compl_appr.md b/mixs6/compl_appr.md index ace92f59..fdd9e31d 100644 --- a/mixs6/compl_appr.md +++ b/mixs6/compl_appr.md @@ -17,9 +17,9 @@ None -> OPT ## Children - * [mimag➞compl_appr](mimag_compl_appr.md) - * [misag➞compl_appr](misag_compl_appr.md) - * [miuvig➞compl_appr](miuvig_compl_appr.md) + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) + * [MISAG➞compl_appr](MISAG_compl_appr.md) + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) ## Used by diff --git a/mixs6/compl_score.md b/mixs6/compl_score.md index ca2822b8..95932536 100644 --- a/mixs6/compl_score.md +++ b/mixs6/compl_score.md @@ -17,14 +17,14 @@ None -> OPT ## Children - * [migs_ba➞compl_score](migs_ba_compl_score.md) - * [migs_eu➞compl_score](migs_eu_compl_score.md) - * [migs_org➞compl_score](migs_org_compl_score.md) - * [migs_pl➞compl_score](migs_pl_compl_score.md) - * [migs_vi➞compl_score](migs_vi_compl_score.md) - * [mimag➞compl_score](mimag_compl_score.md) - * [misag➞compl_score](misag_compl_score.md) - * [miuvig➞compl_score](miuvig_compl_score.md) + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) + * [MIGS org➞compl_score](MIGS_org_compl_score.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) + * [MIMAG➞compl_score](MIMAG_compl_score.md) + * [MISAG➞compl_score](MISAG_compl_score.md) + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) ## Used by diff --git a/mixs6/compl_software.md b/mixs6/compl_software.md index 105beeae..87bfdb6b 100644 --- a/mixs6/compl_software.md +++ b/mixs6/compl_software.md @@ -17,14 +17,14 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞compl_software](migs_ba_compl_software.md) - * [migs_eu➞compl_software](migs_eu_compl_software.md) - * [migs_org➞compl_software](migs_org_compl_software.md) - * [migs_pl➞compl_software](migs_pl_compl_software.md) - * [migs_vi➞compl_software](migs_vi_compl_software.md) - * [mimag➞compl_software](mimag_compl_software.md) - * [misag➞compl_software](misag_compl_software.md) - * [miuvig➞compl_software](miuvig_compl_software.md) + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) + * [MIGS org➞compl_software](MIGS_org_compl_software.md) + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) + * [MIMAG➞compl_software](MIMAG_compl_software.md) + * [MISAG➞compl_software](MISAG_compl_software.md) + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) ## Used by diff --git a/mixs6/conduc.md b/mixs6/conduc.md index 453023a0..0d335b24 100644 --- a/mixs6/conduc.md +++ b/mixs6/conduc.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/contam_score.md b/mixs6/contam_score.md index a6dcf17f..16367a49 100644 --- a/mixs6/contam_score.md +++ b/mixs6/contam_score.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞contam_score](mimag_contam_score.md) - * [misag➞contam_score](misag_contam_score.md) + * [MIMAG➞contam_score](MIMAG_contam_score.md) + * [MISAG➞contam_score](MISAG_contam_score.md) ## Used by diff --git a/mixs6/contam_screen_input.md b/mixs6/contam_screen_input.md index 66b29ac4..2f7bdfd1 100644 --- a/mixs6/contam_screen_input.md +++ b/mixs6/contam_screen_input.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) - * [misag➞contam_screen_input](misag_contam_screen_input.md) + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) ## Used by diff --git a/mixs6/contam_screen_param.md b/mixs6/contam_screen_param.md index 9186ca1f..580099ea 100644 --- a/mixs6/contam_screen_param.md +++ b/mixs6/contam_screen_param.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) - * [misag➞contam_screen_param](misag_contam_screen_param.md) + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) ## Used by diff --git a/mixs6/cool_syst_id.md b/mixs6/cool_syst_id.md index ea0df443..04fb27b2 100644 --- a/mixs6/cool_syst_id.md +++ b/mixs6/cool_syst_id.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/crop_rotation.md b/mixs6/crop_rotation.md index 7c173c2d..b38cd615 100644 --- a/mixs6/crop_rotation.md +++ b/mixs6/crop_rotation.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/cult_root_med.md b/mixs6/cult_root_med.md index 6fccf609..ee62b67d 100644 --- a/mixs6/cult_root_med.md +++ b/mixs6/cult_root_med.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/cur_land_use.md b/mixs6/cur_land_use.md index eaceee06..59cbb5b3 100644 --- a/mixs6/cur_land_use.md +++ b/mixs6/cur_land_use.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/cur_vegetation.md b/mixs6/cur_vegetation.md index 75035705..02b777e8 100644 --- a/mixs6/cur_vegetation.md +++ b/mixs6/cur_vegetation.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/cur_vegetation_meth.md b/mixs6/cur_vegetation_meth.md index 716eb5c9..f2e34850 100644 --- a/mixs6/cur_vegetation_meth.md +++ b/mixs6/cur_vegetation_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/date_last_rain.md b/mixs6/date_last_rain.md index 80cf783f..b8f6730d 100644 --- a/mixs6/date_last_rain.md +++ b/mixs6/date_last_rain.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/decontam_software.md b/mixs6/decontam_software.md index eb591646..e22ac5c7 100644 --- a/mixs6/decontam_software.md +++ b/mixs6/decontam_software.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [mimag➞decontam_software](mimag_decontam_software.md) - * [misag➞decontam_software](misag_decontam_software.md) + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) + * [MISAG➞decontam_software](MISAG_decontam_software.md) ## Used by diff --git a/mixs6/density.md b/mixs6/density.md index f41e5d82..536177a0 100644 --- a/mixs6/density.md +++ b/mixs6/density.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/depos_env.md b/mixs6/depos_env.md index ab7fec57..d5eb3d7b 100644 --- a/mixs6/depos_env.md +++ b/mixs6/depos_env.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/depth.md b/mixs6/depth.md index c30044ad..38719f8c 100644 --- a/mixs6/depth.md +++ b/mixs6/depth.md @@ -21,210 +21,210 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/dermatology_disord.md b/mixs6/dermatology_disord.md index 2246abde..84e28700 100644 --- a/mixs6/dermatology_disord.md +++ b/mixs6/dermatology_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) ## Other properties diff --git a/mixs6/detec_type.md b/mixs6/detec_type.md index e23e2995..0486ac30 100644 --- a/mixs6/detec_type.md +++ b/mixs6/detec_type.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞detec_type](miuvig_detec_type.md) + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) ## Used by diff --git a/mixs6/dew_point.md b/mixs6/dew_point.md index 518fc0fd..a87af384 100644 --- a/mixs6/dew_point.md +++ b/mixs6/dew_point.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/diet_last_six_month.md b/mixs6/diet_last_six_month.md index 2eb41553..b2556907 100644 --- a/mixs6/diet_last_six_month.md +++ b/mixs6/diet_last_six_month.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/diether_lipids.md b/mixs6/diether_lipids.md index 139e9095..7bb3e9d2 100644 --- a/mixs6/diether_lipids.md +++ b/mixs6/diether_lipids.md @@ -21,53 +21,53 @@ None -> OPT [String](types/String.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_carb_dioxide.md b/mixs6/diss_carb_dioxide.md index ae56721d..b59f53b9 100644 --- a/mixs6/diss_carb_dioxide.md +++ b/mixs6/diss_carb_dioxide.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_hydrogen.md b/mixs6/diss_hydrogen.md index bfb38fdd..b6c21d0b 100644 --- a/mixs6/diss_hydrogen.md +++ b/mixs6/diss_hydrogen.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_inorg_carb.md b/mixs6/diss_inorg_carb.md index 612c28bf..6a98db1d 100644 --- a/mixs6/diss_inorg_carb.md +++ b/mixs6/diss_inorg_carb.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_inorg_nitro.md b/mixs6/diss_inorg_nitro.md index 71fd2597..7298a917 100644 --- a/mixs6/diss_inorg_nitro.md +++ b/mixs6/diss_inorg_nitro.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_inorg_phosp.md b/mixs6/diss_inorg_phosp.md index 723cec6e..b3b8e71e 100644 --- a/mixs6/diss_inorg_phosp.md +++ b/mixs6/diss_inorg_phosp.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_iron.md b/mixs6/diss_iron.md index 2d9684c9..67c3eb46 100644 --- a/mixs6/diss_iron.md +++ b/mixs6/diss_iron.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/diss_org_carb.md b/mixs6/diss_org_carb.md index fd9eb0dd..eb592270 100644 --- a/mixs6/diss_org_carb.md +++ b/mixs6/diss_org_carb.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_org_nitro.md b/mixs6/diss_org_nitro.md index 09ff556e..90fa24c2 100644 --- a/mixs6/diss_org_nitro.md +++ b/mixs6/diss_org_nitro.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_oxygen.md b/mixs6/diss_oxygen.md index a3d1afb3..3928c304 100644 --- a/mixs6/diss_oxygen.md +++ b/mixs6/diss_oxygen.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/diss_oxygen_fluid.md b/mixs6/diss_oxygen_fluid.md index c8b0f036..a0cb4d8d 100644 --- a/mixs6/diss_oxygen_fluid.md +++ b/mixs6/diss_oxygen_fluid.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/dominant_hand.md b/mixs6/dominant_hand.md index 958915f0..2f19bf50 100644 --- a/mixs6/dominant_hand.md +++ b/mixs6/dominant_hand.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) ## Other properties diff --git a/mixs6/door_comp_type.md b/mixs6/door_comp_type.md index de01d432..61c00fa8 100644 --- a/mixs6/door_comp_type.md +++ b/mixs6/door_comp_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_cond.md b/mixs6/door_cond.md index a812eec7..a8e64b86 100644 --- a/mixs6/door_cond.md +++ b/mixs6/door_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_direct.md b/mixs6/door_direct.md index 6a156d0a..c04cdecb 100644 --- a/mixs6/door_direct.md +++ b/mixs6/door_direct.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_loc.md b/mixs6/door_loc.md index fd41886d..df9bad24 100644 --- a/mixs6/door_loc.md +++ b/mixs6/door_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_mat.md b/mixs6/door_mat.md index 307cfb3b..30b61ae7 100644 --- a/mixs6/door_mat.md +++ b/mixs6/door_mat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_move.md b/mixs6/door_move.md index 62a9737a..b8a78d81 100644 --- a/mixs6/door_move.md +++ b/mixs6/door_move.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_size.md b/mixs6/door_size.md index e96360b1..4c8ea631 100644 --- a/mixs6/door_size.md +++ b/mixs6/door_size.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_type.md b/mixs6/door_type.md index ab9936a1..0d6eeb65 100644 --- a/mixs6/door_type.md +++ b/mixs6/door_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_type_metal.md b/mixs6/door_type_metal.md index e2415020..7cdd369d 100644 --- a/mixs6/door_type_metal.md +++ b/mixs6/door_type_metal.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_type_wood.md b/mixs6/door_type_wood.md index ebde396f..874c2478 100644 --- a/mixs6/door_type_wood.md +++ b/mixs6/door_type_wood.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/door_water_mold.md b/mixs6/door_water_mold.md index 711cf015..b17c0d21 100644 --- a/mixs6/door_water_mold.md +++ b/mixs6/door_water_mold.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/douche.md b/mixs6/douche.md index b9ddbdca..3d8fc7a0 100644 --- a/mixs6/douche.md +++ b/mixs6/douche.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/down_par.md b/mixs6/down_par.md index e9acfb0d..686b9a8f 100644 --- a/mixs6/down_par.md +++ b/mixs6/down_par.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/drainage_class.md b/mixs6/drainage_class.md index c809966f..38f62e78 100644 --- a/mixs6/drainage_class.md +++ b/mixs6/drainage_class.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/drawings.md b/mixs6/drawings.md index dafde8ff..2a8456e4 100644 --- a/mixs6/drawings.md +++ b/mixs6/drawings.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/drug_usage.md b/mixs6/drug_usage.md index 44d51d83..02d850a4 100644 --- a/mixs6/drug_usage.md +++ b/mixs6/drug_usage.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/efficiency_percent.md b/mixs6/efficiency_percent.md index 61219952..5d0e785f 100644 --- a/mixs6/efficiency_percent.md +++ b/mixs6/efficiency_percent.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/elev.md b/mixs6/elev.md index 21b6adc5..9b78443f 100644 --- a/mixs6/elev.md +++ b/mixs6/elev.md @@ -21,210 +21,210 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/elevator.md b/mixs6/elevator.md index 56e00131..f33a0dbf 100644 --- a/mixs6/elevator.md +++ b/mixs6/elevator.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/emulsions.md b/mixs6/emulsions.md index a15278d1..016f91ca 100644 --- a/mixs6/emulsions.md +++ b/mixs6/emulsions.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/encoded_traits.md b/mixs6/encoded_traits.md index e095d968..6116064c 100644 --- a/mixs6/encoded_traits.md +++ b/mixs6/encoded_traits.md @@ -17,9 +17,9 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) ## Used by diff --git a/mixs6/env_broad_scale.md b/mixs6/env_broad_scale.md index 946dee0a..9afd7322 100644 --- a/mixs6/env_broad_scale.md +++ b/mixs6/env_broad_scale.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞env_broad_scale](me_env_broad_scale.md) - * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) - * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) - * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) - * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) - * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) - * [mimag➞env_broad_scale](mimag_env_broad_scale.md) - * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) - * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) - * [misag➞env_broad_scale](misag_env_broad_scale.md) - * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) + * [ME➞env_broad_scale](ME_env_broad_scale.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/env_local_scale.md b/mixs6/env_local_scale.md index cffffbad..1835d064 100644 --- a/mixs6/env_local_scale.md +++ b/mixs6/env_local_scale.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞env_local_scale](me_env_local_scale.md) - * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) - * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) - * [migs_org➞env_local_scale](migs_org_env_local_scale.md) - * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) - * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) - * [mimag➞env_local_scale](mimag_env_local_scale.md) - * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) - * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) - * [misag➞env_local_scale](misag_env_local_scale.md) - * [miuvig➞env_local_scale](miuvig_env_local_scale.md) + * [ME➞env_local_scale](ME_env_local_scale.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/env_medium.md b/mixs6/env_medium.md index 16615e78..c5122dc9 100644 --- a/mixs6/env_medium.md +++ b/mixs6/env_medium.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞env_medium](me_env_medium.md) - * [migs_ba➞env_medium](migs_ba_env_medium.md) - * [migs_eu➞env_medium](migs_eu_env_medium.md) - * [migs_org➞env_medium](migs_org_env_medium.md) - * [migs_pl➞env_medium](migs_pl_env_medium.md) - * [migs_vi➞env_medium](migs_vi_env_medium.md) - * [mimag➞env_medium](mimag_env_medium.md) - * [mimarks_c➞env_medium](mimarks_c_env_medium.md) - * [mimarks_s➞env_medium](mimarks_s_env_medium.md) - * [misag➞env_medium](misag_env_medium.md) - * [miuvig➞env_medium](miuvig_env_medium.md) + * [ME➞env_medium](ME_env_medium.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) + * [MIGS org➞env_medium](MIGS_org_env_medium.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) + * [MIMAG➞env_medium](MIMAG_env_medium.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) + * [MISAG➞env_medium](MISAG_env_medium.md) + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/env_package.md b/mixs6/env_package.md index 223b5b77..d49de2ea 100644 --- a/mixs6/env_package.md +++ b/mixs6/env_package.md @@ -17,17 +17,17 @@ None -> OPT ## Children - * [me➞env_package](me_env_package.md) - * [migs_ba➞env_package](migs_ba_env_package.md) - * [migs_eu➞env_package](migs_eu_env_package.md) - * [migs_org➞env_package](migs_org_env_package.md) - * [migs_pl➞env_package](migs_pl_env_package.md) - * [migs_vi➞env_package](migs_vi_env_package.md) - * [mimag➞env_package](mimag_env_package.md) - * [mimarks_c➞env_package](mimarks_c_env_package.md) - * [mimarks_s➞env_package](mimarks_s_env_package.md) - * [misag➞env_package](misag_env_package.md) - * [miuvig➞env_package](miuvig_env_package.md) + * [ME➞env_package](ME_env_package.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) + * [MIGS org➞env_package](MIGS_org_env_package.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) + * [MIMAG➞env_package](MIMAG_env_package.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) + * [MISAG➞env_package](MISAG_env_package.md) + * [MIUVIG➞env_package](MIUVIG_env_package.md) ## Used by diff --git a/mixs6/escalator.md b/mixs6/escalator.md index 6986d7cc..d69fbe22 100644 --- a/mixs6/escalator.md +++ b/mixs6/escalator.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/estimated_size.md b/mixs6/estimated_size.md index de2c2f2b..3644ffdb 100644 --- a/mixs6/estimated_size.md +++ b/mixs6/estimated_size.md @@ -17,12 +17,12 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) - * [migs_org➞estimated_size](migs_org_estimated_size.md) - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) - * [miuvig➞estimated_size](miuvig_estimated_size.md) + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) ## Used by diff --git a/mixs6/ethylbenzene.md b/mixs6/ethylbenzene.md index 7e2e99d9..420d3c5f 100644 --- a/mixs6/ethylbenzene.md +++ b/mixs6/ethylbenzene.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/exp_duct.md b/mixs6/exp_duct.md index 6459e4a3..75e28fc0 100644 --- a/mixs6/exp_duct.md +++ b/mixs6/exp_duct.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/exp_pipe.md b/mixs6/exp_pipe.md index bd876343..d460e03b 100644 --- a/mixs6/exp_pipe.md +++ b/mixs6/exp_pipe.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/experimental_factor.md b/mixs6/experimental_factor.md index b9b12c97..138dc29a 100644 --- a/mixs6/experimental_factor.md +++ b/mixs6/experimental_factor.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞experimental_factor](me_experimental_factor.md) - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) - * [mimag➞experimental_factor](mimag_experimental_factor.md) - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) - * [misag➞experimental_factor](misag_experimental_factor.md) - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) + * [ME➞experimental_factor](ME_experimental_factor.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) ## Used by diff --git a/mixs6/ext_door.md b/mixs6/ext_door.md index 6d75f0d4..2599ee16 100644 --- a/mixs6/ext_door.md +++ b/mixs6/ext_door.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ext_wall_orient.md b/mixs6/ext_wall_orient.md index 9f079fe7..1534acde 100644 --- a/mixs6/ext_wall_orient.md +++ b/mixs6/ext_wall_orient.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/ext_window_orient.md b/mixs6/ext_window_orient.md index f737bd19..badefdb7 100644 --- a/mixs6/ext_window_orient.md +++ b/mixs6/ext_window_orient.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/extrachrom_elements.md b/mixs6/extrachrom_elements.md index 4cd5459c..0b76fdd6 100644 --- a/mixs6/extrachrom_elements.md +++ b/mixs6/extrachrom_elements.md @@ -17,10 +17,10 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) ## Used by diff --git a/mixs6/extreme_event.md b/mixs6/extreme_event.md index 568ba318..8d8d1fb8 100644 --- a/mixs6/extreme_event.md +++ b/mixs6/extreme_event.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/extreme_salinity.md b/mixs6/extreme_salinity.md index 796bd326..56d12f9a 100644 --- a/mixs6/extreme_salinity.md +++ b/mixs6/extreme_salinity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/fao_class.md b/mixs6/fao_class.md index b59acaf9..e73e92bc 100644 --- a/mixs6/fao_class.md +++ b/mixs6/fao_class.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/feat_pred.md b/mixs6/feat_pred.md index b25e0fea..8c27738d 100644 --- a/mixs6/feat_pred.md +++ b/mixs6/feat_pred.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞feat_pred](me_feat_pred.md) - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) - * [migs_org➞feat_pred](migs_org_feat_pred.md) - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) - * [mimag➞feat_pred](mimag_feat_pred.md) - * [misag➞feat_pred](misag_feat_pred.md) - * [miuvig➞feat_pred](miuvig_feat_pred.md) + * [ME➞feat_pred](ME_feat_pred.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) + * [MISAG➞feat_pred](MISAG_feat_pred.md) + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) ## Used by diff --git a/mixs6/fertilizer_regm.md b/mixs6/fertilizer_regm.md index 23d253c5..718f7634 100644 --- a/mixs6/fertilizer_regm.md +++ b/mixs6/fertilizer_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/field.md b/mixs6/field.md index d7f62d81..908346ff 100644 --- a/mixs6/field.md +++ b/mixs6/field.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/filter_type.md b/mixs6/filter_type.md index fa2d9e7e..5643ca53 100644 --- a/mixs6/filter_type.md +++ b/mixs6/filter_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/fire.md b/mixs6/fire.md index 92544840..b3299ae9 100644 --- a/mixs6/fire.md +++ b/mixs6/fire.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/fireplace_type.md b/mixs6/fireplace_type.md index ee9a91e5..78de7cd4 100644 --- a/mixs6/fireplace_type.md +++ b/mixs6/fireplace_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/flooding.md b/mixs6/flooding.md index 04adfbfe..7d8311b9 100644 --- a/mixs6/flooding.md +++ b/mixs6/flooding.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/floor_age.md b/mixs6/floor_age.md index 9acf8207..978f27fc 100644 --- a/mixs6/floor_age.md +++ b/mixs6/floor_age.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_area.md b/mixs6/floor_area.md index 662e03ae..801b852f 100644 --- a/mixs6/floor_area.md +++ b/mixs6/floor_area.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_cond.md b/mixs6/floor_cond.md index 3ec9d7c0..e2e22157 100644 --- a/mixs6/floor_cond.md +++ b/mixs6/floor_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_count.md b/mixs6/floor_count.md index f41602e3..f2d5a11b 100644 --- a/mixs6/floor_count.md +++ b/mixs6/floor_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_finish_mat.md b/mixs6/floor_finish_mat.md index d903c531..e41d8b77 100644 --- a/mixs6/floor_finish_mat.md +++ b/mixs6/floor_finish_mat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_struc.md b/mixs6/floor_struc.md index 44101067..9ec56e18 100644 --- a/mixs6/floor_struc.md +++ b/mixs6/floor_struc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_thermal_mass.md b/mixs6/floor_thermal_mass.md index e7ca97de..2141422b 100644 --- a/mixs6/floor_thermal_mass.md +++ b/mixs6/floor_thermal_mass.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/floor_water_mold.md b/mixs6/floor_water_mold.md index 1a846cf3..e5a30a5b 100644 --- a/mixs6/floor_water_mold.md +++ b/mixs6/floor_water_mold.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/fluor.md b/mixs6/fluor.md index c4d2ef80..7983ead9 100644 --- a/mixs6/fluor.md +++ b/mixs6/fluor.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/foetal_health_stat.md b/mixs6/foetal_health_stat.md index 7d841982..ac8897d4 100644 --- a/mixs6/foetal_health_stat.md +++ b/mixs6/foetal_health_stat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/freq_clean.md b/mixs6/freq_clean.md index 48ce37dd..b29c6191 100644 --- a/mixs6/freq_clean.md +++ b/mixs6/freq_clean.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/freq_cook.md b/mixs6/freq_cook.md index 6cb1368c..04e89d01 100644 --- a/mixs6/freq_cook.md +++ b/mixs6/freq_cook.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/fungicide_regm.md b/mixs6/fungicide_regm.md index f2e2c415..28b93c47 100644 --- a/mixs6/fungicide_regm.md +++ b/mixs6/fungicide_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/furniture.md b/mixs6/furniture.md index 3f89862d..c06ea3ff 100644 --- a/mixs6/furniture.md +++ b/mixs6/furniture.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/gaseous_environment.md b/mixs6/gaseous_environment.md index 64445188..73d8b0fd 100644 --- a/mixs6/gaseous_environment.md +++ b/mixs6/gaseous_environment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/gaseous_substances.md b/mixs6/gaseous_substances.md index ed9cd10a..8927a05a 100644 --- a/mixs6/gaseous_substances.md +++ b/mixs6/gaseous_substances.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/gastrointest_disord.md b/mixs6/gastrointest_disord.md index 7f0fcb3c..af3ca822 100644 --- a/mixs6/gastrointest_disord.md +++ b/mixs6/gastrointest_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) ## Other properties diff --git a/mixs6/gender_restroom.md b/mixs6/gender_restroom.md index 80f52ba5..cd8a4b1f 100644 --- a/mixs6/gender_restroom.md +++ b/mixs6/gender_restroom.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/genetic_mod.md b/mixs6/genetic_mod.md index dc4a3b2b..adc06b42 100644 --- a/mixs6/genetic_mod.md +++ b/mixs6/genetic_mod.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/geo_loc_name.md b/mixs6/geo_loc_name.md index 4a83654f..9a057a46 100644 --- a/mixs6/geo_loc_name.md +++ b/mixs6/geo_loc_name.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞geo_loc_name](me_geo_loc_name.md) - * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) - * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) - * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) - * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) - * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) - * [mimag➞geo_loc_name](mimag_geo_loc_name.md) - * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) - * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) - * [misag➞geo_loc_name](misag_geo_loc_name.md) - * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) + * [ME➞geo_loc_name](ME_geo_loc_name.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/gestation_state.md b/mixs6/gestation_state.md index 98e2124a..bccec130 100644 --- a/mixs6/gestation_state.md +++ b/mixs6/gestation_state.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/glucosidase_act.md b/mixs6/glucosidase_act.md index e95340b6..13722d14 100644 --- a/mixs6/glucosidase_act.md +++ b/mixs6/glucosidase_act.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/gravidity.md b/mixs6/gravidity.md index ffb13e58..c49da4f8 100644 --- a/mixs6/gravidity.md +++ b/mixs6/gravidity.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/gravity.md b/mixs6/gravity.md index 3078caa3..131514e6 100644 --- a/mixs6/gravity.md +++ b/mixs6/gravity.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/growth_facil.md b/mixs6/growth_facil.md index d8c693d8..7e50da26 100644 --- a/mixs6/growth_facil.md +++ b/mixs6/growth_facil.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/growth_habit.md b/mixs6/growth_habit.md index 8b276654..14b3625b 100644 --- a/mixs6/growth_habit.md +++ b/mixs6/growth_habit.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/growth_hormone_regm.md b/mixs6/growth_hormone_regm.md index b2d5d302..d1d3ff70 100644 --- a/mixs6/growth_hormone_regm.md +++ b/mixs6/growth_hormone_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/gynecologic_disord.md b/mixs6/gynecologic_disord.md index 00bf339f..bb4101dd 100644 --- a/mixs6/gynecologic_disord.md +++ b/mixs6/gynecologic_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/hall_count.md b/mixs6/hall_count.md index 53889b1e..d01aec98 100644 --- a/mixs6/hall_count.md +++ b/mixs6/hall_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/handidness.md b/mixs6/handidness.md index 9147485c..c1d76548 100644 --- a/mixs6/handidness.md +++ b/mixs6/handidness.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/hc_produced.md b/mixs6/hc_produced.md index dd8a7419..d138fcfd 100644 --- a/mixs6/hc_produced.md +++ b/mixs6/hc_produced.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/hcr.md b/mixs6/hcr.md index 1189e26b..d7c44faf 100644 --- a/mixs6/hcr.md +++ b/mixs6/hcr.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/hcr_fw_salinity.md b/mixs6/hcr_fw_salinity.md index 88563d61..2667d108 100644 --- a/mixs6/hcr_fw_salinity.md +++ b/mixs6/hcr_fw_salinity.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/hcr_geol_age.md b/mixs6/hcr_geol_age.md index ca4e1d5b..17882d43 100644 --- a/mixs6/hcr_geol_age.md +++ b/mixs6/hcr_geol_age.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/hcr_pressure.md b/mixs6/hcr_pressure.md index cd3e54a5..227c8502 100644 --- a/mixs6/hcr_pressure.md +++ b/mixs6/hcr_pressure.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/hcr_temp.md b/mixs6/hcr_temp.md index 7ada3e0c..2f21b65b 100644 --- a/mixs6/hcr_temp.md +++ b/mixs6/hcr_temp.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/health_disease_stat.md b/mixs6/health_disease_stat.md index 7e6669f1..c86da601 100644 --- a/mixs6/health_disease_stat.md +++ b/mixs6/health_disease_stat.md @@ -17,9 +17,9 @@ None -> OPT ## Children - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) ## Used by diff --git a/mixs6/heat_cool_type.md b/mixs6/heat_cool_type.md index e1fca8e7..3e0c0699 100644 --- a/mixs6/heat_cool_type.md +++ b/mixs6/heat_cool_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/heat_deliv_loc.md b/mixs6/heat_deliv_loc.md index cad0af42..cc4311b3 100644 --- a/mixs6/heat_deliv_loc.md +++ b/mixs6/heat_deliv_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/heat_system_deliv_meth.md b/mixs6/heat_system_deliv_meth.md index 66ecfd68..c97543d7 100644 --- a/mixs6/heat_system_deliv_meth.md +++ b/mixs6/heat_system_deliv_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/heat_system_id.md b/mixs6/heat_system_id.md index 8e5e881a..c95b6d06 100644 --- a/mixs6/heat_system_id.md +++ b/mixs6/heat_system_id.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/heavy_metals.md b/mixs6/heavy_metals.md index c97ea7f0..73587be8 100644 --- a/mixs6/heavy_metals.md +++ b/mixs6/heavy_metals.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/heavy_metals_meth.md b/mixs6/heavy_metals_meth.md index e95e25d6..666c564a 100644 --- a/mixs6/heavy_metals_meth.md +++ b/mixs6/heavy_metals_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/height_carper_fiber.md b/mixs6/height_carper_fiber.md index 00346395..de9662ea 100644 --- a/mixs6/height_carper_fiber.md +++ b/mixs6/height_carper_fiber.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/herbicide_regm.md b/mixs6/herbicide_regm.md index bb63e842..ab186797 100644 --- a/mixs6/herbicide_regm.md +++ b/mixs6/herbicide_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/horizon.md b/mixs6/horizon.md index d6fb8a92..f2cd1b1f 100644 --- a/mixs6/horizon.md +++ b/mixs6/horizon.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/horizon_meth.md b/mixs6/horizon_meth.md index 5744514d..93eb6e42 100644 --- a/mixs6/horizon_meth.md +++ b/mixs6/horizon_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/host_age.md b/mixs6/host_age.md index 72a6309e..a270f7b2 100644 --- a/mixs6/host_age.md +++ b/mixs6/host_age.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_blood_press_diast.md b/mixs6/host_blood_press_diast.md index cc8e73a1..396c307e 100644 --- a/mixs6/host_blood_press_diast.md +++ b/mixs6/host_blood_press_diast.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_blood_press_syst.md b/mixs6/host_blood_press_syst.md index 913bbfde..f159d87e 100644 --- a/mixs6/host_blood_press_syst.md +++ b/mixs6/host_blood_press_syst.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_body_habitat.md b/mixs6/host_body_habitat.md index 3038a403..c2e584d0 100644 --- a/mixs6/host_body_habitat.md +++ b/mixs6/host_body_habitat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_body_mass_index.md b/mixs6/host_body_mass_index.md index eeeba402..93b1d543 100644 --- a/mixs6/host_body_mass_index.md +++ b/mixs6/host_body_mass_index.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_body_product.md b/mixs6/host_body_product.md index d4bf41f7..c683c72a 100644 --- a/mixs6/host_body_product.md +++ b/mixs6/host_body_product.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_body_site.md b/mixs6/host_body_site.md index 5597d18e..14318e23 100644 --- a/mixs6/host_body_site.md +++ b/mixs6/host_body_site.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_body_temp.md b/mixs6/host_body_temp.md index f0613e63..e8080437 100644 --- a/mixs6/host_body_temp.md +++ b/mixs6/host_body_temp.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_color.md b/mixs6/host_color.md index de0c697c..f24afc35 100644 --- a/mixs6/host_color.md +++ b/mixs6/host_color.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_common_name.md b/mixs6/host_common_name.md index 34716f20..fc22c21f 100644 --- a/mixs6/host_common_name.md +++ b/mixs6/host_common_name.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_diet.md b/mixs6/host_diet.md index 8523f285..0f4bbe4a 100644 --- a/mixs6/host_diet.md +++ b/mixs6/host_diet.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_disease_stat.md b/mixs6/host_disease_stat.md index be1e8340..65b3e1d0 100644 --- a/mixs6/host_disease_stat.md +++ b/mixs6/host_disease_stat.md @@ -21,89 +21,89 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_dry_mass.md b/mixs6/host_dry_mass.md index 7a0b3644..0e393bd9 100644 --- a/mixs6/host_dry_mass.md +++ b/mixs6/host_dry_mass.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_family_relationship.md b/mixs6/host_family_relationship.md index 4e1556db..a1768590 100644 --- a/mixs6/host_family_relationship.md +++ b/mixs6/host_family_relationship.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_genotype.md b/mixs6/host_genotype.md index 9902da5b..1bce480e 100644 --- a/mixs6/host_genotype.md +++ b/mixs6/host_genotype.md @@ -21,89 +21,89 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_growth_cond.md b/mixs6/host_growth_cond.md index e3465f99..4671f26d 100644 --- a/mixs6/host_growth_cond.md +++ b/mixs6/host_growth_cond.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_height.md b/mixs6/host_height.md index f1223f2e..89444236 100644 --- a/mixs6/host_height.md +++ b/mixs6/host_height.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_hiv_stat.md b/mixs6/host_hiv_stat.md index 87cbd93a..049b1e47 100644 --- a/mixs6/host_hiv_stat.md +++ b/mixs6/host_hiv_stat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_infra_specific_name.md b/mixs6/host_infra_specific_name.md index ea57ca68..00bc2ab9 100644 --- a/mixs6/host_infra_specific_name.md +++ b/mixs6/host_infra_specific_name.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_infra_specific_rank.md b/mixs6/host_infra_specific_rank.md index 1bdd10ff..085ef2ae 100644 --- a/mixs6/host_infra_specific_rank.md +++ b/mixs6/host_infra_specific_rank.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_last_meal.md b/mixs6/host_last_meal.md index 19e06ae5..a1353f06 100644 --- a/mixs6/host_last_meal.md +++ b/mixs6/host_last_meal.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_length.md b/mixs6/host_length.md index f1b3506b..bf535024 100644 --- a/mixs6/host_length.md +++ b/mixs6/host_length.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_life_stage.md b/mixs6/host_life_stage.md index 63a29a51..8fe0a7c4 100644 --- a/mixs6/host_life_stage.md +++ b/mixs6/host_life_stage.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_occupation.md b/mixs6/host_occupation.md index 8122c112..d8683d7d 100644 --- a/mixs6/host_occupation.md +++ b/mixs6/host_occupation.md @@ -21,65 +21,65 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_phenotype.md b/mixs6/host_phenotype.md index c013a434..97e88954 100644 --- a/mixs6/host_phenotype.md +++ b/mixs6/host_phenotype.md @@ -21,89 +21,89 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_pred_appr.md b/mixs6/host_pred_appr.md index 8ae50929..0cd7066a 100644 --- a/mixs6/host_pred_appr.md +++ b/mixs6/host_pred_appr.md @@ -17,7 +17,7 @@ None -> OPT ## Children - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) ## Used by diff --git a/mixs6/host_pred_est_acc.md b/mixs6/host_pred_est_acc.md index 3edf10c6..09051028 100644 --- a/mixs6/host_pred_est_acc.md +++ b/mixs6/host_pred_est_acc.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) ## Used by diff --git a/mixs6/host_pulse.md b/mixs6/host_pulse.md index 211698b9..1df4295c 100644 --- a/mixs6/host_pulse.md +++ b/mixs6/host_pulse.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_sex.md b/mixs6/host_sex.md index 47d5df4f..eb965052 100644 --- a/mixs6/host_sex.md +++ b/mixs6/host_sex.md @@ -21,77 +21,77 @@ None -> OPT ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_shape.md b/mixs6/host_shape.md index b721bf62..43913364 100644 --- a/mixs6/host_shape.md +++ b/mixs6/host_shape.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_spec_range.md b/mixs6/host_spec_range.md index 5543fa70..60d81251 100644 --- a/mixs6/host_spec_range.md +++ b/mixs6/host_spec_range.md @@ -17,11 +17,11 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) ## Used by diff --git a/mixs6/host_subject_id.md b/mixs6/host_subject_id.md index 7e30b6ce..dfe62039 100644 --- a/mixs6/host_subject_id.md +++ b/mixs6/host_subject_id.md @@ -21,77 +21,77 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/host_substrate.md b/mixs6/host_substrate.md index b68e7f48..0d2c8ffd 100644 --- a/mixs6/host_substrate.md +++ b/mixs6/host_substrate.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_taxid.md b/mixs6/host_taxid.md index 39c3f412..8f3dce1c 100644 --- a/mixs6/host_taxid.md +++ b/mixs6/host_taxid.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_tot_mass.md b/mixs6/host_tot_mass.md index 6c014e6c..748f559b 100644 --- a/mixs6/host_tot_mass.md +++ b/mixs6/host_tot_mass.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/host_wet_mass.md b/mixs6/host_wet_mass.md index 9b149d0a..2f683df2 100644 --- a/mixs6/host_wet_mass.md +++ b/mixs6/host_wet_mass.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/hrt.md b/mixs6/hrt.md index 0821186e..03aaa9ec 100644 --- a/mixs6/hrt.md +++ b/mixs6/hrt.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/humidity.md b/mixs6/humidity.md index c7058a60..13fd8237 100644 --- a/mixs6/humidity.md +++ b/mixs6/humidity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/humidity_regm.md b/mixs6/humidity_regm.md index 8fd9aab5..5d804f97 100644 --- a/mixs6/humidity_regm.md +++ b/mixs6/humidity_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/hysterectomy.md b/mixs6/hysterectomy.md index 9a2daa50..a003a702 100644 --- a/mixs6/hysterectomy.md +++ b/mixs6/hysterectomy.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/ihmc_ethnicity.md b/mixs6/ihmc_ethnicity.md index aaf9c335..4e94adfa 100644 --- a/mixs6/ihmc_ethnicity.md +++ b/mixs6/ihmc_ethnicity.md @@ -21,65 +21,65 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/ihmc_medication_code.md b/mixs6/ihmc_medication_code.md index 2bbcf53f..5abcdb78 100644 --- a/mixs6/ihmc_medication_code.md +++ b/mixs6/ihmc_medication_code.md @@ -21,65 +21,65 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/index.md b/mixs6/index.md index 5e65871a..694b39c1 100644 --- a/mixs6/index.md +++ b/mixs6/index.md @@ -8,241 +8,241 @@ MIxS 6 linkml rendering ### Classes * [Air](Air.md) - air - * [AirMe](AirMe.md) - Combinatorial checklist for air with me - * [AirMigsBa](AirMigsBa.md) - Combinatorial checklist for air with migs_ba - * [AirMigsEu](AirMigsEu.md) - Combinatorial checklist for air with migs_eu - * [AirMigsOrg](AirMigsOrg.md) - Combinatorial checklist for air with migs_org - * [AirMigsPl](AirMigsPl.md) - Combinatorial checklist for air with migs_pl - * [AirMigsVi](AirMigsVi.md) - Combinatorial checklist for air with migs_vi - * [AirMimag](AirMimag.md) - Combinatorial checklist for air with mimag - * [AirMimarksC](AirMimarksC.md) - Combinatorial checklist for air with mimarks_c - * [AirMimarksS](AirMimarksS.md) - Combinatorial checklist for air with mimarks_s - * [AirMisag](AirMisag.md) - Combinatorial checklist for air with misag - * [AirMiuvig](AirMiuvig.md) - Combinatorial checklist for air with miuvig + * [AirME](AirME.md) - Combinatorial checklist Metagenome or Environmental with environmental package air + * [AirMIGSBacteria](AirMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [AirMIGSEukaryote](AirMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package air + * [AirMIGSOrg](AirMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package air + * [AirMIGSPlant](AirMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package air + * [AirMIGSVirus](AirMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package air + * [AirMIMAG](AirMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package air + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package air + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package air + * [AirMISAG](AirMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package air + * [AirMIUVIG](AirMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package air * [BuiltEnvironment](BuiltEnvironment.md) - built environment - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - Combinatorial checklist for built environment with me - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - Combinatorial checklist for built environment with migs_ba - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - Combinatorial checklist for built environment with migs_eu - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - Combinatorial checklist for built environment with migs_org - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - Combinatorial checklist for built environment with migs_pl - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - Combinatorial checklist for built environment with migs_vi - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - Combinatorial checklist for built environment with mimag - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - Combinatorial checklist for built environment with mimarks_c - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - Combinatorial checklist for built environment with mimarks_s - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - Combinatorial checklist for built environment with misag - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) - Combinatorial checklist for built environment with miuvig + * [BuiltEnvironmentME](BuiltEnvironmentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package built environment + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package built environment + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package built environment + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package built environment + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package built environment + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package built environment + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package built environment + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment * [Core](Core.md) - Core package. Do not use this directly, this is used to build other packages * [Host-associated](Host-associated.md) - host-associated - * [Host-associatedMe](Host-associatedMe.md) - Combinatorial checklist for host-associated with me - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - Combinatorial checklist for host-associated with migs_ba - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - Combinatorial checklist for host-associated with migs_eu - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - Combinatorial checklist for host-associated with migs_org - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - Combinatorial checklist for host-associated with migs_pl - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - Combinatorial checklist for host-associated with migs_vi - * [Host-associatedMimag](Host-associatedMimag.md) - Combinatorial checklist for host-associated with mimag - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - Combinatorial checklist for host-associated with mimarks_c - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - Combinatorial checklist for host-associated with mimarks_s - * [Host-associatedMisag](Host-associatedMisag.md) - Combinatorial checklist for host-associated with misag - * [Host-associatedMiuvig](Host-associatedMiuvig.md) - Combinatorial checklist for host-associated with miuvig + * [Host-associatedME](Host-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package host-associated + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package host-associated + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package host-associated + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package host-associated + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package host-associated + * [Host-associatedMIMAG](Host-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package host-associated + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package host-associated + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package host-associated + * [Host-associatedMISAG](Host-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package host-associated + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package host-associated * [Human-associated](Human-associated.md) - human-associated - * [Human-associatedMe](Human-associatedMe.md) - Combinatorial checklist for human-associated with me - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - Combinatorial checklist for human-associated with migs_ba - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - Combinatorial checklist for human-associated with migs_eu - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - Combinatorial checklist for human-associated with migs_org - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - Combinatorial checklist for human-associated with migs_pl - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - Combinatorial checklist for human-associated with migs_vi - * [Human-associatedMimag](Human-associatedMimag.md) - Combinatorial checklist for human-associated with mimag - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - Combinatorial checklist for human-associated with mimarks_c - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - Combinatorial checklist for human-associated with mimarks_s - * [Human-associatedMisag](Human-associatedMisag.md) - Combinatorial checklist for human-associated with misag - * [Human-associatedMiuvig](Human-associatedMiuvig.md) - Combinatorial checklist for human-associated with miuvig + * [Human-associatedME](Human-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-associated + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-associated + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-associated + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-associated + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-associated + * [Human-associatedMIMAG](Human-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-associated + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-associated + * [Human-associatedMISAG](Human-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-associated + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-associated * [Human-gut](Human-gut.md) - human-gut - * [Human-gutMe](Human-gutMe.md) - Combinatorial checklist for human-gut with me - * [Human-gutMigsBa](Human-gutMigsBa.md) - Combinatorial checklist for human-gut with migs_ba - * [Human-gutMigsEu](Human-gutMigsEu.md) - Combinatorial checklist for human-gut with migs_eu - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - Combinatorial checklist for human-gut with migs_org - * [Human-gutMigsPl](Human-gutMigsPl.md) - Combinatorial checklist for human-gut with migs_pl - * [Human-gutMigsVi](Human-gutMigsVi.md) - Combinatorial checklist for human-gut with migs_vi - * [Human-gutMimag](Human-gutMimag.md) - Combinatorial checklist for human-gut with mimag - * [Human-gutMimarksC](Human-gutMimarksC.md) - Combinatorial checklist for human-gut with mimarks_c - * [Human-gutMimarksS](Human-gutMimarksS.md) - Combinatorial checklist for human-gut with mimarks_s - * [Human-gutMisag](Human-gutMisag.md) - Combinatorial checklist for human-gut with misag - * [Human-gutMiuvig](Human-gutMiuvig.md) - Combinatorial checklist for human-gut with miuvig + * [Human-gutME](Human-gutME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-gut + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-gut + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-gut + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-gut + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-gut + * [Human-gutMIMAG](Human-gutMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-gut + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-gut + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-gut + * [Human-gutMISAG](Human-gutMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut + * [Human-gutMIUVIG](Human-gutMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-gut * [Human-oral](Human-oral.md) - human-oral - * [Human-oralMe](Human-oralMe.md) - Combinatorial checklist for human-oral with me - * [Human-oralMigsBa](Human-oralMigsBa.md) - Combinatorial checklist for human-oral with migs_ba - * [Human-oralMigsEu](Human-oralMigsEu.md) - Combinatorial checklist for human-oral with migs_eu - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - Combinatorial checklist for human-oral with migs_org - * [Human-oralMigsPl](Human-oralMigsPl.md) - Combinatorial checklist for human-oral with migs_pl - * [Human-oralMigsVi](Human-oralMigsVi.md) - Combinatorial checklist for human-oral with migs_vi - * [Human-oralMimag](Human-oralMimag.md) - Combinatorial checklist for human-oral with mimag - * [Human-oralMimarksC](Human-oralMimarksC.md) - Combinatorial checklist for human-oral with mimarks_c - * [Human-oralMimarksS](Human-oralMimarksS.md) - Combinatorial checklist for human-oral with mimarks_s - * [Human-oralMisag](Human-oralMisag.md) - Combinatorial checklist for human-oral with misag - * [Human-oralMiuvig](Human-oralMiuvig.md) - Combinatorial checklist for human-oral with miuvig + * [Human-oralME](Human-oralME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-oral + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-oral + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-oral + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-oral + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-oral + * [Human-oralMIMAG](Human-oralMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-oral + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-oral + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-oral + * [Human-oralMISAG](Human-oralMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-oral + * [Human-oralMIUVIG](Human-oralMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-oral * [Human-skin](Human-skin.md) - human-skin - * [Human-skinMe](Human-skinMe.md) - Combinatorial checklist for human-skin with me - * [Human-skinMigsBa](Human-skinMigsBa.md) - Combinatorial checklist for human-skin with migs_ba - * [Human-skinMigsEu](Human-skinMigsEu.md) - Combinatorial checklist for human-skin with migs_eu - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - Combinatorial checklist for human-skin with migs_org - * [Human-skinMigsPl](Human-skinMigsPl.md) - Combinatorial checklist for human-skin with migs_pl - * [Human-skinMigsVi](Human-skinMigsVi.md) - Combinatorial checklist for human-skin with migs_vi - * [Human-skinMimag](Human-skinMimag.md) - Combinatorial checklist for human-skin with mimag - * [Human-skinMimarksC](Human-skinMimarksC.md) - Combinatorial checklist for human-skin with mimarks_c - * [Human-skinMimarksS](Human-skinMimarksS.md) - Combinatorial checklist for human-skin with mimarks_s - * [Human-skinMisag](Human-skinMisag.md) - Combinatorial checklist for human-skin with misag - * [Human-skinMiuvig](Human-skinMiuvig.md) - Combinatorial checklist for human-skin with miuvig + * [Human-skinME](Human-skinME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-skin + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-skin + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-skin + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-skin + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-skin + * [Human-skinMIMAG](Human-skinMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-skin + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-skin + * [Human-skinMISAG](Human-skinMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-skin + * [Human-skinMIUVIG](Human-skinMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-skin * [Human-vaginal](Human-vaginal.md) - human-vaginal - * [Human-vaginalMe](Human-vaginalMe.md) - Combinatorial checklist for human-vaginal with me - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - Combinatorial checklist for human-vaginal with migs_ba - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - Combinatorial checklist for human-vaginal with migs_eu - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - Combinatorial checklist for human-vaginal with migs_org - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - Combinatorial checklist for human-vaginal with migs_pl - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - Combinatorial checklist for human-vaginal with migs_vi - * [Human-vaginalMimag](Human-vaginalMimag.md) - Combinatorial checklist for human-vaginal with mimag - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - Combinatorial checklist for human-vaginal with mimarks_c - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - Combinatorial checklist for human-vaginal with mimarks_s - * [Human-vaginalMisag](Human-vaginalMisag.md) - Combinatorial checklist for human-vaginal with misag - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) - Combinatorial checklist for human-vaginal with miuvig + * [Human-vaginalME](Human-vaginalME.md) - Combinatorial checklist Metagenome or Environmental with environmental package human-vaginal + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package human-vaginal + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package human-vaginal + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package human-vaginal + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package human-vaginal + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package human-vaginal + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-vaginal + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package human-vaginal + * [Human-vaginalMISAG](Human-vaginalMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-vaginal + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package human-vaginal * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - Combinatorial checklist for hydrocarbon resources-cores with me - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_ba - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_eu - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_org - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_pl - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - Combinatorial checklist for hydrocarbon resources-cores with migs_vi - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - Combinatorial checklist for hydrocarbon resources-cores with mimag - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_c - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_s - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - Combinatorial checklist for hydrocarbon resources-cores with misag - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) - Combinatorial checklist for hydrocarbon resources-cores with miuvig + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-cores + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-cores * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with me - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_org - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimag - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with misag - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with miuvig + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) - Combinatorial checklist Metagenome or Environmental with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package hydrocarbon resources-fluids_swabs + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package hydrocarbon resources-fluids_swabs * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - Combinatorial checklist for microbial mat_biofilm with me - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - Combinatorial checklist for microbial mat_biofilm with migs_ba - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - Combinatorial checklist for microbial mat_biofilm with migs_eu - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - Combinatorial checklist for microbial mat_biofilm with migs_org - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - Combinatorial checklist for microbial mat_biofilm with migs_pl - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - Combinatorial checklist for microbial mat_biofilm with migs_vi - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - Combinatorial checklist for microbial mat_biofilm with mimag - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_c - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - Combinatorial checklist for microbial mat_biofilm with mimarks_s - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - Combinatorial checklist for microbial mat_biofilm with misag - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) - Combinatorial checklist for microbial mat_biofilm with miuvig + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) - Combinatorial checklist Metagenome or Environmental with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package microbial mat_biofilm + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package microbial mat_biofilm * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - Combinatorial checklist for miscellaneous natural or artificial environment with me - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_org - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimag - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - Combinatorial checklist for miscellaneous natural or artificial environment with misag - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) - Combinatorial checklist for miscellaneous natural or artificial environment with miuvig + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment * [Plant-associated](Plant-associated.md) - plant-associated - * [Plant-associatedMe](Plant-associatedMe.md) - Combinatorial checklist for plant-associated with me - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - Combinatorial checklist for plant-associated with migs_ba - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - Combinatorial checklist for plant-associated with migs_eu - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - Combinatorial checklist for plant-associated with migs_org - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - Combinatorial checklist for plant-associated with migs_pl - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - Combinatorial checklist for plant-associated with migs_vi - * [Plant-associatedMimag](Plant-associatedMimag.md) - Combinatorial checklist for plant-associated with mimag - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - Combinatorial checklist for plant-associated with mimarks_c - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - Combinatorial checklist for plant-associated with mimarks_s - * [Plant-associatedMisag](Plant-associatedMisag.md) - Combinatorial checklist for plant-associated with misag - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) - Combinatorial checklist for plant-associated with miuvig + * [Plant-associatedME](Plant-associatedME.md) - Combinatorial checklist Metagenome or Environmental with environmental package plant-associated + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package plant-associated + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package plant-associated + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package plant-associated + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package plant-associated + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package plant-associated + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package plant-associated + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package plant-associated + * [Plant-associatedMISAG](Plant-associatedMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package plant-associated + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package plant-associated * [QuantityValue](QuantityValue.md) - used to record a measurement * [Sediment](Sediment.md) - sediment - * [SedimentMe](SedimentMe.md) - Combinatorial checklist for sediment with me - * [SedimentMigsBa](SedimentMigsBa.md) - Combinatorial checklist for sediment with migs_ba - * [SedimentMigsEu](SedimentMigsEu.md) - Combinatorial checklist for sediment with migs_eu - * [SedimentMigsOrg](SedimentMigsOrg.md) - Combinatorial checklist for sediment with migs_org - * [SedimentMigsPl](SedimentMigsPl.md) - Combinatorial checklist for sediment with migs_pl - * [SedimentMigsVi](SedimentMigsVi.md) - Combinatorial checklist for sediment with migs_vi - * [SedimentMimag](SedimentMimag.md) - Combinatorial checklist for sediment with mimag - * [SedimentMimarksC](SedimentMimarksC.md) - Combinatorial checklist for sediment with mimarks_c - * [SedimentMimarksS](SedimentMimarksS.md) - Combinatorial checklist for sediment with mimarks_s - * [SedimentMisag](SedimentMisag.md) - Combinatorial checklist for sediment with misag - * [SedimentMiuvig](SedimentMiuvig.md) - Combinatorial checklist for sediment with miuvig + * [SedimentME](SedimentME.md) - Combinatorial checklist Metagenome or Environmental with environmental package sediment + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment + * [SedimentMIGSOrg](SedimentMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment + * [SedimentMIGSPlant](SedimentMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment + * [SedimentMIGSVirus](SedimentMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment + * [SedimentMIMAG](SedimentMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment + * [SedimentMISAG](SedimentMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment + * [SedimentMIUVIG](SedimentMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment * [Soil](Soil.md) - soil - * [SoilMe](SoilMe.md) - Combinatorial checklist for soil with me - * [SoilMigsBa](SoilMigsBa.md) - Combinatorial checklist for soil with migs_ba - * [SoilMigsEu](SoilMigsEu.md) - Combinatorial checklist for soil with migs_eu - * [SoilMigsOrg](SoilMigsOrg.md) - Combinatorial checklist for soil with migs_org - * [SoilMigsPl](SoilMigsPl.md) - Combinatorial checklist for soil with migs_pl - * [SoilMigsVi](SoilMigsVi.md) - Combinatorial checklist for soil with migs_vi - * [SoilMimag](SoilMimag.md) - Combinatorial checklist for soil with mimag - * [SoilMimarksC](SoilMimarksC.md) - Combinatorial checklist for soil with mimarks_c - * [SoilMimarksS](SoilMimarksS.md) - Combinatorial checklist for soil with mimarks_s - * [SoilMisag](SoilMisag.md) - Combinatorial checklist for soil with misag - * [SoilMiuvig](SoilMiuvig.md) - Combinatorial checklist for soil with miuvig + * [SoilME](SoilME.md) - Combinatorial checklist Metagenome or Environmental with environmental package soil + * [SoilMIGSBacteria](SoilMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil + * [SoilMIGSOrg](SoilMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil + * [SoilMIGSPlant](SoilMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil + * [SoilMIGSVirus](SoilMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil + * [SoilMIMAG](SoilMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil + * [SoilMISAG](SoilMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil + * [SoilMIUVIG](SoilMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil * [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - Combinatorial checklist for wastewater_sludge with me - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - Combinatorial checklist for wastewater_sludge with migs_ba - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - Combinatorial checklist for wastewater_sludge with migs_eu - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - Combinatorial checklist for wastewater_sludge with migs_org - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - Combinatorial checklist for wastewater_sludge with migs_pl - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - Combinatorial checklist for wastewater_sludge with migs_vi - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - Combinatorial checklist for wastewater_sludge with mimag - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - Combinatorial checklist for wastewater_sludge with mimarks_c - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - Combinatorial checklist for wastewater_sludge with mimarks_s - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - Combinatorial checklist for wastewater_sludge with misag - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) - Combinatorial checklist for wastewater_sludge with miuvig + * [WastewaterSludgeME](WastewaterSludgeME.md) - Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge * [Water](Water.md) - water - * [WaterMe](WaterMe.md) - Combinatorial checklist for water with me - * [WaterMigsBa](WaterMigsBa.md) - Combinatorial checklist for water with migs_ba - * [WaterMigsEu](WaterMigsEu.md) - Combinatorial checklist for water with migs_eu - * [WaterMigsOrg](WaterMigsOrg.md) - Combinatorial checklist for water with migs_org - * [WaterMigsPl](WaterMigsPl.md) - Combinatorial checklist for water with migs_pl - * [WaterMigsVi](WaterMigsVi.md) - Combinatorial checklist for water with migs_vi - * [WaterMimag](WaterMimag.md) - Combinatorial checklist for water with mimag - * [WaterMimarksC](WaterMimarksC.md) - Combinatorial checklist for water with mimarks_c - * [WaterMimarksS](WaterMimarksS.md) - Combinatorial checklist for water with mimarks_s - * [WaterMisag](WaterMisag.md) - Combinatorial checklist for water with misag - * [WaterMiuvig](WaterMiuvig.md) - Combinatorial checklist for water with miuvig + * [WaterME](WaterME.md) - Combinatorial checklist Metagenome or Environmental with environmental package water + * [WaterMIGSBacteria](WaterMIGSBacteria.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package water + * [WaterMIGSOrg](WaterMIGSOrg.md) - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package water + * [WaterMIGSPlant](WaterMIGSPlant.md) - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package water + * [WaterMIGSVirus](WaterMIGSVirus.md) - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package water + * [WaterMIMAG](WaterMIMAG.md) - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package water + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package water + * [WaterMISAG](WaterMISAG.md) - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package water + * [WaterMIUVIG](WaterMIUVIG.md) - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package water ### Mixins - * [Me](Me.md) - me Checklist - * [MigsBa](MigsBa.md) - migs_ba Checklist - * [MigsEu](MigsEu.md) - migs_eu Checklist - * [MigsOrg](MigsOrg.md) - migs_org Checklist - * [MigsPl](MigsPl.md) - migs_pl Checklist - * [MigsVi](MigsVi.md) - migs_vi Checklist - * [Mimag](Mimag.md) - mimag Checklist - * [MimarksC](MimarksC.md) - mimarks_c Checklist - * [MimarksS](MimarksS.md) - mimarks_s Checklist - * [Misag](Misag.md) - misag Checklist - * [Miuvig](Miuvig.md) - miuvig Checklist + * [ME](ME.md) - Metagenome or Environmental + * [MIGSBacteria](MIGSBacteria.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + * [MIGSEukaryote](MIGSEukaryote.md) - Minimal Information about a Genome Sequence: eukaryote + * [MIGSOrg](MIGSOrg.md) - Minimal Information about a Genome Sequence: org + * [MIGSPlant](MIGSPlant.md) - Minimal Information about a Genome Sequence: plant + * [MIGSVirus](MIGSVirus.md) - Minimal Information about a Genome Sequence: cultured bacteria/archaea + * [MIMAG](MIMAG.md) - Minimum Information About a Metagenome-Assembled Genome + * [MIMARKSSpecimen](MIMARKSSpecimen.md) - Minimal Information about a Marker Specimen: specimen + * [MIMARKSSurvey](MIMARKSSurvey.md) - Minimal Information about a Marker Specimen: survey + * [MISAG](MISAG.md) - Minimum Information About a Single Amplified Genome + * [MIUVIG](MIUVIG.md) - Minimum Information About an Uncultivated Virus Genome ### Slots * [core field](core_field.md) - basic fields * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * [me➞sample_name](me_sample_name.md) - * [migs_ba➞sample_name](migs_ba_sample_name.md) - * [migs_eu➞sample_name](migs_eu_sample_name.md) - * [migs_org➞sample_name](migs_org_sample_name.md) - * [migs_pl➞sample_name](migs_pl_sample_name.md) - * [migs_vi➞sample_name](migs_vi_sample_name.md) - * [mimag➞sample_name](mimag_sample_name.md) - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) - * [misag➞sample_name](misag_sample_name.md) - * [miuvig➞sample_name](miuvig_sample_name.md) + * [ME➞sample_name](ME_sample_name.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) + * [MISAG➞sample_name](MISAG_sample_name.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) * [environment field](environment_field.md) - field describing environmental aspect of a sample * [abs_air_humidity](abs_air_humidity.md) - Actual mass of water vapor - mh20 - present in the air water vapor mixture * [add_recov_method](add_recov_method.md) - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field @@ -320,17 +320,17 @@ MIxS 6 linkml rendering * [chlorophyll](chlorophyll.md) - Concentration of chlorophyll * [climate_environment](climate_environment.md) - Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates * [collection_date](collection_date.md) - The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * [me➞collection_date](me_collection_date.md) - * [migs_ba➞collection_date](migs_ba_collection_date.md) - * [migs_eu➞collection_date](migs_eu_collection_date.md) - * [migs_org➞collection_date](migs_org_collection_date.md) - * [migs_pl➞collection_date](migs_pl_collection_date.md) - * [migs_vi➞collection_date](migs_vi_collection_date.md) - * [mimag➞collection_date](mimag_collection_date.md) - * [mimarks_c➞collection_date](mimarks_c_collection_date.md) - * [mimarks_s➞collection_date](mimarks_s_collection_date.md) - * [misag➞collection_date](misag_collection_date.md) - * [miuvig➞collection_date](miuvig_collection_date.md) + * [ME➞collection_date](ME_collection_date.md) + * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) + * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) + * [MIGS org➞collection_date](MIGS_org_collection_date.md) + * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) + * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) + * [MIMAG➞collection_date](MIMAG_collection_date.md) + * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) + * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) + * [MISAG➞collection_date](MISAG_collection_date.md) + * [MIUVIG➞collection_date](MIUVIG_collection_date.md) * [conduc](conduc.md) - Electrical conductivity of water * [cool_syst_id](cool_syst_id.md) - The cooling system identifier * [crop_rotation](crop_rotation.md) - Whether or not crop is rotated, and if yes, rotation schedule @@ -378,41 +378,41 @@ MIxS 6 linkml rendering * [elevator](elevator.md) - The number of elevators within the built structure * [emulsions](emulsions.md) - Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types * [env_broad_scale](env_broad_scale.md) - In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * [me➞env_broad_scale](me_env_broad_scale.md) - * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) - * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) - * [migs_org➞env_broad_scale](migs_org_env_broad_scale.md) - * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) - * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) - * [mimag➞env_broad_scale](mimag_env_broad_scale.md) - * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) - * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) - * [misag➞env_broad_scale](misag_env_broad_scale.md) - * [miuvig➞env_broad_scale](miuvig_env_broad_scale.md) + * [ME➞env_broad_scale](ME_env_broad_scale.md) + * [MIGS bacteria➞env_broad_scale](MIGS_bacteria_env_broad_scale.md) + * [MIGS eukaryote➞env_broad_scale](MIGS_eukaryote_env_broad_scale.md) + * [MIGS org➞env_broad_scale](MIGS_org_env_broad_scale.md) + * [MIGS plant➞env_broad_scale](MIGS_plant_env_broad_scale.md) + * [MIGS virus➞env_broad_scale](MIGS_virus_env_broad_scale.md) + * [MIMAG➞env_broad_scale](MIMAG_env_broad_scale.md) + * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) + * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) + * [MISAG➞env_broad_scale](MISAG_env_broad_scale.md) + * [MIUVIG➞env_broad_scale](MIUVIG_env_broad_scale.md) * [env_local_scale](env_local_scale.md) - In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * [me➞env_local_scale](me_env_local_scale.md) - * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) - * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) - * [migs_org➞env_local_scale](migs_org_env_local_scale.md) - * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) - * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) - * [mimag➞env_local_scale](mimag_env_local_scale.md) - * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) - * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) - * [misag➞env_local_scale](misag_env_local_scale.md) - * [miuvig➞env_local_scale](miuvig_env_local_scale.md) + * [ME➞env_local_scale](ME_env_local_scale.md) + * [MIGS bacteria➞env_local_scale](MIGS_bacteria_env_local_scale.md) + * [MIGS eukaryote➞env_local_scale](MIGS_eukaryote_env_local_scale.md) + * [MIGS org➞env_local_scale](MIGS_org_env_local_scale.md) + * [MIGS plant➞env_local_scale](MIGS_plant_env_local_scale.md) + * [MIGS virus➞env_local_scale](MIGS_virus_env_local_scale.md) + * [MIMAG➞env_local_scale](MIMAG_env_local_scale.md) + * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) + * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) + * [MISAG➞env_local_scale](MISAG_env_local_scale.md) + * [MIUVIG➞env_local_scale](MIUVIG_env_local_scale.md) * [env_medium](env_medium.md) - In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * [me➞env_medium](me_env_medium.md) - * [migs_ba➞env_medium](migs_ba_env_medium.md) - * [migs_eu➞env_medium](migs_eu_env_medium.md) - * [migs_org➞env_medium](migs_org_env_medium.md) - * [migs_pl➞env_medium](migs_pl_env_medium.md) - * [migs_vi➞env_medium](migs_vi_env_medium.md) - * [mimag➞env_medium](mimag_env_medium.md) - * [mimarks_c➞env_medium](mimarks_c_env_medium.md) - * [mimarks_s➞env_medium](mimarks_s_env_medium.md) - * [misag➞env_medium](misag_env_medium.md) - * [miuvig➞env_medium](miuvig_env_medium.md) + * [ME➞env_medium](ME_env_medium.md) + * [MIGS bacteria➞env_medium](MIGS_bacteria_env_medium.md) + * [MIGS eukaryote➞env_medium](MIGS_eukaryote_env_medium.md) + * [MIGS org➞env_medium](MIGS_org_env_medium.md) + * [MIGS plant➞env_medium](MIGS_plant_env_medium.md) + * [MIGS virus➞env_medium](MIGS_virus_env_medium.md) + * [MIMAG➞env_medium](MIMAG_env_medium.md) + * [MIMARKS specimen➞env_medium](MIMARKS_specimen_env_medium.md) + * [MIMARKS survey➞env_medium](MIMARKS_survey_env_medium.md) + * [MISAG➞env_medium](MISAG_env_medium.md) + * [MIUVIG➞env_medium](MIUVIG_env_medium.md) * [escalator](escalator.md) - The number of escalators within the built structure * [ethylbenzene](ethylbenzene.md) - Concentration of ethylbenzene in the sample * [exp_duct](exp_duct.md) - The amount of exposed ductwork in the room @@ -449,17 +449,17 @@ MIxS 6 linkml rendering * [gender_restroom](gender_restroom.md) - The gender type of the restroom * [genetic_mod](genetic_mod.md) - Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection * [geo_loc_name](geo_loc_name.md) - The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * [me➞geo_loc_name](me_geo_loc_name.md) - * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) - * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) - * [migs_org➞geo_loc_name](migs_org_geo_loc_name.md) - * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) - * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) - * [mimag➞geo_loc_name](mimag_geo_loc_name.md) - * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) - * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) - * [misag➞geo_loc_name](misag_geo_loc_name.md) - * [miuvig➞geo_loc_name](miuvig_geo_loc_name.md) + * [ME➞geo_loc_name](ME_geo_loc_name.md) + * [MIGS bacteria➞geo_loc_name](MIGS_bacteria_geo_loc_name.md) + * [MIGS eukaryote➞geo_loc_name](MIGS_eukaryote_geo_loc_name.md) + * [MIGS org➞geo_loc_name](MIGS_org_geo_loc_name.md) + * [MIGS plant➞geo_loc_name](MIGS_plant_geo_loc_name.md) + * [MIGS virus➞geo_loc_name](MIGS_virus_geo_loc_name.md) + * [MIMAG➞geo_loc_name](MIMAG_geo_loc_name.md) + * [MIMARKS specimen➞geo_loc_name](MIMARKS_specimen_geo_loc_name.md) + * [MIMARKS survey➞geo_loc_name](MIMARKS_survey_geo_loc_name.md) + * [MISAG➞geo_loc_name](MISAG_geo_loc_name.md) + * [MIUVIG➞geo_loc_name](MIUVIG_geo_loc_name.md) * [gestation_state](gestation_state.md) - Specification of the gestation state * [glucosidase_act](glucosidase_act.md) - Measurement of glucosidase activity * [gravidity](gravidity.md) - Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used @@ -535,17 +535,17 @@ MIxS 6 linkml rendering * [iwf](iwf.md) - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) * [last_clean](last_clean.md) - The last time the floor was cleaned (swept, mopped, vacuumed) * [lat_lon](lat_lon.md) - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * [me➞lat_lon](me_lat_lon.md) - * [migs_ba➞lat_lon](migs_ba_lat_lon.md) - * [migs_eu➞lat_lon](migs_eu_lat_lon.md) - * [migs_org➞lat_lon](migs_org_lat_lon.md) - * [migs_pl➞lat_lon](migs_pl_lat_lon.md) - * [migs_vi➞lat_lon](migs_vi_lat_lon.md) - * [mimag➞lat_lon](mimag_lat_lon.md) - * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) - * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) - * [misag➞lat_lon](misag_lat_lon.md) - * [miuvig➞lat_lon](miuvig_lat_lon.md) + * [ME➞lat_lon](ME_lat_lon.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) + * [MISAG➞lat_lon](MISAG_lat_lon.md) + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) * [light_intensity](light_intensity.md) - Measurement of light intensity * [light_regm](light_regm.md) - Information about treatment(s) involving exposure to light, including both light intensity and quality. * [light_type](light_type.md) - Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light @@ -826,561 +826,561 @@ MIxS 6 linkml rendering * [xylene](xylene.md) - Concentration of xylene in the sample * [investigation field](investigation_field.md) - field describing aspect of the investigation/study to which the sample belongs * [experimental_factor](experimental_factor.md) - Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * [me➞experimental_factor](me_experimental_factor.md) - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) - * [migs_org➞experimental_factor](migs_org_experimental_factor.md) - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) - * [mimag➞experimental_factor](mimag_experimental_factor.md) - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) - * [misag➞experimental_factor](misag_experimental_factor.md) - * [miuvig➞experimental_factor](miuvig_experimental_factor.md) + * [ME➞experimental_factor](ME_experimental_factor.md) + * [MIGS bacteria➞experimental_factor](MIGS_bacteria_experimental_factor.md) + * [MIGS eukaryote➞experimental_factor](MIGS_eukaryote_experimental_factor.md) + * [MIGS org➞experimental_factor](MIGS_org_experimental_factor.md) + * [MIGS plant➞experimental_factor](MIGS_plant_experimental_factor.md) + * [MIGS virus➞experimental_factor](MIGS_virus_experimental_factor.md) + * [MIMAG➞experimental_factor](MIMAG_experimental_factor.md) + * [MIMARKS specimen➞experimental_factor](MIMARKS_specimen_experimental_factor.md) + * [MIMARKS survey➞experimental_factor](MIMARKS_survey_experimental_factor.md) + * [MISAG➞experimental_factor](MISAG_experimental_factor.md) + * [MIUVIG➞experimental_factor](MIUVIG_experimental_factor.md) * [investigation_type](investigation_type.md) - Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * [me➞investigation_type](me_investigation_type.md) - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) - * [migs_org➞investigation_type](migs_org_investigation_type.md) - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) - * [mimag➞investigation_type](mimag_investigation_type.md) - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) - * [misag➞investigation_type](misag_investigation_type.md) - * [miuvig➞investigation_type](miuvig_investigation_type.md) + * [ME➞investigation_type](ME_investigation_type.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) + * [MISAG➞investigation_type](MISAG_investigation_type.md) + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) * [project_name](project_name.md) - Name of the project within which the sequencing was organized - * [me➞project_name](me_project_name.md) - * [migs_ba➞project_name](migs_ba_project_name.md) - * [migs_eu➞project_name](migs_eu_project_name.md) - * [migs_org➞project_name](migs_org_project_name.md) - * [migs_pl➞project_name](migs_pl_project_name.md) - * [migs_vi➞project_name](migs_vi_project_name.md) - * [mimag➞project_name](mimag_project_name.md) - * [mimarks_c➞project_name](mimarks_c_project_name.md) - * [mimarks_s➞project_name](mimarks_s_project_name.md) - * [misag➞project_name](misag_project_name.md) - * [miuvig➞project_name](miuvig_project_name.md) + * [ME➞project_name](ME_project_name.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) + * [MIGS org➞project_name](MIGS_org_project_name.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) + * [MIMAG➞project_name](MIMAG_project_name.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) + * [MISAG➞project_name](MISAG_project_name.md) + * [MIUVIG➞project_name](MIUVIG_project_name.md) * [submitted_to_insdc](submitted_to_insdc.md) - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) * [mixs extension field](mixs_extension_field.md) * [env_package](env_package.md) - MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * [me➞env_package](me_env_package.md) - * [migs_ba➞env_package](migs_ba_env_package.md) - * [migs_eu➞env_package](migs_eu_env_package.md) - * [migs_org➞env_package](migs_org_env_package.md) - * [migs_pl➞env_package](migs_pl_env_package.md) - * [migs_vi➞env_package](migs_vi_env_package.md) - * [mimag➞env_package](mimag_env_package.md) - * [mimarks_c➞env_package](mimarks_c_env_package.md) - * [mimarks_s➞env_package](mimarks_s_env_package.md) - * [misag➞env_package](misag_env_package.md) - * [miuvig➞env_package](miuvig_env_package.md) + * [ME➞env_package](ME_env_package.md) + * [MIGS bacteria➞env_package](MIGS_bacteria_env_package.md) + * [MIGS eukaryote➞env_package](MIGS_eukaryote_env_package.md) + * [MIGS org➞env_package](MIGS_org_env_package.md) + * [MIGS plant➞env_package](MIGS_plant_env_package.md) + * [MIGS virus➞env_package](MIGS_virus_env_package.md) + * [MIMAG➞env_package](MIMAG_env_package.md) + * [MIMARKS specimen➞env_package](MIMARKS_specimen_env_package.md) + * [MIMARKS survey➞env_package](MIMARKS_survey_env_package.md) + * [MISAG➞env_package](MISAG_env_package.md) + * [MIUVIG➞env_package](MIUVIG_env_package.md) * [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) * [biotic_relationship](biotic_relationship.md) - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) - * [miuvig➞biotic_relationship](miuvig_biotic_relationship.md) + * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) + * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) + * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) + * [MIMARKS survey➞biotic_relationship](MIMARKS_survey_biotic_relationship.md) + * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) * [encoded_traits](encoded_traits.md) - Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) + * [MIGS bacteria➞encoded_traits](MIGS_bacteria_encoded_traits.md) + * [MIGS plant➞encoded_traits](MIGS_plant_encoded_traits.md) + * [MIGS virus➞encoded_traits](MIGS_virus_encoded_traits.md) * [estimated_size](estimated_size.md) - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) - * [migs_org➞estimated_size](migs_org_estimated_size.md) - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) - * [miuvig➞estimated_size](miuvig_estimated_size.md) + * [MIGS bacteria➞estimated_size](MIGS_bacteria_estimated_size.md) + * [MIGS eukaryote➞estimated_size](MIGS_eukaryote_estimated_size.md) + * [MIGS org➞estimated_size](MIGS_org_estimated_size.md) + * [MIGS plant➞estimated_size](MIGS_plant_estimated_size.md) + * [MIGS virus➞estimated_size](MIGS_virus_estimated_size.md) + * [MIUVIG➞estimated_size](MIUVIG_estimated_size.md) * [extrachrom_elements](extrachrom_elements.md) - Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) - * [migs_org➞extrachrom_elements](migs_org_extrachrom_elements.md) - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) + * [MIGS bacteria➞extrachrom_elements](MIGS_bacteria_extrachrom_elements.md) + * [MIGS eukaryote➞extrachrom_elements](MIGS_eukaryote_extrachrom_elements.md) + * [MIGS org➞extrachrom_elements](MIGS_org_extrachrom_elements.md) + * [MIMARKS survey➞extrachrom_elements](MIMARKS_survey_extrachrom_elements.md) * [health_disease_stat](health_disease_stat.md) - Health or disease status of specific host at time of collection - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) + * [MIGS bacteria➞health_disease_stat](MIGS_bacteria_health_disease_stat.md) + * [MIGS eukaryote➞health_disease_stat](MIGS_eukaryote_health_disease_stat.md) + * [MIGS virus➞health_disease_stat](MIGS_virus_health_disease_stat.md) * [host_spec_range](host_spec_range.md) - The NCBI taxonomy identifier of the specific host if it is known - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) - * [miuvig➞host_spec_range](miuvig_host_spec_range.md) + * [MIGS bacteria➞host_spec_range](MIGS_bacteria_host_spec_range.md) + * [MIGS eukaryote➞host_spec_range](MIGS_eukaryote_host_spec_range.md) + * [MIGS plant➞host_spec_range](MIGS_plant_host_spec_range.md) + * [MIGS virus➞host_spec_range](MIGS_virus_host_spec_range.md) + * [MIUVIG➞host_spec_range](MIUVIG_host_spec_range.md) * [isol_growth_condt](isol_growth_condt.md) - Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) * [num_replicons](num_replicons.md) - Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) * [pathogenicity](pathogenicity.md) - To what is the entity pathogenic - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) * [ploidy](ploidy.md) - The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * [migs_eu➞ploidy](migs_eu_ploidy.md) + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) * [propagation](propagation.md) - This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * [migs_eu➞propagation](migs_eu_propagation.md) - * [migs_pl➞propagation](migs_pl_propagation.md) - * [migs_vi➞propagation](migs_vi_propagation.md) + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) * [ref_biomaterial](ref_biomaterial.md) - Primary publication if isolated before genome publication; otherwise, primary genome report - * [me➞ref_biomaterial](me_ref_biomaterial.md) - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) * [rel_to_oxygen](rel_to_oxygen.md) - Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) * [samp_collect_device](samp_collect_device.md) - The method or device employed for collecting the sample - * [me➞samp_collect_device](me_samp_collect_device.md) - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) - * [misag➞samp_collect_device](misag_samp_collect_device.md) - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) + * [ME➞samp_collect_device](ME_samp_collect_device.md) + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) * [samp_mat_process](samp_mat_process.md) - Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * [me➞samp_mat_process](me_samp_mat_process.md) - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) - * [misag➞samp_mat_process](misag_samp_mat_process.md) - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) + * [ME➞samp_mat_process](ME_samp_mat_process.md) + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) * [samp_size](samp_size.md) - Amount or size of sample (volume, mass or area) that was collected - * [me➞samp_size](me_samp_size.md) - * [migs_ba➞samp_size](migs_ba_samp_size.md) - * [migs_eu➞samp_size](migs_eu_samp_size.md) - * [migs_org➞samp_size](migs_org_samp_size.md) - * [migs_pl➞samp_size](migs_pl_samp_size.md) - * [migs_vi➞samp_size](migs_vi_samp_size.md) - * [mimag➞samp_size](mimag_samp_size.md) - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) - * [misag➞samp_size](misag_samp_size.md) - * [miuvig➞samp_size](miuvig_samp_size.md) + * [ME➞samp_size](ME_samp_size.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) + * [MIGS org➞samp_size](MIGS_org_samp_size.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) + * [MIMAG➞samp_size](MIMAG_samp_size.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) + * [MISAG➞samp_size](MISAG_samp_size.md) + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) * [size_frac](size_frac.md) - Filtering pore size used in sample preparation - * [me➞size_frac](me_size_frac.md) - * [mimag➞size_frac](mimag_size_frac.md) - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) - * [misag➞size_frac](misag_size_frac.md) - * [miuvig➞size_frac](miuvig_size_frac.md) + * [ME➞size_frac](ME_size_frac.md) + * [MIMAG➞size_frac](MIMAG_size_frac.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) + * [MISAG➞size_frac](MISAG_size_frac.md) + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) * [source_mat_id](source_mat_id.md) - A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * [me➞source_mat_id](me_source_mat_id.md) - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) - * [mimag➞source_mat_id](mimag_source_mat_id.md) - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) - * [misag➞source_mat_id](misag_source_mat_id.md) - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) + * [ME➞source_mat_id](ME_source_mat_id.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) * [source_uvig](source_uvig.md) - Type of dataset from which the UViG was obtained - * [miuvig➞source_uvig](miuvig_source_uvig.md) + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) * [specific_host](specific_host.md) - If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * [migs_ba➞specific_host](migs_ba_specific_host.md) - * [migs_eu➞specific_host](migs_eu_specific_host.md) - * [migs_pl➞specific_host](migs_pl_specific_host.md) - * [migs_vi➞specific_host](migs_vi_specific_host.md) - * [miuvig➞specific_host](miuvig_specific_host.md) + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) * [subspecf_gen_lin](subspecf_gen_lin.md) - This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) * [trophic_level](trophic_level.md) - Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) * [virus_enrich_appr](virus_enrich_appr.md) - List of approaches used to enrich the sample for viruses, if any - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) * [➞has numeric value](quantityValue__has_numeric_value.md) * [➞has raw value](quantityValue__has_raw_value.md) * [➞has unit](quantityValue__has_unit.md) - Example "m" * [sequencing field](sequencing_field.md) * [adapters](adapters.md) - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * [me➞adapters](me_adapters.md) - * [migs_ba➞adapters](migs_ba_adapters.md) - * [migs_eu➞adapters](migs_eu_adapters.md) - * [migs_org➞adapters](migs_org_adapters.md) - * [migs_pl➞adapters](migs_pl_adapters.md) - * [migs_vi➞adapters](migs_vi_adapters.md) - * [mimag➞adapters](mimag_adapters.md) - * [mimarks_s➞adapters](mimarks_s_adapters.md) - * [misag➞adapters](misag_adapters.md) - * [miuvig➞adapters](miuvig_adapters.md) + * [ME➞adapters](ME_adapters.md) + * [MIGS bacteria➞adapters](MIGS_bacteria_adapters.md) + * [MIGS eukaryote➞adapters](MIGS_eukaryote_adapters.md) + * [MIGS org➞adapters](MIGS_org_adapters.md) + * [MIGS plant➞adapters](MIGS_plant_adapters.md) + * [MIGS virus➞adapters](MIGS_virus_adapters.md) + * [MIMAG➞adapters](MIMAG_adapters.md) + * [MIMARKS specimen➞adapters](MIMARKS_specimen_adapters.md) + * [MISAG➞adapters](MISAG_adapters.md) + * [MIUVIG➞adapters](MIUVIG_adapters.md) * [annot](annot.md) - Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * [me➞annot](me_annot.md) - * [migs_ba➞annot](migs_ba_annot.md) - * [migs_eu➞annot](migs_eu_annot.md) - * [migs_org➞annot](migs_org_annot.md) - * [migs_pl➞annot](migs_pl_annot.md) - * [migs_vi➞annot](migs_vi_annot.md) - * [mimag➞annot](mimag_annot.md) - * [misag➞annot](misag_annot.md) - * [miuvig➞annot](miuvig_annot.md) + * [ME➞annot](ME_annot.md) + * [MIGS bacteria➞annot](MIGS_bacteria_annot.md) + * [MIGS eukaryote➞annot](MIGS_eukaryote_annot.md) + * [MIGS org➞annot](MIGS_org_annot.md) + * [MIGS plant➞annot](MIGS_plant_annot.md) + * [MIGS virus➞annot](MIGS_virus_annot.md) + * [MIMAG➞annot](MIMAG_annot.md) + * [MISAG➞annot](MISAG_annot.md) + * [MIUVIG➞annot](MIUVIG_annot.md) * [assembly_name](assembly_name.md) - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * [me➞assembly_name](me_assembly_name.md) - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) - * [migs_org➞assembly_name](migs_org_assembly_name.md) - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) - * [mimag➞assembly_name](mimag_assembly_name.md) - * [misag➞assembly_name](misag_assembly_name.md) - * [miuvig➞assembly_name](miuvig_assembly_name.md) + * [ME➞assembly_name](ME_assembly_name.md) + * [MIGS bacteria➞assembly_name](MIGS_bacteria_assembly_name.md) + * [MIGS eukaryote➞assembly_name](MIGS_eukaryote_assembly_name.md) + * [MIGS org➞assembly_name](MIGS_org_assembly_name.md) + * [MIGS plant➞assembly_name](MIGS_plant_assembly_name.md) + * [MIGS virus➞assembly_name](MIGS_virus_assembly_name.md) + * [MIMAG➞assembly_name](MIMAG_assembly_name.md) + * [MISAG➞assembly_name](MISAG_assembly_name.md) + * [MIUVIG➞assembly_name](MIUVIG_assembly_name.md) * [assembly_qual](assembly_qual.md) - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * [me➞assembly_qual](me_assembly_qual.md) - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) - * [migs_org➞assembly_qual](migs_org_assembly_qual.md) - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) - * [mimag➞assembly_qual](mimag_assembly_qual.md) - * [misag➞assembly_qual](misag_assembly_qual.md) - * [miuvig➞assembly_qual](miuvig_assembly_qual.md) + * [ME➞assembly_qual](ME_assembly_qual.md) + * [MIGS bacteria➞assembly_qual](MIGS_bacteria_assembly_qual.md) + * [MIGS eukaryote➞assembly_qual](MIGS_eukaryote_assembly_qual.md) + * [MIGS org➞assembly_qual](MIGS_org_assembly_qual.md) + * [MIGS plant➞assembly_qual](MIGS_plant_assembly_qual.md) + * [MIGS virus➞assembly_qual](MIGS_virus_assembly_qual.md) + * [MIMAG➞assembly_qual](MIMAG_assembly_qual.md) + * [MISAG➞assembly_qual](MISAG_assembly_qual.md) + * [MIUVIG➞assembly_qual](MIUVIG_assembly_qual.md) * [assembly_software](assembly_software.md) - Tool(s) used for assembly, including version number and parameters - * [me➞assembly_software](me_assembly_software.md) - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) - * [migs_org➞assembly_software](migs_org_assembly_software.md) - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) - * [mimag➞assembly_software](mimag_assembly_software.md) - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) - * [misag➞assembly_software](misag_assembly_software.md) - * [miuvig➞assembly_software](miuvig_assembly_software.md) + * [ME➞assembly_software](ME_assembly_software.md) + * [MIGS bacteria➞assembly_software](MIGS_bacteria_assembly_software.md) + * [MIGS eukaryote➞assembly_software](MIGS_eukaryote_assembly_software.md) + * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) + * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) + * [MIGS virus➞assembly_software](MIGS_virus_assembly_software.md) + * [MIMAG➞assembly_software](MIMAG_assembly_software.md) + * [MIMARKS specimen➞assembly_software](MIMARKS_specimen_assembly_software.md) + * [MISAG➞assembly_software](MISAG_assembly_software.md) + * [MIUVIG➞assembly_software](MIUVIG_assembly_software.md) * [bin_param](bin_param.md) - The parameters that have been applied during the extraction of genomes from metagenomic datasets - * [mimag➞bin_param](mimag_bin_param.md) - * [miuvig➞bin_param](miuvig_bin_param.md) + * [MIMAG➞bin_param](MIMAG_bin_param.md) + * [MIUVIG➞bin_param](MIUVIG_bin_param.md) * [bin_software](bin_software.md) - Tool(s) used for the extraction of genomes from metagenomic datasets - * [mimag➞bin_software](mimag_bin_software.md) - * [miuvig➞bin_software](miuvig_bin_software.md) + * [MIMAG➞bin_software](MIMAG_bin_software.md) + * [MIUVIG➞bin_software](MIUVIG_bin_software.md) * [chimera_check](chimera_check.md) - A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) + * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) + * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) * [compl_appr](compl_appr.md) - The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * [mimag➞compl_appr](mimag_compl_appr.md) - * [misag➞compl_appr](misag_compl_appr.md) - * [miuvig➞compl_appr](miuvig_compl_appr.md) + * [MIMAG➞compl_appr](MIMAG_compl_appr.md) + * [MISAG➞compl_appr](MISAG_compl_appr.md) + * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) * [compl_score](compl_score.md) - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * [migs_ba➞compl_score](migs_ba_compl_score.md) - * [migs_eu➞compl_score](migs_eu_compl_score.md) - * [migs_org➞compl_score](migs_org_compl_score.md) - * [migs_pl➞compl_score](migs_pl_compl_score.md) - * [migs_vi➞compl_score](migs_vi_compl_score.md) - * [mimag➞compl_score](mimag_compl_score.md) - * [misag➞compl_score](misag_compl_score.md) - * [miuvig➞compl_score](miuvig_compl_score.md) + * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) + * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) + * [MIGS org➞compl_score](MIGS_org_compl_score.md) + * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) + * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) + * [MIMAG➞compl_score](MIMAG_compl_score.md) + * [MISAG➞compl_score](MISAG_compl_score.md) + * [MIUVIG➞compl_score](MIUVIG_compl_score.md) * [compl_software](compl_software.md) - Tools used for completion estimate, i.e. checkm, anvi'o, busco - * [migs_ba➞compl_software](migs_ba_compl_software.md) - * [migs_eu➞compl_software](migs_eu_compl_software.md) - * [migs_org➞compl_software](migs_org_compl_software.md) - * [migs_pl➞compl_software](migs_pl_compl_software.md) - * [migs_vi➞compl_software](migs_vi_compl_software.md) - * [mimag➞compl_software](mimag_compl_software.md) - * [misag➞compl_software](misag_compl_software.md) - * [miuvig➞compl_software](miuvig_compl_software.md) + * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) + * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) + * [MIGS org➞compl_software](MIGS_org_compl_software.md) + * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) + * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) + * [MIMAG➞compl_software](MIMAG_compl_software.md) + * [MISAG➞compl_software](MISAG_compl_software.md) + * [MIUVIG➞compl_software](MIUVIG_compl_software.md) * [contam_score](contam_score.md) - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * [mimag➞contam_score](mimag_contam_score.md) - * [misag➞contam_score](misag_contam_score.md) + * [MIMAG➞contam_score](MIMAG_contam_score.md) + * [MISAG➞contam_score](MISAG_contam_score.md) * [contam_screen_input](contam_screen_input.md) - The type of sequence data used as input - * [mimag➞contam_screen_input](mimag_contam_screen_input.md) - * [misag➞contam_screen_input](misag_contam_screen_input.md) + * [MIMAG➞contam_screen_input](MIMAG_contam_screen_input.md) + * [MISAG➞contam_screen_input](MISAG_contam_screen_input.md) * [contam_screen_param](contam_screen_param.md) - Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * [mimag➞contam_screen_param](mimag_contam_screen_param.md) - * [misag➞contam_screen_param](misag_contam_screen_param.md) + * [MIMAG➞contam_screen_param](MIMAG_contam_screen_param.md) + * [MISAG➞contam_screen_param](MISAG_contam_screen_param.md) * [decontam_software](decontam_software.md) - Tool(s) used in contamination screening - * [mimag➞decontam_software](mimag_decontam_software.md) - * [misag➞decontam_software](misag_decontam_software.md) + * [MIMAG➞decontam_software](MIMAG_decontam_software.md) + * [MISAG➞decontam_software](MISAG_decontam_software.md) * [detec_type](detec_type.md) - Type of UViG detection - * [miuvig➞detec_type](miuvig_detec_type.md) + * [MIUVIG➞detec_type](MIUVIG_detec_type.md) * [feat_pred](feat_pred.md) - Method used to predict UViGs features such as ORFs, integration site, etc. - * [me➞feat_pred](me_feat_pred.md) - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) - * [migs_org➞feat_pred](migs_org_feat_pred.md) - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) - * [mimag➞feat_pred](mimag_feat_pred.md) - * [misag➞feat_pred](misag_feat_pred.md) - * [miuvig➞feat_pred](miuvig_feat_pred.md) + * [ME➞feat_pred](ME_feat_pred.md) + * [MIGS bacteria➞feat_pred](MIGS_bacteria_feat_pred.md) + * [MIGS eukaryote➞feat_pred](MIGS_eukaryote_feat_pred.md) + * [MIGS org➞feat_pred](MIGS_org_feat_pred.md) + * [MIGS plant➞feat_pred](MIGS_plant_feat_pred.md) + * [MIGS virus➞feat_pred](MIGS_virus_feat_pred.md) + * [MIMAG➞feat_pred](MIMAG_feat_pred.md) + * [MISAG➞feat_pred](MISAG_feat_pred.md) + * [MIUVIG➞feat_pred](MIUVIG_feat_pred.md) * [host_pred_appr](host_pred_appr.md) - Tool or approach used for host prediction - * [miuvig➞host_pred_appr](miuvig_host_pred_appr.md) + * [MIUVIG➞host_pred_appr](MIUVIG_host_pred_appr.md) * [host_pred_est_acc](host_pred_est_acc.md) - For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * [miuvig➞host_pred_est_acc](miuvig_host_pred_est_acc.md) + * [MIUVIG➞host_pred_est_acc](MIUVIG_host_pred_est_acc.md) * [lib_layout](lib_layout.md) - Specify whether to expect single, paired, or other configuration of reads - * [me➞lib_layout](me_lib_layout.md) - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) - * [migs_org➞lib_layout](migs_org_lib_layout.md) - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) - * [mimag➞lib_layout](mimag_lib_layout.md) - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) - * [misag➞lib_layout](misag_lib_layout.md) - * [miuvig➞lib_layout](miuvig_lib_layout.md) + * [ME➞lib_layout](ME_lib_layout.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) + * [MISAG➞lib_layout](MISAG_lib_layout.md) + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) * [lib_reads_seqd](lib_reads_seqd.md) - Total number of clones sequenced from the library - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) * [lib_screen](lib_screen.md) - Specific enrichment or screening methods applied before and/or after creating libraries - * [me➞lib_screen](me_lib_screen.md) - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) - * [migs_org➞lib_screen](migs_org_lib_screen.md) - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) - * [mimag➞lib_screen](mimag_lib_screen.md) - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) - * [misag➞lib_screen](misag_lib_screen.md) - * [miuvig➞lib_screen](miuvig_lib_screen.md) + * [ME➞lib_screen](ME_lib_screen.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) + * [MISAG➞lib_screen](MISAG_lib_screen.md) + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) * [lib_size](lib_size.md) - Total number of clones in the library prepared for the project - * [me➞lib_size](me_lib_size.md) - * [migs_ba➞lib_size](migs_ba_lib_size.md) - * [migs_eu➞lib_size](migs_eu_lib_size.md) - * [migs_org➞lib_size](migs_org_lib_size.md) - * [migs_pl➞lib_size](migs_pl_lib_size.md) - * [migs_vi➞lib_size](migs_vi_lib_size.md) - * [mimag➞lib_size](mimag_lib_size.md) - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) - * [misag➞lib_size](misag_lib_size.md) - * [miuvig➞lib_size](miuvig_lib_size.md) + * [ME➞lib_size](ME_lib_size.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) + * [MIGS org➞lib_size](MIGS_org_lib_size.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) + * [MIMAG➞lib_size](MIMAG_lib_size.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) + * [MISAG➞lib_size](MISAG_lib_size.md) + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) * [lib_vector](lib_vector.md) - Cloning vector type(s) used in construction of libraries - * [me➞lib_vector](me_lib_vector.md) - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) - * [migs_org➞lib_vector](migs_org_lib_vector.md) - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) - * [mimag➞lib_vector](mimag_lib_vector.md) - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) - * [misag➞lib_vector](misag_lib_vector.md) - * [miuvig➞lib_vector](miuvig_lib_vector.md) + * [ME➞lib_vector](ME_lib_vector.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) + * [MISAG➞lib_vector](MISAG_lib_vector.md) + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) * [mag_cov_software](mag_cov_software.md) - Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) * [mid](mid.md) - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * [me➞mid](me_mid.md) - * [mimag➞mid](mimag_mid.md) - * [mimarks_s➞mid](mimarks_s_mid.md) - * [misag➞mid](misag_mid.md) - * [miuvig➞mid](miuvig_mid.md) + * [ME➞mid](ME_mid.md) + * [MIMAG➞mid](MIMAG_mid.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) + * [MISAG➞mid](MISAG_mid.md) + * [MIUVIG➞mid](MIUVIG_mid.md) * [nucl_acid_amp](nucl_acid_amp.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) * [nucl_acid_ext](nucl_acid_ext.md) - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) * [number_contig](number_contig.md) - Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * [me➞number_contig](me_number_contig.md) - * [migs_ba➞number_contig](migs_ba_number_contig.md) - * [migs_eu➞number_contig](migs_eu_number_contig.md) - * [migs_org➞number_contig](migs_org_number_contig.md) - * [migs_pl➞number_contig](migs_pl_number_contig.md) - * [migs_vi➞number_contig](migs_vi_number_contig.md) - * [mimag➞number_contig](mimag_number_contig.md) - * [misag➞number_contig](misag_number_contig.md) - * [miuvig➞number_contig](miuvig_number_contig.md) + * [ME➞number_contig](ME_number_contig.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) + * [MIGS org➞number_contig](MIGS_org_number_contig.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) + * [MIMAG➞number_contig](MIMAG_number_contig.md) + * [MISAG➞number_contig](MISAG_number_contig.md) + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) * [pcr_cond](pcr_cond.md) - Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) * [pcr_primers](pcr_primers.md) - PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) * [pred_genome_struc](pred_genome_struc.md) - Expected structure of the viral genome - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) * [pred_genome_type](pred_genome_type.md) - Type of genome predicted for the UViG - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) * [reassembly_bin](reassembly_bin.md) - Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) * [ref_db](ref_db.md) - List of database(s) used for ORF annotation, along with version number and reference to website or publication - * [me➞ref_db](me_ref_db.md) - * [migs_ba➞ref_db](migs_ba_ref_db.md) - * [migs_eu➞ref_db](migs_eu_ref_db.md) - * [migs_org➞ref_db](migs_org_ref_db.md) - * [migs_pl➞ref_db](migs_pl_ref_db.md) - * [migs_vi➞ref_db](migs_vi_ref_db.md) - * [mimag➞ref_db](mimag_ref_db.md) - * [misag➞ref_db](misag_ref_db.md) - * [miuvig➞ref_db](miuvig_ref_db.md) + * [ME➞ref_db](ME_ref_db.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) + * [MIGS org➞ref_db](MIGS_org_ref_db.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) + * [MIMAG➞ref_db](MIMAG_ref_db.md) + * [MISAG➞ref_db](MISAG_ref_db.md) + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) * [seq_meth](seq_meth.md) - Sequencing method used; e.g. Sanger, ABI-solid - * [me➞seq_meth](me_seq_meth.md) - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) - * [migs_org➞seq_meth](migs_org_seq_meth.md) - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) - * [mimag➞seq_meth](mimag_seq_meth.md) - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) - * [misag➞seq_meth](misag_seq_meth.md) - * [miuvig➞seq_meth](miuvig_seq_meth.md) + * [ME➞seq_meth](ME_seq_meth.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) + * [MISAG➞seq_meth](MISAG_seq_meth.md) + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) * [seq_quality_check](seq_quality_check.md) - Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) * [sim_search_meth](sim_search_meth.md) - Tool used to compare ORFs with database, along with version and cutoffs used - * [me➞sim_search_meth](me_sim_search_meth.md) - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) - * [misag➞sim_search_meth](misag_sim_search_meth.md) - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) + * [ME➞sim_search_meth](ME_sim_search_meth.md) + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) * [single_cell_lysis_appr](single_cell_lysis_appr.md) - Method used to free DNA from interior of the cell(s) or particle(s) - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) * [single_cell_lysis_prot](single_cell_lysis_prot.md) - Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) * [sop](sop.md) - Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * [me➞sop](me_sop.md) - * [migs_ba➞sop](migs_ba_sop.md) - * [migs_eu➞sop](migs_eu_sop.md) - * [migs_org➞sop](migs_org_sop.md) - * [migs_pl➞sop](migs_pl_sop.md) - * [migs_vi➞sop](migs_vi_sop.md) - * [mimag➞sop](mimag_sop.md) - * [mimarks_c➞sop](mimarks_c_sop.md) - * [mimarks_s➞sop](mimarks_s_sop.md) - * [misag➞sop](misag_sop.md) - * [miuvig➞sop](miuvig_sop.md) + * [ME➞sop](ME_sop.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) + * [MIGS org➞sop](MIGS_org_sop.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) + * [MIMAG➞sop](MIMAG_sop.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) + * [MISAG➞sop](MISAG_sop.md) + * [MIUVIG➞sop](MIUVIG_sop.md) * [sort_tech](sort_tech.md) - Method used to sort/isolate cells or particles of interest - * [misag➞sort_tech](misag_sort_tech.md) - * [miuvig➞sort_tech](miuvig_sort_tech.md) + * [MISAG➞sort_tech](MISAG_sort_tech.md) + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) * [target_gene](target_gene.md) - Targeted gene or locus name for marker gene studies - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) * [target_subfragment](target_subfragment.md) - Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) * [tax_class](tax_class.md) - Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * [me➞tax_class](me_tax_class.md) - * [migs_ba➞tax_class](migs_ba_tax_class.md) - * [migs_eu➞tax_class](migs_eu_tax_class.md) - * [migs_org➞tax_class](migs_org_tax_class.md) - * [migs_pl➞tax_class](migs_pl_tax_class.md) - * [migs_vi➞tax_class](migs_vi_tax_class.md) - * [mimag➞tax_class](mimag_tax_class.md) - * [misag➞tax_class](misag_tax_class.md) - * [miuvig➞tax_class](miuvig_tax_class.md) + * [ME➞tax_class](ME_tax_class.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) + * [MIGS org➞tax_class](MIGS_org_tax_class.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) + * [MIMAG➞tax_class](MIMAG_tax_class.md) + * [MISAG➞tax_class](MISAG_tax_class.md) + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) * [tax_ident](tax_ident.md) - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) - * [migs_org➞tax_ident](migs_org_tax_ident.md) - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) - * [mimag➞tax_ident](mimag_tax_ident.md) - * [misag➞tax_ident](misag_tax_ident.md) - * [miuvig➞tax_ident](miuvig_tax_ident.md) + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) + * [MISAG➞tax_ident](MISAG_tax_ident.md) + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) * [trna_ext_software](trna_ext_software.md) - Tools used for tRNA identification - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) - * [misag➞trna_ext_software](misag_trna_ext_software.md) - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) * [trnas](trnas.md) - The total number of tRNAs identified from the SAG or MAG - * [mimag➞trnas](mimag_trnas.md) - * [misag➞trnas](misag_trnas.md) - * [miuvig➞trnas](miuvig_trnas.md) + * [MIMAG➞trnas](MIMAG_trnas.md) + * [MISAG➞trnas](MISAG_trnas.md) + * [MIUVIG➞trnas](MIUVIG_trnas.md) * [url](url.md) - * [me➞url](me_url.md) - * [migs_ba➞url](migs_ba_url.md) - * [migs_eu➞url](migs_eu_url.md) - * [migs_org➞url](migs_org_url.md) - * [migs_pl➞url](migs_pl_url.md) - * [migs_vi➞url](migs_vi_url.md) - * [mimag➞url](mimag_url.md) - * [mimarks_c➞url](mimarks_c_url.md) - * [mimarks_s➞url](mimarks_s_url.md) - * [misag➞url](misag_url.md) - * [miuvig➞url](miuvig_url.md) + * [ME➞url](ME_url.md) + * [MIGS bacteria➞url](MIGS_bacteria_url.md) + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) + * [MIGS org➞url](MIGS_org_url.md) + * [MIGS plant➞url](MIGS_plant_url.md) + * [MIGS virus➞url](MIGS_virus_url.md) + * [MIMAG➞url](MIMAG_url.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) + * [MIMARKS survey➞url](MIMARKS_survey_url.md) + * [MISAG➞url](MISAG_url.md) + * [MIUVIG➞url](MIUVIG_url.md) * [vir_ident_software](vir_ident_software.md) - Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) * [votu_class_appr](votu_class_appr.md) - Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) * [votu_db](votu_db.md) - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * [miuvig➞votu_db](miuvig_votu_db.md) + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) * [votu_seq_comp_appr](votu_seq_comp_appr.md) - Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) * [wga_amp_appr](wga_amp_appr.md) - Method used to amplify genomic DNA in preparation for sequencing - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) * [wga_amp_kit](wga_amp_kit.md) - Kit used to amplify genomic DNA in preparation for sequencing - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) * [x_16s_recover](x_16s_recover.md) - Can a 16S gene be recovered from the submitted SAG or MAG? - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) - * [misag➞x_16s_recover](misag_x_16s_recover.md) + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) * [x_16s_recover_software](x_16s_recover_software.md) - Tools used for 16S rRNA gene extraction - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) ### Types diff --git a/mixs6/indoor_space.md b/mixs6/indoor_space.md index 91553d87..69cfb616 100644 --- a/mixs6/indoor_space.md +++ b/mixs6/indoor_space.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/indoor_surf.md b/mixs6/indoor_surf.md index 73241b96..1f291ce5 100644 --- a/mixs6/indoor_surf.md +++ b/mixs6/indoor_surf.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/indust_eff_percent.md b/mixs6/indust_eff_percent.md index fc9b9352..ff3d740c 100644 --- a/mixs6/indust_eff_percent.md +++ b/mixs6/indust_eff_percent.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/inorg_particles.md b/mixs6/inorg_particles.md index df735cfc..23618072 100644 --- a/mixs6/inorg_particles.md +++ b/mixs6/inorg_particles.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/inside_lux.md b/mixs6/inside_lux.md index 2c22b8bc..2817e59c 100644 --- a/mixs6/inside_lux.md +++ b/mixs6/inside_lux.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/int_wall_cond.md b/mixs6/int_wall_cond.md index ddda6ae5..bf11725f 100644 --- a/mixs6/int_wall_cond.md +++ b/mixs6/int_wall_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/investigation_type.md b/mixs6/investigation_type.md index 8a7ae30d..0ddf3662 100644 --- a/mixs6/investigation_type.md +++ b/mixs6/investigation_type.md @@ -17,17 +17,17 @@ None -> OPT ## Children - * [me➞investigation_type](me_investigation_type.md) - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) - * [migs_org➞investigation_type](migs_org_investigation_type.md) - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) - * [mimag➞investigation_type](mimag_investigation_type.md) - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) - * [misag➞investigation_type](misag_investigation_type.md) - * [miuvig➞investigation_type](miuvig_investigation_type.md) + * [ME➞investigation_type](ME_investigation_type.md) + * [MIGS bacteria➞investigation_type](MIGS_bacteria_investigation_type.md) + * [MIGS eukaryote➞investigation_type](MIGS_eukaryote_investigation_type.md) + * [MIGS org➞investigation_type](MIGS_org_investigation_type.md) + * [MIGS plant➞investigation_type](MIGS_plant_investigation_type.md) + * [MIGS virus➞investigation_type](MIGS_virus_investigation_type.md) + * [MIMAG➞investigation_type](MIMAG_investigation_type.md) + * [MIMARKS specimen➞investigation_type](MIMARKS_specimen_investigation_type.md) + * [MIMARKS survey➞investigation_type](MIMARKS_survey_investigation_type.md) + * [MISAG➞investigation_type](MISAG_investigation_type.md) + * [MIUVIG➞investigation_type](MIUVIG_investigation_type.md) ## Used by diff --git a/mixs6/isol_growth_condt.md b/mixs6/isol_growth_condt.md index 5113ed09..923d6ef8 100644 --- a/mixs6/isol_growth_condt.md +++ b/mixs6/isol_growth_condt.md @@ -17,12 +17,12 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) - * [migs_org➞isol_growth_condt](migs_org_isol_growth_condt.md) - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) + * [MIGS bacteria➞isol_growth_condt](MIGS_bacteria_isol_growth_condt.md) + * [MIGS eukaryote➞isol_growth_condt](MIGS_eukaryote_isol_growth_condt.md) + * [MIGS org➞isol_growth_condt](MIGS_org_isol_growth_condt.md) + * [MIGS plant➞isol_growth_condt](MIGS_plant_isol_growth_condt.md) + * [MIGS virus➞isol_growth_condt](MIGS_virus_isol_growth_condt.md) + * [MIMARKS survey➞isol_growth_condt](MIMARKS_survey_isol_growth_condt.md) ## Used by diff --git a/mixs6/iw_bt_date_well.md b/mixs6/iw_bt_date_well.md index 8b7ad3a3..b77d48c4 100644 --- a/mixs6/iw_bt_date_well.md +++ b/mixs6/iw_bt_date_well.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/iwf.md b/mixs6/iwf.md index 39f690b5..85a1a71d 100644 --- a/mixs6/iwf.md +++ b/mixs6/iwf.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/last_clean.md b/mixs6/last_clean.md index 92a9ea09..eee67a47 100644 --- a/mixs6/last_clean.md +++ b/mixs6/last_clean.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/lat_lon.md b/mixs6/lat_lon.md index d6c931b5..c1650030 100644 --- a/mixs6/lat_lon.md +++ b/mixs6/lat_lon.md @@ -17,225 +17,225 @@ None -> OPT [String](types/String.md) ## Children - * [me➞lat_lon](me_lat_lon.md) - * [migs_ba➞lat_lon](migs_ba_lat_lon.md) - * [migs_eu➞lat_lon](migs_eu_lat_lon.md) - * [migs_org➞lat_lon](migs_org_lat_lon.md) - * [migs_pl➞lat_lon](migs_pl_lat_lon.md) - * [migs_vi➞lat_lon](migs_vi_lat_lon.md) - * [mimag➞lat_lon](mimag_lat_lon.md) - * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) - * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) - * [misag➞lat_lon](misag_lat_lon.md) - * [miuvig➞lat_lon](miuvig_lat_lon.md) + * [ME➞lat_lon](ME_lat_lon.md) + * [MIGS bacteria➞lat_lon](MIGS_bacteria_lat_lon.md) + * [MIGS eukaryote➞lat_lon](MIGS_eukaryote_lat_lon.md) + * [MIGS org➞lat_lon](MIGS_org_lat_lon.md) + * [MIGS plant➞lat_lon](MIGS_plant_lat_lon.md) + * [MIGS virus➞lat_lon](MIGS_virus_lat_lon.md) + * [MIMAG➞lat_lon](MIMAG_lat_lon.md) + * [MIMARKS specimen➞lat_lon](MIMARKS_specimen_lat_lon.md) + * [MIMARKS survey➞lat_lon](MIMARKS_survey_lat_lon.md) + * [MISAG➞lat_lon](MISAG_lat_lon.md) + * [MIUVIG➞lat_lon](MIUVIG_lat_lon.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Core](Core.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/lib_layout.md b/mixs6/lib_layout.md index 5932a10c..5ad862b5 100644 --- a/mixs6/lib_layout.md +++ b/mixs6/lib_layout.md @@ -17,16 +17,16 @@ None -> OPT ## Children - * [me➞lib_layout](me_lib_layout.md) - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) - * [migs_org➞lib_layout](migs_org_lib_layout.md) - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) - * [mimag➞lib_layout](mimag_lib_layout.md) - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) - * [misag➞lib_layout](misag_lib_layout.md) - * [miuvig➞lib_layout](miuvig_lib_layout.md) + * [ME➞lib_layout](ME_lib_layout.md) + * [MIGS bacteria➞lib_layout](MIGS_bacteria_lib_layout.md) + * [MIGS eukaryote➞lib_layout](MIGS_eukaryote_lib_layout.md) + * [MIGS org➞lib_layout](MIGS_org_lib_layout.md) + * [MIGS plant➞lib_layout](MIGS_plant_lib_layout.md) + * [MIGS virus➞lib_layout](MIGS_virus_lib_layout.md) + * [MIMAG➞lib_layout](MIMAG_lib_layout.md) + * [MIMARKS specimen➞lib_layout](MIMARKS_specimen_lib_layout.md) + * [MISAG➞lib_layout](MISAG_lib_layout.md) + * [MIUVIG➞lib_layout](MIUVIG_lib_layout.md) ## Used by diff --git a/mixs6/lib_reads_seqd.md b/mixs6/lib_reads_seqd.md index c9b29727..2c0606d5 100644 --- a/mixs6/lib_reads_seqd.md +++ b/mixs6/lib_reads_seqd.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞lib_reads_seqd](me_lib_reads_seqd.md) - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) - * [migs_org➞lib_reads_seqd](migs_org_lib_reads_seqd.md) - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) - * [mimag➞lib_reads_seqd](mimag_lib_reads_seqd.md) - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) - * [misag➞lib_reads_seqd](misag_lib_reads_seqd.md) - * [miuvig➞lib_reads_seqd](miuvig_lib_reads_seqd.md) + * [ME➞lib_reads_seqd](ME_lib_reads_seqd.md) + * [MIGS bacteria➞lib_reads_seqd](MIGS_bacteria_lib_reads_seqd.md) + * [MIGS eukaryote➞lib_reads_seqd](MIGS_eukaryote_lib_reads_seqd.md) + * [MIGS org➞lib_reads_seqd](MIGS_org_lib_reads_seqd.md) + * [MIGS plant➞lib_reads_seqd](MIGS_plant_lib_reads_seqd.md) + * [MIGS virus➞lib_reads_seqd](MIGS_virus_lib_reads_seqd.md) + * [MIMAG➞lib_reads_seqd](MIMAG_lib_reads_seqd.md) + * [MIMARKS specimen➞lib_reads_seqd](MIMARKS_specimen_lib_reads_seqd.md) + * [MISAG➞lib_reads_seqd](MISAG_lib_reads_seqd.md) + * [MIUVIG➞lib_reads_seqd](MIUVIG_lib_reads_seqd.md) ## Used by diff --git a/mixs6/lib_screen.md b/mixs6/lib_screen.md index 64c65f62..1280445b 100644 --- a/mixs6/lib_screen.md +++ b/mixs6/lib_screen.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞lib_screen](me_lib_screen.md) - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) - * [migs_org➞lib_screen](migs_org_lib_screen.md) - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) - * [mimag➞lib_screen](mimag_lib_screen.md) - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) - * [misag➞lib_screen](misag_lib_screen.md) - * [miuvig➞lib_screen](miuvig_lib_screen.md) + * [ME➞lib_screen](ME_lib_screen.md) + * [MIGS bacteria➞lib_screen](MIGS_bacteria_lib_screen.md) + * [MIGS eukaryote➞lib_screen](MIGS_eukaryote_lib_screen.md) + * [MIGS org➞lib_screen](MIGS_org_lib_screen.md) + * [MIGS plant➞lib_screen](MIGS_plant_lib_screen.md) + * [MIGS virus➞lib_screen](MIGS_virus_lib_screen.md) + * [MIMAG➞lib_screen](MIMAG_lib_screen.md) + * [MIMARKS specimen➞lib_screen](MIMARKS_specimen_lib_screen.md) + * [MISAG➞lib_screen](MISAG_lib_screen.md) + * [MIUVIG➞lib_screen](MIUVIG_lib_screen.md) ## Used by diff --git a/mixs6/lib_size.md b/mixs6/lib_size.md index 38355583..410443ad 100644 --- a/mixs6/lib_size.md +++ b/mixs6/lib_size.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞lib_size](me_lib_size.md) - * [migs_ba➞lib_size](migs_ba_lib_size.md) - * [migs_eu➞lib_size](migs_eu_lib_size.md) - * [migs_org➞lib_size](migs_org_lib_size.md) - * [migs_pl➞lib_size](migs_pl_lib_size.md) - * [migs_vi➞lib_size](migs_vi_lib_size.md) - * [mimag➞lib_size](mimag_lib_size.md) - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) - * [misag➞lib_size](misag_lib_size.md) - * [miuvig➞lib_size](miuvig_lib_size.md) + * [ME➞lib_size](ME_lib_size.md) + * [MIGS bacteria➞lib_size](MIGS_bacteria_lib_size.md) + * [MIGS eukaryote➞lib_size](MIGS_eukaryote_lib_size.md) + * [MIGS org➞lib_size](MIGS_org_lib_size.md) + * [MIGS plant➞lib_size](MIGS_plant_lib_size.md) + * [MIGS virus➞lib_size](MIGS_virus_lib_size.md) + * [MIMAG➞lib_size](MIMAG_lib_size.md) + * [MIMARKS specimen➞lib_size](MIMARKS_specimen_lib_size.md) + * [MISAG➞lib_size](MISAG_lib_size.md) + * [MIUVIG➞lib_size](MIUVIG_lib_size.md) ## Used by diff --git a/mixs6/lib_vector.md b/mixs6/lib_vector.md index dc09b669..7fb8c386 100644 --- a/mixs6/lib_vector.md +++ b/mixs6/lib_vector.md @@ -17,16 +17,16 @@ None -> OPT [String](types/String.md) ## Children - * [me➞lib_vector](me_lib_vector.md) - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) - * [migs_org➞lib_vector](migs_org_lib_vector.md) - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) - * [mimag➞lib_vector](mimag_lib_vector.md) - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) - * [misag➞lib_vector](misag_lib_vector.md) - * [miuvig➞lib_vector](miuvig_lib_vector.md) + * [ME➞lib_vector](ME_lib_vector.md) + * [MIGS bacteria➞lib_vector](MIGS_bacteria_lib_vector.md) + * [MIGS eukaryote➞lib_vector](MIGS_eukaryote_lib_vector.md) + * [MIGS org➞lib_vector](MIGS_org_lib_vector.md) + * [MIGS plant➞lib_vector](MIGS_plant_lib_vector.md) + * [MIGS virus➞lib_vector](MIGS_virus_lib_vector.md) + * [MIMAG➞lib_vector](MIMAG_lib_vector.md) + * [MIMARKS specimen➞lib_vector](MIMARKS_specimen_lib_vector.md) + * [MISAG➞lib_vector](MISAG_lib_vector.md) + * [MIUVIG➞lib_vector](MIUVIG_lib_vector.md) ## Used by diff --git a/mixs6/light_intensity.md b/mixs6/light_intensity.md index 297d8254..0f9887aa 100644 --- a/mixs6/light_intensity.md +++ b/mixs6/light_intensity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/light_regm.md b/mixs6/light_regm.md index 9a084aef..6c3e54f3 100644 --- a/mixs6/light_regm.md +++ b/mixs6/light_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/light_type.md b/mixs6/light_type.md index 04c31f5b..3978cb36 100644 --- a/mixs6/light_type.md +++ b/mixs6/light_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/link_addit_analys.md b/mixs6/link_addit_analys.md index d88fc2d5..49ba804f 100644 --- a/mixs6/link_addit_analys.md +++ b/mixs6/link_addit_analys.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/link_class_info.md b/mixs6/link_class_info.md index a27979a9..1f7d3219 100644 --- a/mixs6/link_class_info.md +++ b/mixs6/link_class_info.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/link_climate_info.md b/mixs6/link_climate_info.md index f3cd1658..6f44bada 100644 --- a/mixs6/link_climate_info.md +++ b/mixs6/link_climate_info.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/lithology.md b/mixs6/lithology.md index cabf4b36..8da76645 100644 --- a/mixs6/lithology.md +++ b/mixs6/lithology.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/liver_disord.md b/mixs6/liver_disord.md index a5fd1a33..8d5add52 100644 --- a/mixs6/liver_disord.md +++ b/mixs6/liver_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) ## Other properties diff --git a/mixs6/local_class.md b/mixs6/local_class.md index d10023b1..88cdcfdb 100644 --- a/mixs6/local_class.md +++ b/mixs6/local_class.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/local_class_meth.md b/mixs6/local_class_meth.md index 7660e2a0..0e612c53 100644 --- a/mixs6/local_class_meth.md +++ b/mixs6/local_class_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/mag_cov_software.md b/mixs6/mag_cov_software.md index 1f1af192..d9447aab 100644 --- a/mixs6/mag_cov_software.md +++ b/mixs6/mag_cov_software.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [mimag➞mag_cov_software](mimag_mag_cov_software.md) - * [miuvig➞mag_cov_software](miuvig_mag_cov_software.md) + * [MIMAG➞mag_cov_software](MIMAG_mag_cov_software.md) + * [MIUVIG➞mag_cov_software](MIUVIG_mag_cov_software.md) ## Used by diff --git a/mixs6/magnesium.md b/mixs6/magnesium.md index b19e9519..e165270a 100644 --- a/mixs6/magnesium.md +++ b/mixs6/magnesium.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/maternal_health_stat.md b/mixs6/maternal_health_stat.md index 67bfa001..4d538bd7 100644 --- a/mixs6/maternal_health_stat.md +++ b/mixs6/maternal_health_stat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/max_occup.md b/mixs6/max_occup.md index 1c5bdefa..22a84b07 100644 --- a/mixs6/max_occup.md +++ b/mixs6/max_occup.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/me_adapters.md b/mixs6/me_adapters.md new file mode 100644 index 00000000..526edf17 --- /dev/null +++ b/mixs6/me_adapters.md @@ -0,0 +1,47 @@ + +# Slot: ME_adapters + + + + +URI: [mixs.vocab:ME_adapters](https://w3id.org/mixs/vocab/ME_adapters) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_annot.md b/mixs6/me_annot.md new file mode 100644 index 00000000..13c11660 --- /dev/null +++ b/mixs6/me_annot.md @@ -0,0 +1,47 @@ + +# Slot: ME_annot + + + + +URI: [mixs.vocab:ME_annot](https://w3id.org/mixs/vocab/ME_annot) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_name.md b/mixs6/me_assembly_name.md new file mode 100644 index 00000000..f896238f --- /dev/null +++ b/mixs6/me_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_name + + + + +URI: [mixs.vocab:ME_assembly_name](https://w3id.org/mixs/vocab/ME_assembly_name) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_qual.md b/mixs6/me_assembly_qual.md new file mode 100644 index 00000000..93adbb66 --- /dev/null +++ b/mixs6/me_assembly_qual.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_qual + + + + +URI: [mixs.vocab:ME_assembly_qual](https://w3id.org/mixs/vocab/ME_assembly_qual) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_assembly_software.md b/mixs6/me_assembly_software.md new file mode 100644 index 00000000..42ea280f --- /dev/null +++ b/mixs6/me_assembly_software.md @@ -0,0 +1,47 @@ + +# Slot: ME_assembly_software + + + + +URI: [mixs.vocab:ME_assembly_software](https://w3id.org/mixs/vocab/ME_assembly_software) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_collection_date.md b/mixs6/me_collection_date.md new file mode 100644 index 00000000..b36dbb32 --- /dev/null +++ b/mixs6/me_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: ME_collection_date + + + + +URI: [mixs.vocab:ME_collection_date](https://w3id.org/mixs/vocab/ME_collection_date) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_broad_scale.md b/mixs6/me_env_broad_scale.md new file mode 100644 index 00000000..1b9efbe2 --- /dev/null +++ b/mixs6/me_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_broad_scale + + + + +URI: [mixs.vocab:ME_env_broad_scale](https://w3id.org/mixs/vocab/ME_env_broad_scale) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_local_scale.md b/mixs6/me_env_local_scale.md new file mode 100644 index 00000000..1373bef6 --- /dev/null +++ b/mixs6/me_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_local_scale + + + + +URI: [mixs.vocab:ME_env_local_scale](https://w3id.org/mixs/vocab/ME_env_local_scale) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_medium.md b/mixs6/me_env_medium.md new file mode 100644 index 00000000..0ec09fe4 --- /dev/null +++ b/mixs6/me_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: ME_env_medium + + + + +URI: [mixs.vocab:ME_env_medium](https://w3id.org/mixs/vocab/ME_env_medium) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_env_package.md b/mixs6/me_env_package.md new file mode 100644 index 00000000..7275e02f --- /dev/null +++ b/mixs6/me_env_package.md @@ -0,0 +1,47 @@ + +# Slot: ME_env_package + + + + +URI: [mixs.vocab:ME_env_package](https://w3id.org/mixs/vocab/ME_env_package) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_experimental_factor.md b/mixs6/me_experimental_factor.md new file mode 100644 index 00000000..cf74336d --- /dev/null +++ b/mixs6/me_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: ME_experimental_factor + + + + +URI: [mixs.vocab:ME_experimental_factor](https://w3id.org/mixs/vocab/ME_experimental_factor) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_feat_pred.md b/mixs6/me_feat_pred.md new file mode 100644 index 00000000..cc611ca0 --- /dev/null +++ b/mixs6/me_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: ME_feat_pred + + + + +URI: [mixs.vocab:ME_feat_pred](https://w3id.org/mixs/vocab/ME_feat_pred) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_geo_loc_name.md b/mixs6/me_geo_loc_name.md new file mode 100644 index 00000000..e2981e26 --- /dev/null +++ b/mixs6/me_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: ME_geo_loc_name + + + + +URI: [mixs.vocab:ME_geo_loc_name](https://w3id.org/mixs/vocab/ME_geo_loc_name) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_investigation_type.md b/mixs6/me_investigation_type.md new file mode 100644 index 00000000..d71fc2db --- /dev/null +++ b/mixs6/me_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: ME_investigation_type + + + + +URI: [mixs.vocab:ME_investigation_type](https://w3id.org/mixs/vocab/ME_investigation_type) + + +## Domain and Range + +[ME](ME.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_lat_lon.md b/mixs6/me_lat_lon.md new file mode 100644 index 00000000..f8104a3d --- /dev/null +++ b/mixs6/me_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: ME_lat_lon + + + + +URI: [mixs.vocab:ME_lat_lon](https://w3id.org/mixs/vocab/ME_lat_lon) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [ME](ME.md) diff --git a/mixs6/me_lib_layout.md b/mixs6/me_lib_layout.md new file mode 100644 index 00000000..c3107257 --- /dev/null +++ b/mixs6/me_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_layout + + + + +URI: [mixs.vocab:ME_lib_layout](https://w3id.org/mixs/vocab/ME_lib_layout) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_reads_seqd.md b/mixs6/me_lib_reads_seqd.md new file mode 100644 index 00000000..86afe779 --- /dev/null +++ b/mixs6/me_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_reads_seqd + + + + +URI: [mixs.vocab:ME_lib_reads_seqd](https://w3id.org/mixs/vocab/ME_lib_reads_seqd) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_screen.md b/mixs6/me_lib_screen.md new file mode 100644 index 00000000..a9bb47b7 --- /dev/null +++ b/mixs6/me_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_screen + + + + +URI: [mixs.vocab:ME_lib_screen](https://w3id.org/mixs/vocab/ME_lib_screen) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_size.md b/mixs6/me_lib_size.md new file mode 100644 index 00000000..2b42366a --- /dev/null +++ b/mixs6/me_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_size + + + + +URI: [mixs.vocab:ME_lib_size](https://w3id.org/mixs/vocab/ME_lib_size) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_lib_vector.md b/mixs6/me_lib_vector.md new file mode 100644 index 00000000..c6f5a82f --- /dev/null +++ b/mixs6/me_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: ME_lib_vector + + + + +URI: [mixs.vocab:ME_lib_vector](https://w3id.org/mixs/vocab/ME_lib_vector) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_mid.md b/mixs6/me_mid.md new file mode 100644 index 00000000..eedad885 --- /dev/null +++ b/mixs6/me_mid.md @@ -0,0 +1,47 @@ + +# Slot: ME_mid + + + + +URI: [mixs.vocab:ME_mid](https://w3id.org/mixs/vocab/ME_mid) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_nucl_acid_amp.md b/mixs6/me_nucl_acid_amp.md new file mode 100644 index 00000000..7f3c653d --- /dev/null +++ b/mixs6/me_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: ME_nucl_acid_amp + + + + +URI: [mixs.vocab:ME_nucl_acid_amp](https://w3id.org/mixs/vocab/ME_nucl_acid_amp) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_nucl_acid_ext.md b/mixs6/me_nucl_acid_ext.md new file mode 100644 index 00000000..13c38ff6 --- /dev/null +++ b/mixs6/me_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: ME_nucl_acid_ext + + + + +URI: [mixs.vocab:ME_nucl_acid_ext](https://w3id.org/mixs/vocab/ME_nucl_acid_ext) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_number_contig.md b/mixs6/me_number_contig.md new file mode 100644 index 00000000..0d2b9f9a --- /dev/null +++ b/mixs6/me_number_contig.md @@ -0,0 +1,47 @@ + +# Slot: ME_number_contig + + + + +URI: [mixs.vocab:ME_number_contig](https://w3id.org/mixs/vocab/ME_number_contig) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_project_name.md b/mixs6/me_project_name.md new file mode 100644 index 00000000..7b988468 --- /dev/null +++ b/mixs6/me_project_name.md @@ -0,0 +1,40 @@ + +# Slot: ME_project_name + + + + +URI: [mixs.vocab:ME_project_name](https://w3id.org/mixs/vocab/ME_project_name) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_ref_biomaterial.md b/mixs6/me_ref_biomaterial.md new file mode 100644 index 00000000..a2f4f7ec --- /dev/null +++ b/mixs6/me_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: ME_ref_biomaterial + + + + +URI: [mixs.vocab:ME_ref_biomaterial](https://w3id.org/mixs/vocab/ME_ref_biomaterial) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_ref_db.md b/mixs6/me_ref_db.md new file mode 100644 index 00000000..1e279f68 --- /dev/null +++ b/mixs6/me_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: ME_ref_db + + + + +URI: [mixs.vocab:ME_ref_db](https://w3id.org/mixs/vocab/ME_ref_db) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_rel_to_oxygen.md b/mixs6/me_rel_to_oxygen.md new file mode 100644 index 00000000..c3b8e0e3 --- /dev/null +++ b/mixs6/me_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: ME_rel_to_oxygen + + + + +URI: [mixs.vocab:ME_rel_to_oxygen](https://w3id.org/mixs/vocab/ME_rel_to_oxygen) + + +## Domain and Range + +[ME](ME.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_samp_collect_device.md b/mixs6/me_samp_collect_device.md new file mode 100644 index 00000000..03911d20 --- /dev/null +++ b/mixs6/me_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: ME_samp_collect_device + + + + +URI: [mixs.vocab:ME_samp_collect_device](https://w3id.org/mixs/vocab/ME_samp_collect_device) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_samp_mat_process.md b/mixs6/me_samp_mat_process.md new file mode 100644 index 00000000..fa65af01 --- /dev/null +++ b/mixs6/me_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: ME_samp_mat_process + + + + +URI: [mixs.vocab:ME_samp_mat_process](https://w3id.org/mixs/vocab/ME_samp_mat_process) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_samp_size.md b/mixs6/me_samp_size.md new file mode 100644 index 00000000..bc9b9d61 --- /dev/null +++ b/mixs6/me_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: ME_samp_size + + + + +URI: [mixs.vocab:ME_samp_size](https://w3id.org/mixs/vocab/ME_samp_size) + + +## Domain and Range + +[ME](ME.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_sample_name.md b/mixs6/me_sample_name.md new file mode 100644 index 00000000..261b70fa --- /dev/null +++ b/mixs6/me_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: ME_sample_name + + + + +URI: [mixs.vocab:ME_sample_name](https://w3id.org/mixs/vocab/ME_sample_name) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_seq_meth.md b/mixs6/me_seq_meth.md new file mode 100644 index 00000000..2e1c3bdd --- /dev/null +++ b/mixs6/me_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: ME_seq_meth + + + + +URI: [mixs.vocab:ME_seq_meth](https://w3id.org/mixs/vocab/ME_seq_meth) + + +## Domain and Range + +[ME](ME.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_sim_search_meth.md b/mixs6/me_sim_search_meth.md new file mode 100644 index 00000000..a721b8a9 --- /dev/null +++ b/mixs6/me_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: ME_sim_search_meth + + + + +URI: [mixs.vocab:ME_sim_search_meth](https://w3id.org/mixs/vocab/ME_sim_search_meth) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_size_frac.md b/mixs6/me_size_frac.md new file mode 100644 index 00000000..361103e6 --- /dev/null +++ b/mixs6/me_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: ME_size_frac + + + + +URI: [mixs.vocab:ME_size_frac](https://w3id.org/mixs/vocab/ME_size_frac) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_sop.md b/mixs6/me_sop.md new file mode 100644 index 00000000..fdfe83f6 --- /dev/null +++ b/mixs6/me_sop.md @@ -0,0 +1,47 @@ + +# Slot: ME_sop + + + + +URI: [mixs.vocab:ME_sop](https://w3id.org/mixs/vocab/ME_sop) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_source_mat_id.md b/mixs6/me_source_mat_id.md new file mode 100644 index 00000000..78bcde31 --- /dev/null +++ b/mixs6/me_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: ME_source_mat_id + + + + +URI: [mixs.vocab:ME_source_mat_id](https://w3id.org/mixs/vocab/ME_source_mat_id) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/me_submitted_to_insdc.md b/mixs6/me_submitted_to_insdc.md new file mode 100644 index 00000000..49cf96a8 --- /dev/null +++ b/mixs6/me_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: ME_submitted_to_insdc + + + + +URI: [mixs.vocab:ME_submitted_to_insdc](https://w3id.org/mixs/vocab/ME_submitted_to_insdc) + + +## Domain and Range + +[ME](ME.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_tax_class.md b/mixs6/me_tax_class.md new file mode 100644 index 00000000..476a0ccc --- /dev/null +++ b/mixs6/me_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: ME_tax_class + + + + +URI: [mixs.vocab:ME_tax_class](https://w3id.org/mixs/vocab/ME_tax_class) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) diff --git a/mixs6/me_url.md b/mixs6/me_url.md new file mode 100644 index 00000000..9e37b8b0 --- /dev/null +++ b/mixs6/me_url.md @@ -0,0 +1,47 @@ + +# Slot: ME_url + + + + +URI: [mixs.vocab:ME_url](https://w3id.org/mixs/vocab/ME_url) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mean_frict_vel.md b/mixs6/mean_frict_vel.md index 784a13ce..ad91c28e 100644 --- a/mixs6/mean_frict_vel.md +++ b/mixs6/mean_frict_vel.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/mean_peak_frict_vel.md b/mixs6/mean_peak_frict_vel.md index f3a1808a..7082cb35 100644 --- a/mixs6/mean_peak_frict_vel.md +++ b/mixs6/mean_peak_frict_vel.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/mech_struc.md b/mixs6/mech_struc.md index 2159bf36..b080f73a 100644 --- a/mixs6/mech_struc.md +++ b/mixs6/mech_struc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/mechanical_damage.md b/mixs6/mechanical_damage.md index 7ee649fb..76fe7967 100644 --- a/mixs6/mechanical_damage.md +++ b/mixs6/mechanical_damage.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/medic_hist_perform.md b/mixs6/medic_hist_perform.md index 199fa03b..87911c14 100644 --- a/mixs6/medic_hist_perform.md +++ b/mixs6/medic_hist_perform.md @@ -21,65 +21,65 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/menarche.md b/mixs6/menarche.md index 9cce0db6..5d19a012 100644 --- a/mixs6/menarche.md +++ b/mixs6/menarche.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/menopause.md b/mixs6/menopause.md index a91bfd9c..c585d5a8 100644 --- a/mixs6/menopause.md +++ b/mixs6/menopause.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/methane.md b/mixs6/methane.md index 31a055da..0a397bca 100644 --- a/mixs6/methane.md +++ b/mixs6/methane.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) ## Other properties diff --git a/mixs6/microbial_biomass.md b/mixs6/microbial_biomass.md index 064693f0..1743fc16 100644 --- a/mixs6/microbial_biomass.md +++ b/mixs6/microbial_biomass.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/microbial_biomass_meth.md b/mixs6/microbial_biomass_meth.md index 8f5be4c2..32829c87 100644 --- a/mixs6/microbial_biomass_meth.md +++ b/mixs6/microbial_biomass_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/mid.md b/mixs6/mid.md index 93462abf..35e3119e 100644 --- a/mixs6/mid.md +++ b/mixs6/mid.md @@ -17,11 +17,11 @@ None -> OPT [String](types/String.md) ## Children - * [me➞mid](me_mid.md) - * [mimag➞mid](mimag_mid.md) - * [mimarks_s➞mid](mimarks_s_mid.md) - * [misag➞mid](misag_mid.md) - * [miuvig➞mid](miuvig_mid.md) + * [ME➞mid](ME_mid.md) + * [MIMAG➞mid](MIMAG_mid.md) + * [MIMARKS specimen➞mid](MIMARKS_specimen_mid.md) + * [MISAG➞mid](MISAG_mid.md) + * [MIUVIG➞mid](MIUVIG_mid.md) ## Used by diff --git a/mixs6/migs_ba_adapters.md b/mixs6/migs_ba_adapters.md new file mode 100644 index 00000000..202a624f --- /dev/null +++ b/mixs6/migs_ba_adapters.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_adapters + + + + +URI: [mixs.vocab:migs_ba_adapters](https://w3id.org/mixs/vocab/migs_ba_adapters) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_annot.md b/mixs6/migs_ba_annot.md new file mode 100644 index 00000000..17b9c14b --- /dev/null +++ b/mixs6/migs_ba_annot.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_annot + + + + +URI: [mixs.vocab:migs_ba_annot](https://w3id.org/mixs/vocab/migs_ba_annot) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_assembly_name.md b/mixs6/migs_ba_assembly_name.md new file mode 100644 index 00000000..550d47b6 --- /dev/null +++ b/mixs6/migs_ba_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_assembly_name + + + + +URI: [mixs.vocab:migs_ba_assembly_name](https://w3id.org/mixs/vocab/migs_ba_assembly_name) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_assembly_qual.md b/mixs6/migs_ba_assembly_qual.md new file mode 100644 index 00000000..53fa4d3c --- /dev/null +++ b/mixs6/migs_ba_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_assembly_qual + + + + +URI: [mixs.vocab:migs_ba_assembly_qual](https://w3id.org/mixs/vocab/migs_ba_assembly_qual) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_assembly_software.md b/mixs6/migs_ba_assembly_software.md new file mode 100644 index 00000000..4d8fc32f --- /dev/null +++ b/mixs6/migs_ba_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_assembly_software + + + + +URI: [mixs.vocab:migs_ba_assembly_software](https://w3id.org/mixs/vocab/migs_ba_assembly_software) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_biotic_relationship.md b/mixs6/migs_ba_biotic_relationship.md new file mode 100644 index 00000000..cf26cd5d --- /dev/null +++ b/mixs6/migs_ba_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_biotic_relationship + + + + +URI: [mixs.vocab:migs_ba_biotic_relationship](https://w3id.org/mixs/vocab/migs_ba_biotic_relationship) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_collection_date.md b/mixs6/migs_ba_collection_date.md new file mode 100644 index 00000000..643cc548 --- /dev/null +++ b/mixs6/migs_ba_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_collection_date + + + + +URI: [mixs.vocab:migs_ba_collection_date](https://w3id.org/mixs/vocab/migs_ba_collection_date) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_compl_score.md b/mixs6/migs_ba_compl_score.md new file mode 100644 index 00000000..bae3d1dd --- /dev/null +++ b/mixs6/migs_ba_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_compl_score + + + + +URI: [mixs.vocab:migs_ba_compl_score](https://w3id.org/mixs/vocab/migs_ba_compl_score) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_compl_software.md b/mixs6/migs_ba_compl_software.md new file mode 100644 index 00000000..8566283a --- /dev/null +++ b/mixs6/migs_ba_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_compl_software + + + + +URI: [mixs.vocab:migs_ba_compl_software](https://w3id.org/mixs/vocab/migs_ba_compl_software) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_encoded_traits.md b/mixs6/migs_ba_encoded_traits.md new file mode 100644 index 00000000..5df21614 --- /dev/null +++ b/mixs6/migs_ba_encoded_traits.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_encoded_traits + + + + +URI: [mixs.vocab:migs_ba_encoded_traits](https://w3id.org/mixs/vocab/migs_ba_encoded_traits) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_env_broad_scale.md b/mixs6/migs_ba_env_broad_scale.md new file mode 100644 index 00000000..9ff91f7b --- /dev/null +++ b/mixs6/migs_ba_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_env_broad_scale + + + + +URI: [mixs.vocab:migs_ba_env_broad_scale](https://w3id.org/mixs/vocab/migs_ba_env_broad_scale) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_local_scale.md b/mixs6/migs_ba_env_local_scale.md new file mode 100644 index 00000000..06d6ecf2 --- /dev/null +++ b/mixs6/migs_ba_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_env_local_scale + + + + +URI: [mixs.vocab:migs_ba_env_local_scale](https://w3id.org/mixs/vocab/migs_ba_env_local_scale) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_medium.md b/mixs6/migs_ba_env_medium.md new file mode 100644 index 00000000..a73b2b86 --- /dev/null +++ b/mixs6/migs_ba_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_env_medium + + + + +URI: [mixs.vocab:migs_ba_env_medium](https://w3id.org/mixs/vocab/migs_ba_env_medium) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_package.md b/mixs6/migs_ba_env_package.md new file mode 100644 index 00000000..073e3fe7 --- /dev/null +++ b/mixs6/migs_ba_env_package.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_env_package + + + + +URI: [mixs.vocab:migs_ba_env_package](https://w3id.org/mixs/vocab/migs_ba_env_package) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_estimated_size.md b/mixs6/migs_ba_estimated_size.md new file mode 100644 index 00000000..fdaaeb89 --- /dev/null +++ b/mixs6/migs_ba_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_estimated_size + + + + +URI: [mixs.vocab:migs_ba_estimated_size](https://w3id.org/mixs/vocab/migs_ba_estimated_size) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_experimental_factor.md b/mixs6/migs_ba_experimental_factor.md new file mode 100644 index 00000000..54f48a26 --- /dev/null +++ b/mixs6/migs_ba_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_experimental_factor + + + + +URI: [mixs.vocab:migs_ba_experimental_factor](https://w3id.org/mixs/vocab/migs_ba_experimental_factor) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_extrachrom_elements.md b/mixs6/migs_ba_extrachrom_elements.md new file mode 100644 index 00000000..b3f7c8cd --- /dev/null +++ b/mixs6/migs_ba_extrachrom_elements.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_extrachrom_elements + + + + +URI: [mixs.vocab:migs_ba_extrachrom_elements](https://w3id.org/mixs/vocab/migs_ba_extrachrom_elements) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_feat_pred.md b/mixs6/migs_ba_feat_pred.md new file mode 100644 index 00000000..c44b9fc0 --- /dev/null +++ b/mixs6/migs_ba_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_feat_pred + + + + +URI: [mixs.vocab:migs_ba_feat_pred](https://w3id.org/mixs/vocab/migs_ba_feat_pred) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_geo_loc_name.md b/mixs6/migs_ba_geo_loc_name.md new file mode 100644 index 00000000..a9af3ee3 --- /dev/null +++ b/mixs6/migs_ba_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_geo_loc_name + + + + +URI: [mixs.vocab:migs_ba_geo_loc_name](https://w3id.org/mixs/vocab/migs_ba_geo_loc_name) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_health_disease_stat.md b/mixs6/migs_ba_health_disease_stat.md new file mode 100644 index 00000000..675f6fe7 --- /dev/null +++ b/mixs6/migs_ba_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_health_disease_stat + + + + +URI: [mixs.vocab:migs_ba_health_disease_stat](https://w3id.org/mixs/vocab/migs_ba_health_disease_stat) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_host_spec_range.md b/mixs6/migs_ba_host_spec_range.md new file mode 100644 index 00000000..4a91bdad --- /dev/null +++ b/mixs6/migs_ba_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_host_spec_range + + + + +URI: [mixs.vocab:migs_ba_host_spec_range](https://w3id.org/mixs/vocab/migs_ba_host_spec_range) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_investigation_type.md b/mixs6/migs_ba_investigation_type.md new file mode 100644 index 00000000..9f9ba46d --- /dev/null +++ b/mixs6/migs_ba_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_investigation_type + + + + +URI: [mixs.vocab:migs_ba_investigation_type](https://w3id.org/mixs/vocab/migs_ba_investigation_type) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_isol_growth_condt.md b/mixs6/migs_ba_isol_growth_condt.md new file mode 100644 index 00000000..5de15014 --- /dev/null +++ b/mixs6/migs_ba_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_isol_growth_condt + + + + +URI: [mixs.vocab:migs_ba_isol_growth_condt](https://w3id.org/mixs/vocab/migs_ba_isol_growth_condt) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lat_lon.md b/mixs6/migs_ba_lat_lon.md new file mode 100644 index 00000000..4259c437 --- /dev/null +++ b/mixs6/migs_ba_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: migs_ba_lat_lon + + + + +URI: [mixs.vocab:migs_ba_lat_lon](https://w3id.org/mixs/vocab/migs_ba_lat_lon) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_lib_layout.md b/mixs6/migs_ba_lib_layout.md new file mode 100644 index 00000000..2829bd6f --- /dev/null +++ b/mixs6/migs_ba_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_lib_layout + + + + +URI: [mixs.vocab:migs_ba_lib_layout](https://w3id.org/mixs/vocab/migs_ba_lib_layout) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_reads_seqd.md b/mixs6/migs_ba_lib_reads_seqd.md new file mode 100644 index 00000000..1c8271d9 --- /dev/null +++ b/mixs6/migs_ba_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_lib_reads_seqd + + + + +URI: [mixs.vocab:migs_ba_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_ba_lib_reads_seqd) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_screen.md b/mixs6/migs_ba_lib_screen.md new file mode 100644 index 00000000..213ecc7a --- /dev/null +++ b/mixs6/migs_ba_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_lib_screen + + + + +URI: [mixs.vocab:migs_ba_lib_screen](https://w3id.org/mixs/vocab/migs_ba_lib_screen) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_size.md b/mixs6/migs_ba_lib_size.md new file mode 100644 index 00000000..71698443 --- /dev/null +++ b/mixs6/migs_ba_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_lib_size + + + + +URI: [mixs.vocab:migs_ba_lib_size](https://w3id.org/mixs/vocab/migs_ba_lib_size) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_vector.md b/mixs6/migs_ba_lib_vector.md new file mode 100644 index 00000000..3c371ef5 --- /dev/null +++ b/mixs6/migs_ba_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_lib_vector + + + + +URI: [mixs.vocab:migs_ba_lib_vector](https://w3id.org/mixs/vocab/migs_ba_lib_vector) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_nucl_acid_amp.md b/mixs6/migs_ba_nucl_acid_amp.md new file mode 100644 index 00000000..a07917c5 --- /dev/null +++ b/mixs6/migs_ba_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_nucl_acid_amp + + + + +URI: [mixs.vocab:migs_ba_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_ba_nucl_acid_amp) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_nucl_acid_ext.md b/mixs6/migs_ba_nucl_acid_ext.md new file mode 100644 index 00000000..2821f8c1 --- /dev/null +++ b/mixs6/migs_ba_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_nucl_acid_ext + + + + +URI: [mixs.vocab:migs_ba_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_ba_nucl_acid_ext) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_num_replicons.md b/mixs6/migs_ba_num_replicons.md new file mode 100644 index 00000000..76a293ba --- /dev/null +++ b/mixs6/migs_ba_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_num_replicons + + + + +URI: [mixs.vocab:migs_ba_num_replicons](https://w3id.org/mixs/vocab/migs_ba_num_replicons) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_number_contig.md b/mixs6/migs_ba_number_contig.md new file mode 100644 index 00000000..f21eb0a8 --- /dev/null +++ b/mixs6/migs_ba_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_number_contig + + + + +URI: [mixs.vocab:migs_ba_number_contig](https://w3id.org/mixs/vocab/migs_ba_number_contig) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_pathogenicity.md b/mixs6/migs_ba_pathogenicity.md new file mode 100644 index 00000000..87a65c57 --- /dev/null +++ b/mixs6/migs_ba_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_pathogenicity + + + + +URI: [mixs.vocab:migs_ba_pathogenicity](https://w3id.org/mixs/vocab/migs_ba_pathogenicity) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_project_name.md b/mixs6/migs_ba_project_name.md new file mode 100644 index 00000000..78c6be58 --- /dev/null +++ b/mixs6/migs_ba_project_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_project_name + + + + +URI: [mixs.vocab:migs_ba_project_name](https://w3id.org/mixs/vocab/migs_ba_project_name) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_ref_biomaterial.md b/mixs6/migs_ba_ref_biomaterial.md new file mode 100644 index 00000000..e812c69e --- /dev/null +++ b/mixs6/migs_ba_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_ref_biomaterial + + + + +URI: [mixs.vocab:migs_ba_ref_biomaterial](https://w3id.org/mixs/vocab/migs_ba_ref_biomaterial) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_ref_db.md b/mixs6/migs_ba_ref_db.md new file mode 100644 index 00000000..040f9750 --- /dev/null +++ b/mixs6/migs_ba_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_ref_db + + + + +URI: [mixs.vocab:migs_ba_ref_db](https://w3id.org/mixs/vocab/migs_ba_ref_db) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_rel_to_oxygen.md b/mixs6/migs_ba_rel_to_oxygen.md new file mode 100644 index 00000000..5f1585f4 --- /dev/null +++ b/mixs6/migs_ba_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_rel_to_oxygen + + + + +URI: [mixs.vocab:migs_ba_rel_to_oxygen](https://w3id.org/mixs/vocab/migs_ba_rel_to_oxygen) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_samp_collect_device.md b/mixs6/migs_ba_samp_collect_device.md new file mode 100644 index 00000000..07b9ddca --- /dev/null +++ b/mixs6/migs_ba_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_samp_collect_device + + + + +URI: [mixs.vocab:migs_ba_samp_collect_device](https://w3id.org/mixs/vocab/migs_ba_samp_collect_device) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_samp_mat_process.md b/mixs6/migs_ba_samp_mat_process.md new file mode 100644 index 00000000..2c50d118 --- /dev/null +++ b/mixs6/migs_ba_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_samp_mat_process + + + + +URI: [mixs.vocab:migs_ba_samp_mat_process](https://w3id.org/mixs/vocab/migs_ba_samp_mat_process) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_samp_size.md b/mixs6/migs_ba_samp_size.md new file mode 100644 index 00000000..5f2ffc11 --- /dev/null +++ b/mixs6/migs_ba_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_samp_size + + + + +URI: [mixs.vocab:migs_ba_samp_size](https://w3id.org/mixs/vocab/migs_ba_samp_size) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sample_name.md b/mixs6/migs_ba_sample_name.md new file mode 100644 index 00000000..ecd122ec --- /dev/null +++ b/mixs6/migs_ba_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_sample_name + + + + +URI: [mixs.vocab:migs_ba_sample_name](https://w3id.org/mixs/vocab/migs_ba_sample_name) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_seq_meth.md b/mixs6/migs_ba_seq_meth.md new file mode 100644 index 00000000..4fbf26cc --- /dev/null +++ b/mixs6/migs_ba_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_seq_meth + + + + +URI: [mixs.vocab:migs_ba_seq_meth](https://w3id.org/mixs/vocab/migs_ba_seq_meth) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sim_search_meth.md b/mixs6/migs_ba_sim_search_meth.md new file mode 100644 index 00000000..5e86deda --- /dev/null +++ b/mixs6/migs_ba_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_sim_search_meth + + + + +URI: [mixs.vocab:migs_ba_sim_search_meth](https://w3id.org/mixs/vocab/migs_ba_sim_search_meth) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sop.md b/mixs6/migs_ba_sop.md new file mode 100644 index 00000000..416172cb --- /dev/null +++ b/mixs6/migs_ba_sop.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_sop + + + + +URI: [mixs.vocab:migs_ba_sop](https://w3id.org/mixs/vocab/migs_ba_sop) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_source_mat_id.md b/mixs6/migs_ba_source_mat_id.md new file mode 100644 index 00000000..074ad9fb --- /dev/null +++ b/mixs6/migs_ba_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_source_mat_id + + + + +URI: [mixs.vocab:migs_ba_source_mat_id](https://w3id.org/mixs/vocab/migs_ba_source_mat_id) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_specific_host.md b/mixs6/migs_ba_specific_host.md new file mode 100644 index 00000000..e8f56721 --- /dev/null +++ b/mixs6/migs_ba_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_specific_host + + + + +URI: [mixs.vocab:migs_ba_specific_host](https://w3id.org/mixs/vocab/migs_ba_specific_host) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_submitted_to_insdc.md b/mixs6/migs_ba_submitted_to_insdc.md new file mode 100644 index 00000000..78f42bb7 --- /dev/null +++ b/mixs6/migs_ba_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_submitted_to_insdc + + + + +URI: [mixs.vocab:migs_ba_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_ba_submitted_to_insdc) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_subspecf_gen_lin.md b/mixs6/migs_ba_subspecf_gen_lin.md new file mode 100644 index 00000000..e4619438 --- /dev/null +++ b/mixs6/migs_ba_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_subspecf_gen_lin + + + + +URI: [mixs.vocab:migs_ba_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_ba_subspecf_gen_lin) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_tax_class.md b/mixs6/migs_ba_tax_class.md new file mode 100644 index 00000000..9518f918 --- /dev/null +++ b/mixs6/migs_ba_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: migs_ba_tax_class + + + + +URI: [mixs.vocab:migs_ba_tax_class](https://w3id.org/mixs/vocab/migs_ba_tax_class) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_tax_ident.md b/mixs6/migs_ba_tax_ident.md new file mode 100644 index 00000000..823bbfbc --- /dev/null +++ b/mixs6/migs_ba_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_tax_ident + + + + +URI: [mixs.vocab:migs_ba_tax_ident](https://w3id.org/mixs/vocab/migs_ba_tax_ident) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_trophic_level.md b/mixs6/migs_ba_trophic_level.md new file mode 100644 index 00000000..69867451 --- /dev/null +++ b/mixs6/migs_ba_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_trophic_level + + + + +URI: [mixs.vocab:migs_ba_trophic_level](https://w3id.org/mixs/vocab/migs_ba_trophic_level) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_ba_url.md b/mixs6/migs_ba_url.md new file mode 100644 index 00000000..e4af5a2f --- /dev/null +++ b/mixs6/migs_ba_url.md @@ -0,0 +1,47 @@ + +# Slot: migs_ba_url + + + + +URI: [mixs.vocab:migs_ba_url](https://w3id.org/mixs/vocab/migs_ba_url) + + +## Domain and Range + +[MigsBa](MigsBa.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMigsBa](AirMigsBa.md) + * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) + * [Host-associatedMigsBa](Host-associatedMigsBa.md) + * [Human-associatedMigsBa](Human-associatedMigsBa.md) + * [Human-gutMigsBa](Human-gutMigsBa.md) + * [Human-oralMigsBa](Human-oralMigsBa.md) + * [Human-skinMigsBa](Human-skinMigsBa.md) + * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) + * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) + * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) + * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) + * [MigsBa](MigsBa.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) + * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) + * [SedimentMigsBa](SedimentMigsBa.md) + * [SoilMigsBa](SoilMigsBa.md) + * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) + * [WaterMigsBa](WaterMigsBa.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_adapters.md b/mixs6/migs_eu_adapters.md new file mode 100644 index 00000000..d69ed764 --- /dev/null +++ b/mixs6/migs_eu_adapters.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_adapters + + + + +URI: [mixs.vocab:migs_eu_adapters](https://w3id.org/mixs/vocab/migs_eu_adapters) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_annot.md b/mixs6/migs_eu_annot.md new file mode 100644 index 00000000..c96d5ea1 --- /dev/null +++ b/mixs6/migs_eu_annot.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_annot + + + + +URI: [mixs.vocab:migs_eu_annot](https://w3id.org/mixs/vocab/migs_eu_annot) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_assembly_name.md b/mixs6/migs_eu_assembly_name.md new file mode 100644 index 00000000..16f06f78 --- /dev/null +++ b/mixs6/migs_eu_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_assembly_name + + + + +URI: [mixs.vocab:migs_eu_assembly_name](https://w3id.org/mixs/vocab/migs_eu_assembly_name) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_assembly_qual.md b/mixs6/migs_eu_assembly_qual.md new file mode 100644 index 00000000..20266c8f --- /dev/null +++ b/mixs6/migs_eu_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_assembly_qual + + + + +URI: [mixs.vocab:migs_eu_assembly_qual](https://w3id.org/mixs/vocab/migs_eu_assembly_qual) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_assembly_software.md b/mixs6/migs_eu_assembly_software.md new file mode 100644 index 00000000..683886b5 --- /dev/null +++ b/mixs6/migs_eu_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_assembly_software + + + + +URI: [mixs.vocab:migs_eu_assembly_software](https://w3id.org/mixs/vocab/migs_eu_assembly_software) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_biotic_relationship.md b/mixs6/migs_eu_biotic_relationship.md new file mode 100644 index 00000000..5d6aa601 --- /dev/null +++ b/mixs6/migs_eu_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_biotic_relationship + + + + +URI: [mixs.vocab:migs_eu_biotic_relationship](https://w3id.org/mixs/vocab/migs_eu_biotic_relationship) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_collection_date.md b/mixs6/migs_eu_collection_date.md new file mode 100644 index 00000000..a965176c --- /dev/null +++ b/mixs6/migs_eu_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_collection_date + + + + +URI: [mixs.vocab:migs_eu_collection_date](https://w3id.org/mixs/vocab/migs_eu_collection_date) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_compl_score.md b/mixs6/migs_eu_compl_score.md new file mode 100644 index 00000000..7b08ab18 --- /dev/null +++ b/mixs6/migs_eu_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_compl_score + + + + +URI: [mixs.vocab:migs_eu_compl_score](https://w3id.org/mixs/vocab/migs_eu_compl_score) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_compl_software.md b/mixs6/migs_eu_compl_software.md new file mode 100644 index 00000000..4cb9ba0d --- /dev/null +++ b/mixs6/migs_eu_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_compl_software + + + + +URI: [mixs.vocab:migs_eu_compl_software](https://w3id.org/mixs/vocab/migs_eu_compl_software) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_env_broad_scale.md b/mixs6/migs_eu_env_broad_scale.md new file mode 100644 index 00000000..60eed904 --- /dev/null +++ b/mixs6/migs_eu_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_env_broad_scale + + + + +URI: [mixs.vocab:migs_eu_env_broad_scale](https://w3id.org/mixs/vocab/migs_eu_env_broad_scale) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_local_scale.md b/mixs6/migs_eu_env_local_scale.md new file mode 100644 index 00000000..2537a8d5 --- /dev/null +++ b/mixs6/migs_eu_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_env_local_scale + + + + +URI: [mixs.vocab:migs_eu_env_local_scale](https://w3id.org/mixs/vocab/migs_eu_env_local_scale) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_medium.md b/mixs6/migs_eu_env_medium.md new file mode 100644 index 00000000..4cb33473 --- /dev/null +++ b/mixs6/migs_eu_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_env_medium + + + + +URI: [mixs.vocab:migs_eu_env_medium](https://w3id.org/mixs/vocab/migs_eu_env_medium) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_package.md b/mixs6/migs_eu_env_package.md new file mode 100644 index 00000000..e36475d2 --- /dev/null +++ b/mixs6/migs_eu_env_package.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_env_package + + + + +URI: [mixs.vocab:migs_eu_env_package](https://w3id.org/mixs/vocab/migs_eu_env_package) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_estimated_size.md b/mixs6/migs_eu_estimated_size.md new file mode 100644 index 00000000..d271aa07 --- /dev/null +++ b/mixs6/migs_eu_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_estimated_size + + + + +URI: [mixs.vocab:migs_eu_estimated_size](https://w3id.org/mixs/vocab/migs_eu_estimated_size) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_experimental_factor.md b/mixs6/migs_eu_experimental_factor.md new file mode 100644 index 00000000..d51ac899 --- /dev/null +++ b/mixs6/migs_eu_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_experimental_factor + + + + +URI: [mixs.vocab:migs_eu_experimental_factor](https://w3id.org/mixs/vocab/migs_eu_experimental_factor) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_extrachrom_elements.md b/mixs6/migs_eu_extrachrom_elements.md new file mode 100644 index 00000000..3b733b18 --- /dev/null +++ b/mixs6/migs_eu_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_extrachrom_elements + + + + +URI: [mixs.vocab:migs_eu_extrachrom_elements](https://w3id.org/mixs/vocab/migs_eu_extrachrom_elements) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_feat_pred.md b/mixs6/migs_eu_feat_pred.md new file mode 100644 index 00000000..fac65b4a --- /dev/null +++ b/mixs6/migs_eu_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_feat_pred + + + + +URI: [mixs.vocab:migs_eu_feat_pred](https://w3id.org/mixs/vocab/migs_eu_feat_pred) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_geo_loc_name.md b/mixs6/migs_eu_geo_loc_name.md new file mode 100644 index 00000000..90e28e73 --- /dev/null +++ b/mixs6/migs_eu_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_geo_loc_name + + + + +URI: [mixs.vocab:migs_eu_geo_loc_name](https://w3id.org/mixs/vocab/migs_eu_geo_loc_name) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_health_disease_stat.md b/mixs6/migs_eu_health_disease_stat.md new file mode 100644 index 00000000..808269b4 --- /dev/null +++ b/mixs6/migs_eu_health_disease_stat.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_health_disease_stat + + + + +URI: [mixs.vocab:migs_eu_health_disease_stat](https://w3id.org/mixs/vocab/migs_eu_health_disease_stat) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_host_spec_range.md b/mixs6/migs_eu_host_spec_range.md new file mode 100644 index 00000000..a3d93322 --- /dev/null +++ b/mixs6/migs_eu_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_host_spec_range + + + + +URI: [mixs.vocab:migs_eu_host_spec_range](https://w3id.org/mixs/vocab/migs_eu_host_spec_range) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_investigation_type.md b/mixs6/migs_eu_investigation_type.md new file mode 100644 index 00000000..ac4a6de6 --- /dev/null +++ b/mixs6/migs_eu_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_investigation_type + + + + +URI: [mixs.vocab:migs_eu_investigation_type](https://w3id.org/mixs/vocab/migs_eu_investigation_type) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_isol_growth_condt.md b/mixs6/migs_eu_isol_growth_condt.md new file mode 100644 index 00000000..78536e14 --- /dev/null +++ b/mixs6/migs_eu_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_isol_growth_condt + + + + +URI: [mixs.vocab:migs_eu_isol_growth_condt](https://w3id.org/mixs/vocab/migs_eu_isol_growth_condt) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lat_lon.md b/mixs6/migs_eu_lat_lon.md new file mode 100644 index 00000000..7b2e5ad2 --- /dev/null +++ b/mixs6/migs_eu_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: migs_eu_lat_lon + + + + +URI: [mixs.vocab:migs_eu_lat_lon](https://w3id.org/mixs/vocab/migs_eu_lat_lon) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_lib_layout.md b/mixs6/migs_eu_lib_layout.md new file mode 100644 index 00000000..ccf40b9e --- /dev/null +++ b/mixs6/migs_eu_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_lib_layout + + + + +URI: [mixs.vocab:migs_eu_lib_layout](https://w3id.org/mixs/vocab/migs_eu_lib_layout) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_reads_seqd.md b/mixs6/migs_eu_lib_reads_seqd.md new file mode 100644 index 00000000..802ae9b6 --- /dev/null +++ b/mixs6/migs_eu_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_lib_reads_seqd + + + + +URI: [mixs.vocab:migs_eu_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_eu_lib_reads_seqd) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_screen.md b/mixs6/migs_eu_lib_screen.md new file mode 100644 index 00000000..75f6ce55 --- /dev/null +++ b/mixs6/migs_eu_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_lib_screen + + + + +URI: [mixs.vocab:migs_eu_lib_screen](https://w3id.org/mixs/vocab/migs_eu_lib_screen) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_size.md b/mixs6/migs_eu_lib_size.md new file mode 100644 index 00000000..57b3b2f5 --- /dev/null +++ b/mixs6/migs_eu_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_lib_size + + + + +URI: [mixs.vocab:migs_eu_lib_size](https://w3id.org/mixs/vocab/migs_eu_lib_size) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_vector.md b/mixs6/migs_eu_lib_vector.md new file mode 100644 index 00000000..4c4e9180 --- /dev/null +++ b/mixs6/migs_eu_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_lib_vector + + + + +URI: [mixs.vocab:migs_eu_lib_vector](https://w3id.org/mixs/vocab/migs_eu_lib_vector) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_nucl_acid_amp.md b/mixs6/migs_eu_nucl_acid_amp.md new file mode 100644 index 00000000..ac30966a --- /dev/null +++ b/mixs6/migs_eu_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_nucl_acid_amp + + + + +URI: [mixs.vocab:migs_eu_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_eu_nucl_acid_amp) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_nucl_acid_ext.md b/mixs6/migs_eu_nucl_acid_ext.md new file mode 100644 index 00000000..d12607e1 --- /dev/null +++ b/mixs6/migs_eu_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_nucl_acid_ext + + + + +URI: [mixs.vocab:migs_eu_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_eu_nucl_acid_ext) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_num_replicons.md b/mixs6/migs_eu_num_replicons.md new file mode 100644 index 00000000..54b2e149 --- /dev/null +++ b/mixs6/migs_eu_num_replicons.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_num_replicons + + + + +URI: [mixs.vocab:migs_eu_num_replicons](https://w3id.org/mixs/vocab/migs_eu_num_replicons) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_number_contig.md b/mixs6/migs_eu_number_contig.md new file mode 100644 index 00000000..fd77b8f2 --- /dev/null +++ b/mixs6/migs_eu_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_number_contig + + + + +URI: [mixs.vocab:migs_eu_number_contig](https://w3id.org/mixs/vocab/migs_eu_number_contig) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_pathogenicity.md b/mixs6/migs_eu_pathogenicity.md new file mode 100644 index 00000000..a49e6b96 --- /dev/null +++ b/mixs6/migs_eu_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_pathogenicity + + + + +URI: [mixs.vocab:migs_eu_pathogenicity](https://w3id.org/mixs/vocab/migs_eu_pathogenicity) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_ploidy.md b/mixs6/migs_eu_ploidy.md new file mode 100644 index 00000000..7e8d9385 --- /dev/null +++ b/mixs6/migs_eu_ploidy.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_ploidy + + + + +URI: [mixs.vocab:migs_eu_ploidy](https://w3id.org/mixs/vocab/migs_eu_ploidy) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ploidy](ploidy.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_project_name.md b/mixs6/migs_eu_project_name.md new file mode 100644 index 00000000..f45e5ae0 --- /dev/null +++ b/mixs6/migs_eu_project_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_project_name + + + + +URI: [mixs.vocab:migs_eu_project_name](https://w3id.org/mixs/vocab/migs_eu_project_name) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_propagation.md b/mixs6/migs_eu_propagation.md new file mode 100644 index 00000000..5879bb44 --- /dev/null +++ b/mixs6/migs_eu_propagation.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_propagation + + + + +URI: [mixs.vocab:migs_eu_propagation](https://w3id.org/mixs/vocab/migs_eu_propagation) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_ref_biomaterial.md b/mixs6/migs_eu_ref_biomaterial.md new file mode 100644 index 00000000..f09f5bb4 --- /dev/null +++ b/mixs6/migs_eu_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_ref_biomaterial + + + + +URI: [mixs.vocab:migs_eu_ref_biomaterial](https://w3id.org/mixs/vocab/migs_eu_ref_biomaterial) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_ref_db.md b/mixs6/migs_eu_ref_db.md new file mode 100644 index 00000000..52a10dd3 --- /dev/null +++ b/mixs6/migs_eu_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_ref_db + + + + +URI: [mixs.vocab:migs_eu_ref_db](https://w3id.org/mixs/vocab/migs_eu_ref_db) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_collect_device.md b/mixs6/migs_eu_samp_collect_device.md new file mode 100644 index 00000000..2c98c723 --- /dev/null +++ b/mixs6/migs_eu_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_samp_collect_device + + + + +URI: [mixs.vocab:migs_eu_samp_collect_device](https://w3id.org/mixs/vocab/migs_eu_samp_collect_device) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_mat_process.md b/mixs6/migs_eu_samp_mat_process.md new file mode 100644 index 00000000..04b56a2f --- /dev/null +++ b/mixs6/migs_eu_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_samp_mat_process + + + + +URI: [mixs.vocab:migs_eu_samp_mat_process](https://w3id.org/mixs/vocab/migs_eu_samp_mat_process) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_size.md b/mixs6/migs_eu_samp_size.md new file mode 100644 index 00000000..1864507e --- /dev/null +++ b/mixs6/migs_eu_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_samp_size + + + + +URI: [mixs.vocab:migs_eu_samp_size](https://w3id.org/mixs/vocab/migs_eu_samp_size) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sample_name.md b/mixs6/migs_eu_sample_name.md new file mode 100644 index 00000000..79acd46f --- /dev/null +++ b/mixs6/migs_eu_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_sample_name + + + + +URI: [mixs.vocab:migs_eu_sample_name](https://w3id.org/mixs/vocab/migs_eu_sample_name) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_seq_meth.md b/mixs6/migs_eu_seq_meth.md new file mode 100644 index 00000000..6ff99b4c --- /dev/null +++ b/mixs6/migs_eu_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_seq_meth + + + + +URI: [mixs.vocab:migs_eu_seq_meth](https://w3id.org/mixs/vocab/migs_eu_seq_meth) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sim_search_meth.md b/mixs6/migs_eu_sim_search_meth.md new file mode 100644 index 00000000..5e139a86 --- /dev/null +++ b/mixs6/migs_eu_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_sim_search_meth + + + + +URI: [mixs.vocab:migs_eu_sim_search_meth](https://w3id.org/mixs/vocab/migs_eu_sim_search_meth) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sop.md b/mixs6/migs_eu_sop.md new file mode 100644 index 00000000..c9299a5e --- /dev/null +++ b/mixs6/migs_eu_sop.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_sop + + + + +URI: [mixs.vocab:migs_eu_sop](https://w3id.org/mixs/vocab/migs_eu_sop) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_source_mat_id.md b/mixs6/migs_eu_source_mat_id.md new file mode 100644 index 00000000..252c0d41 --- /dev/null +++ b/mixs6/migs_eu_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_source_mat_id + + + + +URI: [mixs.vocab:migs_eu_source_mat_id](https://w3id.org/mixs/vocab/migs_eu_source_mat_id) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_specific_host.md b/mixs6/migs_eu_specific_host.md new file mode 100644 index 00000000..542ac0e4 --- /dev/null +++ b/mixs6/migs_eu_specific_host.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_specific_host + + + + +URI: [mixs.vocab:migs_eu_specific_host](https://w3id.org/mixs/vocab/migs_eu_specific_host) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_submitted_to_insdc.md b/mixs6/migs_eu_submitted_to_insdc.md new file mode 100644 index 00000000..469ff0e4 --- /dev/null +++ b/mixs6/migs_eu_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_submitted_to_insdc + + + + +URI: [mixs.vocab:migs_eu_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_eu_submitted_to_insdc) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_subspecf_gen_lin.md b/mixs6/migs_eu_subspecf_gen_lin.md new file mode 100644 index 00000000..91ea5605 --- /dev/null +++ b/mixs6/migs_eu_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_subspecf_gen_lin + + + + +URI: [mixs.vocab:migs_eu_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_eu_subspecf_gen_lin) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_tax_class.md b/mixs6/migs_eu_tax_class.md new file mode 100644 index 00000000..92632da9 --- /dev/null +++ b/mixs6/migs_eu_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: migs_eu_tax_class + + + + +URI: [mixs.vocab:migs_eu_tax_class](https://w3id.org/mixs/vocab/migs_eu_tax_class) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_tax_ident.md b/mixs6/migs_eu_tax_ident.md new file mode 100644 index 00000000..ee9ab943 --- /dev/null +++ b/mixs6/migs_eu_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_tax_ident + + + + +URI: [mixs.vocab:migs_eu_tax_ident](https://w3id.org/mixs/vocab/migs_eu_tax_ident) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_trophic_level.md b/mixs6/migs_eu_trophic_level.md new file mode 100644 index 00000000..5c6fac76 --- /dev/null +++ b/mixs6/migs_eu_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_trophic_level + + + + +URI: [mixs.vocab:migs_eu_trophic_level](https://w3id.org/mixs/vocab/migs_eu_trophic_level) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_eu_url.md b/mixs6/migs_eu_url.md new file mode 100644 index 00000000..6a7a49b6 --- /dev/null +++ b/mixs6/migs_eu_url.md @@ -0,0 +1,47 @@ + +# Slot: migs_eu_url + + + + +URI: [mixs.vocab:migs_eu_url](https://w3id.org/mixs/vocab/migs_eu_url) + + +## Domain and Range + +[MigsEu](MigsEu.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMigsEu](AirMigsEu.md) + * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) + * [Host-associatedMigsEu](Host-associatedMigsEu.md) + * [Human-associatedMigsEu](Human-associatedMigsEu.md) + * [Human-gutMigsEu](Human-gutMigsEu.md) + * [Human-oralMigsEu](Human-oralMigsEu.md) + * [Human-skinMigsEu](Human-skinMigsEu.md) + * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) + * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) + * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) + * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) + * [MigsEu](MigsEu.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) + * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) + * [SedimentMigsEu](SedimentMigsEu.md) + * [SoilMigsEu](SoilMigsEu.md) + * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) + * [WaterMigsEu](WaterMigsEu.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_adapters.md b/mixs6/migs_org_adapters.md new file mode 100644 index 00000000..a28fe001 --- /dev/null +++ b/mixs6/migs_org_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_adapters + + + + +URI: [mixs.vocab:MIGS_org_adapters](https://w3id.org/mixs/vocab/MIGS_org_adapters) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_annot.md b/mixs6/migs_org_annot.md new file mode 100644 index 00000000..3a6ec145 --- /dev/null +++ b/mixs6/migs_org_annot.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_annot + + + + +URI: [mixs.vocab:MIGS_org_annot](https://w3id.org/mixs/vocab/MIGS_org_annot) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_assembly_name.md b/mixs6/migs_org_assembly_name.md new file mode 100644 index 00000000..7fd76fae --- /dev/null +++ b/mixs6/migs_org_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_assembly_name + + + + +URI: [mixs.vocab:MIGS_org_assembly_name](https://w3id.org/mixs/vocab/MIGS_org_assembly_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_assembly_qual.md b/mixs6/migs_org_assembly_qual.md new file mode 100644 index 00000000..6d3f890e --- /dev/null +++ b/mixs6/migs_org_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_assembly_qual + + + + +URI: [mixs.vocab:MIGS_org_assembly_qual](https://w3id.org/mixs/vocab/MIGS_org_assembly_qual) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_assembly_software.md b/mixs6/migs_org_assembly_software.md new file mode 100644 index 00000000..376e5c55 --- /dev/null +++ b/mixs6/migs_org_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_assembly_software + + + + +URI: [mixs.vocab:MIGS_org_assembly_software](https://w3id.org/mixs/vocab/MIGS_org_assembly_software) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_collection_date.md b/mixs6/migs_org_collection_date.md new file mode 100644 index 00000000..ea3647f7 --- /dev/null +++ b/mixs6/migs_org_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_collection_date + + + + +URI: [mixs.vocab:MIGS_org_collection_date](https://w3id.org/mixs/vocab/MIGS_org_collection_date) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_compl_score.md b/mixs6/migs_org_compl_score.md new file mode 100644 index 00000000..0f839e58 --- /dev/null +++ b/mixs6/migs_org_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_compl_score + + + + +URI: [mixs.vocab:MIGS_org_compl_score](https://w3id.org/mixs/vocab/MIGS_org_compl_score) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_compl_software.md b/mixs6/migs_org_compl_software.md new file mode 100644 index 00000000..8024e1d3 --- /dev/null +++ b/mixs6/migs_org_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_compl_software + + + + +URI: [mixs.vocab:MIGS_org_compl_software](https://w3id.org/mixs/vocab/MIGS_org_compl_software) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_env_broad_scale.md b/mixs6/migs_org_env_broad_scale.md new file mode 100644 index 00000000..84a4487b --- /dev/null +++ b/mixs6/migs_org_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_broad_scale + + + + +URI: [mixs.vocab:MIGS_org_env_broad_scale](https://w3id.org/mixs/vocab/MIGS_org_env_broad_scale) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_local_scale.md b/mixs6/migs_org_env_local_scale.md new file mode 100644 index 00000000..522c0f2f --- /dev/null +++ b/mixs6/migs_org_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_local_scale + + + + +URI: [mixs.vocab:MIGS_org_env_local_scale](https://w3id.org/mixs/vocab/MIGS_org_env_local_scale) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_medium.md b/mixs6/migs_org_env_medium.md new file mode 100644 index 00000000..bd2df2e3 --- /dev/null +++ b/mixs6/migs_org_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_env_medium + + + + +URI: [mixs.vocab:MIGS_org_env_medium](https://w3id.org/mixs/vocab/MIGS_org_env_medium) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_env_package.md b/mixs6/migs_org_env_package.md new file mode 100644 index 00000000..37bce3a7 --- /dev/null +++ b/mixs6/migs_org_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_env_package + + + + +URI: [mixs.vocab:MIGS_org_env_package](https://w3id.org/mixs/vocab/MIGS_org_env_package) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_estimated_size.md b/mixs6/migs_org_estimated_size.md new file mode 100644 index 00000000..42e6877d --- /dev/null +++ b/mixs6/migs_org_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_estimated_size + + + + +URI: [mixs.vocab:MIGS_org_estimated_size](https://w3id.org/mixs/vocab/MIGS_org_estimated_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_experimental_factor.md b/mixs6/migs_org_experimental_factor.md new file mode 100644 index 00000000..df513b32 --- /dev/null +++ b/mixs6/migs_org_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_experimental_factor + + + + +URI: [mixs.vocab:MIGS_org_experimental_factor](https://w3id.org/mixs/vocab/MIGS_org_experimental_factor) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_extrachrom_elements.md b/mixs6/migs_org_extrachrom_elements.md new file mode 100644 index 00000000..c3c07183 --- /dev/null +++ b/mixs6/migs_org_extrachrom_elements.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_extrachrom_elements + + + + +URI: [mixs.vocab:MIGS_org_extrachrom_elements](https://w3id.org/mixs/vocab/MIGS_org_extrachrom_elements) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_feat_pred.md b/mixs6/migs_org_feat_pred.md new file mode 100644 index 00000000..3c781cff --- /dev/null +++ b/mixs6/migs_org_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_feat_pred + + + + +URI: [mixs.vocab:MIGS_org_feat_pred](https://w3id.org/mixs/vocab/MIGS_org_feat_pred) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_geo_loc_name.md b/mixs6/migs_org_geo_loc_name.md new file mode 100644 index 00000000..dc43148f --- /dev/null +++ b/mixs6/migs_org_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_geo_loc_name + + + + +URI: [mixs.vocab:MIGS_org_geo_loc_name](https://w3id.org/mixs/vocab/MIGS_org_geo_loc_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_investigation_type.md b/mixs6/migs_org_investigation_type.md new file mode 100644 index 00000000..e70b04be --- /dev/null +++ b/mixs6/migs_org_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_investigation_type + + + + +URI: [mixs.vocab:MIGS_org_investigation_type](https://w3id.org/mixs/vocab/MIGS_org_investigation_type) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_isol_growth_condt.md b/mixs6/migs_org_isol_growth_condt.md new file mode 100644 index 00000000..aa130ab9 --- /dev/null +++ b/mixs6/migs_org_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_isol_growth_condt + + + + +URI: [mixs.vocab:MIGS_org_isol_growth_condt](https://w3id.org/mixs/vocab/MIGS_org_isol_growth_condt) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lat_lon.md b/mixs6/migs_org_lat_lon.md new file mode 100644 index 00000000..cfad477f --- /dev/null +++ b/mixs6/migs_org_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIGS_org_lat_lon + + + + +URI: [mixs.vocab:MIGS_org_lat_lon](https://w3id.org/mixs/vocab/MIGS_org_lat_lon) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) diff --git a/mixs6/migs_org_lib_layout.md b/mixs6/migs_org_lib_layout.md new file mode 100644 index 00000000..5030e4e2 --- /dev/null +++ b/mixs6/migs_org_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_layout + + + + +URI: [mixs.vocab:MIGS_org_lib_layout](https://w3id.org/mixs/vocab/MIGS_org_lib_layout) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_reads_seqd.md b/mixs6/migs_org_lib_reads_seqd.md new file mode 100644 index 00000000..2297ac3b --- /dev/null +++ b/mixs6/migs_org_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_reads_seqd + + + + +URI: [mixs.vocab:MIGS_org_lib_reads_seqd](https://w3id.org/mixs/vocab/MIGS_org_lib_reads_seqd) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_screen.md b/mixs6/migs_org_lib_screen.md new file mode 100644 index 00000000..e0d119a0 --- /dev/null +++ b/mixs6/migs_org_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_screen + + + + +URI: [mixs.vocab:MIGS_org_lib_screen](https://w3id.org/mixs/vocab/MIGS_org_lib_screen) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_size.md b/mixs6/migs_org_lib_size.md new file mode 100644 index 00000000..67f1bdc9 --- /dev/null +++ b/mixs6/migs_org_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_size + + + + +URI: [mixs.vocab:MIGS_org_lib_size](https://w3id.org/mixs/vocab/MIGS_org_lib_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_lib_vector.md b/mixs6/migs_org_lib_vector.md new file mode 100644 index 00000000..f0bacaf9 --- /dev/null +++ b/mixs6/migs_org_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_lib_vector + + + + +URI: [mixs.vocab:MIGS_org_lib_vector](https://w3id.org/mixs/vocab/MIGS_org_lib_vector) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_nucl_acid_amp.md b/mixs6/migs_org_nucl_acid_amp.md new file mode 100644 index 00000000..c8043784 --- /dev/null +++ b/mixs6/migs_org_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_nucl_acid_amp + + + + +URI: [mixs.vocab:MIGS_org_nucl_acid_amp](https://w3id.org/mixs/vocab/MIGS_org_nucl_acid_amp) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_nucl_acid_ext.md b/mixs6/migs_org_nucl_acid_ext.md new file mode 100644 index 00000000..b429d808 --- /dev/null +++ b/mixs6/migs_org_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_nucl_acid_ext + + + + +URI: [mixs.vocab:MIGS_org_nucl_acid_ext](https://w3id.org/mixs/vocab/MIGS_org_nucl_acid_ext) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_number_contig.md b/mixs6/migs_org_number_contig.md new file mode 100644 index 00000000..57f35064 --- /dev/null +++ b/mixs6/migs_org_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_number_contig + + + + +URI: [mixs.vocab:MIGS_org_number_contig](https://w3id.org/mixs/vocab/MIGS_org_number_contig) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_project_name.md b/mixs6/migs_org_project_name.md new file mode 100644 index 00000000..9fa9c971 --- /dev/null +++ b/mixs6/migs_org_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_project_name + + + + +URI: [mixs.vocab:MIGS_org_project_name](https://w3id.org/mixs/vocab/MIGS_org_project_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_ref_biomaterial.md b/mixs6/migs_org_ref_biomaterial.md new file mode 100644 index 00000000..1d5e8643 --- /dev/null +++ b/mixs6/migs_org_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_ref_biomaterial + + + + +URI: [mixs.vocab:MIGS_org_ref_biomaterial](https://w3id.org/mixs/vocab/MIGS_org_ref_biomaterial) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_ref_db.md b/mixs6/migs_org_ref_db.md new file mode 100644 index 00000000..1c94ff68 --- /dev/null +++ b/mixs6/migs_org_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_ref_db + + + + +URI: [mixs.vocab:MIGS_org_ref_db](https://w3id.org/mixs/vocab/MIGS_org_ref_db) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_samp_collect_device.md b/mixs6/migs_org_samp_collect_device.md new file mode 100644 index 00000000..00baf73d --- /dev/null +++ b/mixs6/migs_org_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_samp_collect_device + + + + +URI: [mixs.vocab:MIGS_org_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_org_samp_collect_device) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_samp_mat_process.md b/mixs6/migs_org_samp_mat_process.md new file mode 100644 index 00000000..ed21c591 --- /dev/null +++ b/mixs6/migs_org_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_samp_mat_process + + + + +URI: [mixs.vocab:MIGS_org_samp_mat_process](https://w3id.org/mixs/vocab/MIGS_org_samp_mat_process) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_samp_size.md b/mixs6/migs_org_samp_size.md new file mode 100644 index 00000000..140213d8 --- /dev/null +++ b/mixs6/migs_org_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_samp_size + + + + +URI: [mixs.vocab:MIGS_org_samp_size](https://w3id.org/mixs/vocab/MIGS_org_samp_size) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sample_name.md b/mixs6/migs_org_sample_name.md new file mode 100644 index 00000000..5e52d127 --- /dev/null +++ b/mixs6/migs_org_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sample_name + + + + +URI: [mixs.vocab:MIGS_org_sample_name](https://w3id.org/mixs/vocab/MIGS_org_sample_name) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_seq_meth.md b/mixs6/migs_org_seq_meth.md new file mode 100644 index 00000000..c242cfa6 --- /dev/null +++ b/mixs6/migs_org_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_seq_meth + + + + +URI: [mixs.vocab:MIGS_org_seq_meth](https://w3id.org/mixs/vocab/MIGS_org_seq_meth) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sim_search_meth.md b/mixs6/migs_org_sim_search_meth.md new file mode 100644 index 00000000..c7853eaf --- /dev/null +++ b/mixs6/migs_org_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sim_search_meth + + + + +URI: [mixs.vocab:MIGS_org_sim_search_meth](https://w3id.org/mixs/vocab/MIGS_org_sim_search_meth) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_sop.md b/mixs6/migs_org_sop.md new file mode 100644 index 00000000..e34c6f3b --- /dev/null +++ b/mixs6/migs_org_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_sop + + + + +URI: [mixs.vocab:MIGS_org_sop](https://w3id.org/mixs/vocab/MIGS_org_sop) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_source_mat_id.md b/mixs6/migs_org_source_mat_id.md new file mode 100644 index 00000000..343e9cc8 --- /dev/null +++ b/mixs6/migs_org_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_source_mat_id + + + + +URI: [mixs.vocab:MIGS_org_source_mat_id](https://w3id.org/mixs/vocab/MIGS_org_source_mat_id) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_submitted_to_insdc.md b/mixs6/migs_org_submitted_to_insdc.md new file mode 100644 index 00000000..29531604 --- /dev/null +++ b/mixs6/migs_org_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_submitted_to_insdc + + + + +URI: [mixs.vocab:MIGS_org_submitted_to_insdc](https://w3id.org/mixs/vocab/MIGS_org_submitted_to_insdc) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_subspecf_gen_lin.md b/mixs6/migs_org_subspecf_gen_lin.md new file mode 100644 index 00000000..2602a635 --- /dev/null +++ b/mixs6/migs_org_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_subspecf_gen_lin + + + + +URI: [mixs.vocab:MIGS_org_subspecf_gen_lin](https://w3id.org/mixs/vocab/MIGS_org_subspecf_gen_lin) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_tax_class.md b/mixs6/migs_org_tax_class.md new file mode 100644 index 00000000..470eac16 --- /dev/null +++ b/mixs6/migs_org_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_tax_class + + + + +URI: [mixs.vocab:MIGS_org_tax_class](https://w3id.org/mixs/vocab/MIGS_org_tax_class) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/migs_org_tax_ident.md b/mixs6/migs_org_tax_ident.md new file mode 100644 index 00000000..d49592dd --- /dev/null +++ b/mixs6/migs_org_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_tax_ident + + + + +URI: [mixs.vocab:MIGS_org_tax_ident](https://w3id.org/mixs/vocab/MIGS_org_tax_ident) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_org_url.md b/mixs6/migs_org_url.md new file mode 100644 index 00000000..c8e99c2c --- /dev/null +++ b/mixs6/migs_org_url.md @@ -0,0 +1,47 @@ + +# Slot: MIGS_org_url + + + + +URI: [mixs.vocab:MIGS_org_url](https://w3id.org/mixs/vocab/MIGS_org_url) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_adapters.md b/mixs6/migs_pl_adapters.md new file mode 100644 index 00000000..944c2422 --- /dev/null +++ b/mixs6/migs_pl_adapters.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_adapters + + + + +URI: [mixs.vocab:migs_pl_adapters](https://w3id.org/mixs/vocab/migs_pl_adapters) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_annot.md b/mixs6/migs_pl_annot.md new file mode 100644 index 00000000..5b3849c4 --- /dev/null +++ b/mixs6/migs_pl_annot.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_annot + + + + +URI: [mixs.vocab:migs_pl_annot](https://w3id.org/mixs/vocab/migs_pl_annot) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_assembly_name.md b/mixs6/migs_pl_assembly_name.md new file mode 100644 index 00000000..ca345509 --- /dev/null +++ b/mixs6/migs_pl_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_assembly_name + + + + +URI: [mixs.vocab:migs_pl_assembly_name](https://w3id.org/mixs/vocab/migs_pl_assembly_name) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_assembly_qual.md b/mixs6/migs_pl_assembly_qual.md new file mode 100644 index 00000000..645db662 --- /dev/null +++ b/mixs6/migs_pl_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_assembly_qual + + + + +URI: [mixs.vocab:migs_pl_assembly_qual](https://w3id.org/mixs/vocab/migs_pl_assembly_qual) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_assembly_software.md b/mixs6/migs_pl_assembly_software.md new file mode 100644 index 00000000..7c4c61af --- /dev/null +++ b/mixs6/migs_pl_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_assembly_software + + + + +URI: [mixs.vocab:migs_pl_assembly_software](https://w3id.org/mixs/vocab/migs_pl_assembly_software) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_collection_date.md b/mixs6/migs_pl_collection_date.md new file mode 100644 index 00000000..58bcba22 --- /dev/null +++ b/mixs6/migs_pl_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_collection_date + + + + +URI: [mixs.vocab:migs_pl_collection_date](https://w3id.org/mixs/vocab/migs_pl_collection_date) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_compl_score.md b/mixs6/migs_pl_compl_score.md new file mode 100644 index 00000000..4bc74c96 --- /dev/null +++ b/mixs6/migs_pl_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_compl_score + + + + +URI: [mixs.vocab:migs_pl_compl_score](https://w3id.org/mixs/vocab/migs_pl_compl_score) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_compl_software.md b/mixs6/migs_pl_compl_software.md new file mode 100644 index 00000000..cfb9b8cb --- /dev/null +++ b/mixs6/migs_pl_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_compl_software + + + + +URI: [mixs.vocab:migs_pl_compl_software](https://w3id.org/mixs/vocab/migs_pl_compl_software) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_encoded_traits.md b/mixs6/migs_pl_encoded_traits.md new file mode 100644 index 00000000..cb56c959 --- /dev/null +++ b/mixs6/migs_pl_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_encoded_traits + + + + +URI: [mixs.vocab:migs_pl_encoded_traits](https://w3id.org/mixs/vocab/migs_pl_encoded_traits) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_env_broad_scale.md b/mixs6/migs_pl_env_broad_scale.md new file mode 100644 index 00000000..cec8b9ee --- /dev/null +++ b/mixs6/migs_pl_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_env_broad_scale + + + + +URI: [mixs.vocab:migs_pl_env_broad_scale](https://w3id.org/mixs/vocab/migs_pl_env_broad_scale) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_local_scale.md b/mixs6/migs_pl_env_local_scale.md new file mode 100644 index 00000000..a0bbfafd --- /dev/null +++ b/mixs6/migs_pl_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_env_local_scale + + + + +URI: [mixs.vocab:migs_pl_env_local_scale](https://w3id.org/mixs/vocab/migs_pl_env_local_scale) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_medium.md b/mixs6/migs_pl_env_medium.md new file mode 100644 index 00000000..470e9c8a --- /dev/null +++ b/mixs6/migs_pl_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_env_medium + + + + +URI: [mixs.vocab:migs_pl_env_medium](https://w3id.org/mixs/vocab/migs_pl_env_medium) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_package.md b/mixs6/migs_pl_env_package.md new file mode 100644 index 00000000..a73e86d9 --- /dev/null +++ b/mixs6/migs_pl_env_package.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_env_package + + + + +URI: [mixs.vocab:migs_pl_env_package](https://w3id.org/mixs/vocab/migs_pl_env_package) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_estimated_size.md b/mixs6/migs_pl_estimated_size.md new file mode 100644 index 00000000..9272d555 --- /dev/null +++ b/mixs6/migs_pl_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_estimated_size + + + + +URI: [mixs.vocab:migs_pl_estimated_size](https://w3id.org/mixs/vocab/migs_pl_estimated_size) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_experimental_factor.md b/mixs6/migs_pl_experimental_factor.md new file mode 100644 index 00000000..f9bc24b9 --- /dev/null +++ b/mixs6/migs_pl_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_experimental_factor + + + + +URI: [mixs.vocab:migs_pl_experimental_factor](https://w3id.org/mixs/vocab/migs_pl_experimental_factor) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_feat_pred.md b/mixs6/migs_pl_feat_pred.md new file mode 100644 index 00000000..96a16907 --- /dev/null +++ b/mixs6/migs_pl_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_feat_pred + + + + +URI: [mixs.vocab:migs_pl_feat_pred](https://w3id.org/mixs/vocab/migs_pl_feat_pred) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_geo_loc_name.md b/mixs6/migs_pl_geo_loc_name.md new file mode 100644 index 00000000..16cea806 --- /dev/null +++ b/mixs6/migs_pl_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_geo_loc_name + + + + +URI: [mixs.vocab:migs_pl_geo_loc_name](https://w3id.org/mixs/vocab/migs_pl_geo_loc_name) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_host_spec_range.md b/mixs6/migs_pl_host_spec_range.md new file mode 100644 index 00000000..3be75f87 --- /dev/null +++ b/mixs6/migs_pl_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_host_spec_range + + + + +URI: [mixs.vocab:migs_pl_host_spec_range](https://w3id.org/mixs/vocab/migs_pl_host_spec_range) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_investigation_type.md b/mixs6/migs_pl_investigation_type.md new file mode 100644 index 00000000..c4a61019 --- /dev/null +++ b/mixs6/migs_pl_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_investigation_type + + + + +URI: [mixs.vocab:migs_pl_investigation_type](https://w3id.org/mixs/vocab/migs_pl_investigation_type) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_isol_growth_condt.md b/mixs6/migs_pl_isol_growth_condt.md new file mode 100644 index 00000000..1d02df0f --- /dev/null +++ b/mixs6/migs_pl_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_isol_growth_condt + + + + +URI: [mixs.vocab:migs_pl_isol_growth_condt](https://w3id.org/mixs/vocab/migs_pl_isol_growth_condt) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lat_lon.md b/mixs6/migs_pl_lat_lon.md new file mode 100644 index 00000000..9734ed6f --- /dev/null +++ b/mixs6/migs_pl_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: migs_pl_lat_lon + + + + +URI: [mixs.vocab:migs_pl_lat_lon](https://w3id.org/mixs/vocab/migs_pl_lat_lon) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_lib_layout.md b/mixs6/migs_pl_lib_layout.md new file mode 100644 index 00000000..86d02d4e --- /dev/null +++ b/mixs6/migs_pl_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_lib_layout + + + + +URI: [mixs.vocab:migs_pl_lib_layout](https://w3id.org/mixs/vocab/migs_pl_lib_layout) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_reads_seqd.md b/mixs6/migs_pl_lib_reads_seqd.md new file mode 100644 index 00000000..22d638a4 --- /dev/null +++ b/mixs6/migs_pl_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_lib_reads_seqd + + + + +URI: [mixs.vocab:migs_pl_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_pl_lib_reads_seqd) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_screen.md b/mixs6/migs_pl_lib_screen.md new file mode 100644 index 00000000..5dadacba --- /dev/null +++ b/mixs6/migs_pl_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_lib_screen + + + + +URI: [mixs.vocab:migs_pl_lib_screen](https://w3id.org/mixs/vocab/migs_pl_lib_screen) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_size.md b/mixs6/migs_pl_lib_size.md new file mode 100644 index 00000000..43e18625 --- /dev/null +++ b/mixs6/migs_pl_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_lib_size + + + + +URI: [mixs.vocab:migs_pl_lib_size](https://w3id.org/mixs/vocab/migs_pl_lib_size) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_vector.md b/mixs6/migs_pl_lib_vector.md new file mode 100644 index 00000000..43c2db4f --- /dev/null +++ b/mixs6/migs_pl_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_lib_vector + + + + +URI: [mixs.vocab:migs_pl_lib_vector](https://w3id.org/mixs/vocab/migs_pl_lib_vector) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_nucl_acid_amp.md b/mixs6/migs_pl_nucl_acid_amp.md new file mode 100644 index 00000000..0d12aac3 --- /dev/null +++ b/mixs6/migs_pl_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_nucl_acid_amp + + + + +URI: [mixs.vocab:migs_pl_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_pl_nucl_acid_amp) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_nucl_acid_ext.md b/mixs6/migs_pl_nucl_acid_ext.md new file mode 100644 index 00000000..a9ced933 --- /dev/null +++ b/mixs6/migs_pl_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_nucl_acid_ext + + + + +URI: [mixs.vocab:migs_pl_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_pl_nucl_acid_ext) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_number_contig.md b/mixs6/migs_pl_number_contig.md new file mode 100644 index 00000000..9d503dda --- /dev/null +++ b/mixs6/migs_pl_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_number_contig + + + + +URI: [mixs.vocab:migs_pl_number_contig](https://w3id.org/mixs/vocab/migs_pl_number_contig) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_project_name.md b/mixs6/migs_pl_project_name.md new file mode 100644 index 00000000..996c6ad3 --- /dev/null +++ b/mixs6/migs_pl_project_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_project_name + + + + +URI: [mixs.vocab:migs_pl_project_name](https://w3id.org/mixs/vocab/migs_pl_project_name) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_propagation.md b/mixs6/migs_pl_propagation.md new file mode 100644 index 00000000..ae2cac79 --- /dev/null +++ b/mixs6/migs_pl_propagation.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_propagation + + + + +URI: [mixs.vocab:migs_pl_propagation](https://w3id.org/mixs/vocab/migs_pl_propagation) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_ref_biomaterial.md b/mixs6/migs_pl_ref_biomaterial.md new file mode 100644 index 00000000..6c766345 --- /dev/null +++ b/mixs6/migs_pl_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_ref_biomaterial + + + + +URI: [mixs.vocab:migs_pl_ref_biomaterial](https://w3id.org/mixs/vocab/migs_pl_ref_biomaterial) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_ref_db.md b/mixs6/migs_pl_ref_db.md new file mode 100644 index 00000000..6de82e45 --- /dev/null +++ b/mixs6/migs_pl_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_ref_db + + + + +URI: [mixs.vocab:migs_pl_ref_db](https://w3id.org/mixs/vocab/migs_pl_ref_db) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_collect_device.md b/mixs6/migs_pl_samp_collect_device.md new file mode 100644 index 00000000..8d164472 --- /dev/null +++ b/mixs6/migs_pl_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_samp_collect_device + + + + +URI: [mixs.vocab:migs_pl_samp_collect_device](https://w3id.org/mixs/vocab/migs_pl_samp_collect_device) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_mat_process.md b/mixs6/migs_pl_samp_mat_process.md new file mode 100644 index 00000000..64420e94 --- /dev/null +++ b/mixs6/migs_pl_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_samp_mat_process + + + + +URI: [mixs.vocab:migs_pl_samp_mat_process](https://w3id.org/mixs/vocab/migs_pl_samp_mat_process) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_size.md b/mixs6/migs_pl_samp_size.md new file mode 100644 index 00000000..a028a032 --- /dev/null +++ b/mixs6/migs_pl_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_samp_size + + + + +URI: [mixs.vocab:migs_pl_samp_size](https://w3id.org/mixs/vocab/migs_pl_samp_size) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sample_name.md b/mixs6/migs_pl_sample_name.md new file mode 100644 index 00000000..7f48e3ee --- /dev/null +++ b/mixs6/migs_pl_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_sample_name + + + + +URI: [mixs.vocab:migs_pl_sample_name](https://w3id.org/mixs/vocab/migs_pl_sample_name) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_seq_meth.md b/mixs6/migs_pl_seq_meth.md new file mode 100644 index 00000000..88490b4d --- /dev/null +++ b/mixs6/migs_pl_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_seq_meth + + + + +URI: [mixs.vocab:migs_pl_seq_meth](https://w3id.org/mixs/vocab/migs_pl_seq_meth) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sim_search_meth.md b/mixs6/migs_pl_sim_search_meth.md new file mode 100644 index 00000000..04219948 --- /dev/null +++ b/mixs6/migs_pl_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_sim_search_meth + + + + +URI: [mixs.vocab:migs_pl_sim_search_meth](https://w3id.org/mixs/vocab/migs_pl_sim_search_meth) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sop.md b/mixs6/migs_pl_sop.md new file mode 100644 index 00000000..b5dc7e06 --- /dev/null +++ b/mixs6/migs_pl_sop.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_sop + + + + +URI: [mixs.vocab:migs_pl_sop](https://w3id.org/mixs/vocab/migs_pl_sop) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_source_mat_id.md b/mixs6/migs_pl_source_mat_id.md new file mode 100644 index 00000000..8db66956 --- /dev/null +++ b/mixs6/migs_pl_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_source_mat_id + + + + +URI: [mixs.vocab:migs_pl_source_mat_id](https://w3id.org/mixs/vocab/migs_pl_source_mat_id) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_specific_host.md b/mixs6/migs_pl_specific_host.md new file mode 100644 index 00000000..9b9051a5 --- /dev/null +++ b/mixs6/migs_pl_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_specific_host + + + + +URI: [mixs.vocab:migs_pl_specific_host](https://w3id.org/mixs/vocab/migs_pl_specific_host) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_submitted_to_insdc.md b/mixs6/migs_pl_submitted_to_insdc.md new file mode 100644 index 00000000..0b12e93d --- /dev/null +++ b/mixs6/migs_pl_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_submitted_to_insdc + + + + +URI: [mixs.vocab:migs_pl_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_pl_submitted_to_insdc) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_subspecf_gen_lin.md b/mixs6/migs_pl_subspecf_gen_lin.md new file mode 100644 index 00000000..15c0df49 --- /dev/null +++ b/mixs6/migs_pl_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_subspecf_gen_lin + + + + +URI: [mixs.vocab:migs_pl_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_pl_subspecf_gen_lin) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_tax_class.md b/mixs6/migs_pl_tax_class.md new file mode 100644 index 00000000..89cb9134 --- /dev/null +++ b/mixs6/migs_pl_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: migs_pl_tax_class + + + + +URI: [mixs.vocab:migs_pl_tax_class](https://w3id.org/mixs/vocab/migs_pl_tax_class) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_tax_ident.md b/mixs6/migs_pl_tax_ident.md new file mode 100644 index 00000000..0f48b229 --- /dev/null +++ b/mixs6/migs_pl_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_tax_ident + + + + +URI: [mixs.vocab:migs_pl_tax_ident](https://w3id.org/mixs/vocab/migs_pl_tax_ident) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_pl_url.md b/mixs6/migs_pl_url.md new file mode 100644 index 00000000..b1bee8c2 --- /dev/null +++ b/mixs6/migs_pl_url.md @@ -0,0 +1,47 @@ + +# Slot: migs_pl_url + + + + +URI: [mixs.vocab:migs_pl_url](https://w3id.org/mixs/vocab/migs_pl_url) + + +## Domain and Range + +[MigsPl](MigsPl.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMigsPl](AirMigsPl.md) + * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) + * [Host-associatedMigsPl](Host-associatedMigsPl.md) + * [Human-associatedMigsPl](Human-associatedMigsPl.md) + * [Human-gutMigsPl](Human-gutMigsPl.md) + * [Human-oralMigsPl](Human-oralMigsPl.md) + * [Human-skinMigsPl](Human-skinMigsPl.md) + * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) + * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) + * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) + * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) + * [MigsPl](MigsPl.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) + * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) + * [SedimentMigsPl](SedimentMigsPl.md) + * [SoilMigsPl](SoilMigsPl.md) + * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) + * [WaterMigsPl](WaterMigsPl.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_adapters.md b/mixs6/migs_vi_adapters.md new file mode 100644 index 00000000..efdf0cb6 --- /dev/null +++ b/mixs6/migs_vi_adapters.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_adapters + + + + +URI: [mixs.vocab:migs_vi_adapters](https://w3id.org/mixs/vocab/migs_vi_adapters) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_annot.md b/mixs6/migs_vi_annot.md new file mode 100644 index 00000000..fb2c3632 --- /dev/null +++ b/mixs6/migs_vi_annot.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_annot + + + + +URI: [mixs.vocab:migs_vi_annot](https://w3id.org/mixs/vocab/migs_vi_annot) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_assembly_name.md b/mixs6/migs_vi_assembly_name.md new file mode 100644 index 00000000..736d5151 --- /dev/null +++ b/mixs6/migs_vi_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_assembly_name + + + + +URI: [mixs.vocab:migs_vi_assembly_name](https://w3id.org/mixs/vocab/migs_vi_assembly_name) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_assembly_qual.md b/mixs6/migs_vi_assembly_qual.md new file mode 100644 index 00000000..5453b781 --- /dev/null +++ b/mixs6/migs_vi_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_assembly_qual + + + + +URI: [mixs.vocab:migs_vi_assembly_qual](https://w3id.org/mixs/vocab/migs_vi_assembly_qual) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_assembly_software.md b/mixs6/migs_vi_assembly_software.md new file mode 100644 index 00000000..87ff40ad --- /dev/null +++ b/mixs6/migs_vi_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_assembly_software + + + + +URI: [mixs.vocab:migs_vi_assembly_software](https://w3id.org/mixs/vocab/migs_vi_assembly_software) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_biotic_relationship.md b/mixs6/migs_vi_biotic_relationship.md new file mode 100644 index 00000000..e721549e --- /dev/null +++ b/mixs6/migs_vi_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_biotic_relationship + + + + +URI: [mixs.vocab:migs_vi_biotic_relationship](https://w3id.org/mixs/vocab/migs_vi_biotic_relationship) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_collection_date.md b/mixs6/migs_vi_collection_date.md new file mode 100644 index 00000000..659f29d4 --- /dev/null +++ b/mixs6/migs_vi_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_collection_date + + + + +URI: [mixs.vocab:migs_vi_collection_date](https://w3id.org/mixs/vocab/migs_vi_collection_date) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_compl_score.md b/mixs6/migs_vi_compl_score.md new file mode 100644 index 00000000..c9b27db7 --- /dev/null +++ b/mixs6/migs_vi_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_compl_score + + + + +URI: [mixs.vocab:migs_vi_compl_score](https://w3id.org/mixs/vocab/migs_vi_compl_score) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_compl_software.md b/mixs6/migs_vi_compl_software.md new file mode 100644 index 00000000..c98a0c06 --- /dev/null +++ b/mixs6/migs_vi_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_compl_software + + + + +URI: [mixs.vocab:migs_vi_compl_software](https://w3id.org/mixs/vocab/migs_vi_compl_software) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_encoded_traits.md b/mixs6/migs_vi_encoded_traits.md new file mode 100644 index 00000000..7d318a7e --- /dev/null +++ b/mixs6/migs_vi_encoded_traits.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_encoded_traits + + + + +URI: [mixs.vocab:migs_vi_encoded_traits](https://w3id.org/mixs/vocab/migs_vi_encoded_traits) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [encoded_traits](encoded_traits.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_env_broad_scale.md b/mixs6/migs_vi_env_broad_scale.md new file mode 100644 index 00000000..90179a66 --- /dev/null +++ b/mixs6/migs_vi_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_env_broad_scale + + + + +URI: [mixs.vocab:migs_vi_env_broad_scale](https://w3id.org/mixs/vocab/migs_vi_env_broad_scale) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_local_scale.md b/mixs6/migs_vi_env_local_scale.md new file mode 100644 index 00000000..b274d51c --- /dev/null +++ b/mixs6/migs_vi_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_env_local_scale + + + + +URI: [mixs.vocab:migs_vi_env_local_scale](https://w3id.org/mixs/vocab/migs_vi_env_local_scale) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_medium.md b/mixs6/migs_vi_env_medium.md new file mode 100644 index 00000000..03d4a7af --- /dev/null +++ b/mixs6/migs_vi_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_env_medium + + + + +URI: [mixs.vocab:migs_vi_env_medium](https://w3id.org/mixs/vocab/migs_vi_env_medium) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_package.md b/mixs6/migs_vi_env_package.md new file mode 100644 index 00000000..e4b1d1e9 --- /dev/null +++ b/mixs6/migs_vi_env_package.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_env_package + + + + +URI: [mixs.vocab:migs_vi_env_package](https://w3id.org/mixs/vocab/migs_vi_env_package) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_estimated_size.md b/mixs6/migs_vi_estimated_size.md new file mode 100644 index 00000000..5aebe8c3 --- /dev/null +++ b/mixs6/migs_vi_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_estimated_size + + + + +URI: [mixs.vocab:migs_vi_estimated_size](https://w3id.org/mixs/vocab/migs_vi_estimated_size) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_experimental_factor.md b/mixs6/migs_vi_experimental_factor.md new file mode 100644 index 00000000..87c4f7ab --- /dev/null +++ b/mixs6/migs_vi_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_experimental_factor + + + + +URI: [mixs.vocab:migs_vi_experimental_factor](https://w3id.org/mixs/vocab/migs_vi_experimental_factor) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_feat_pred.md b/mixs6/migs_vi_feat_pred.md new file mode 100644 index 00000000..e6b3da8f --- /dev/null +++ b/mixs6/migs_vi_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_feat_pred + + + + +URI: [mixs.vocab:migs_vi_feat_pred](https://w3id.org/mixs/vocab/migs_vi_feat_pred) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_geo_loc_name.md b/mixs6/migs_vi_geo_loc_name.md new file mode 100644 index 00000000..e9710dbe --- /dev/null +++ b/mixs6/migs_vi_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_geo_loc_name + + + + +URI: [mixs.vocab:migs_vi_geo_loc_name](https://w3id.org/mixs/vocab/migs_vi_geo_loc_name) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_health_disease_stat.md b/mixs6/migs_vi_health_disease_stat.md new file mode 100644 index 00000000..5fa7d4c5 --- /dev/null +++ b/mixs6/migs_vi_health_disease_stat.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_health_disease_stat + + + + +URI: [mixs.vocab:migs_vi_health_disease_stat](https://w3id.org/mixs/vocab/migs_vi_health_disease_stat) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [health_disease_stat](health_disease_stat.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_host_spec_range.md b/mixs6/migs_vi_host_spec_range.md new file mode 100644 index 00000000..4a5d3190 --- /dev/null +++ b/mixs6/migs_vi_host_spec_range.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_host_spec_range + + + + +URI: [mixs.vocab:migs_vi_host_spec_range](https://w3id.org/mixs/vocab/migs_vi_host_spec_range) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_investigation_type.md b/mixs6/migs_vi_investigation_type.md new file mode 100644 index 00000000..2c56ce70 --- /dev/null +++ b/mixs6/migs_vi_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_investigation_type + + + + +URI: [mixs.vocab:migs_vi_investigation_type](https://w3id.org/mixs/vocab/migs_vi_investigation_type) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_isol_growth_condt.md b/mixs6/migs_vi_isol_growth_condt.md new file mode 100644 index 00000000..13fb2b04 --- /dev/null +++ b/mixs6/migs_vi_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_isol_growth_condt + + + + +URI: [mixs.vocab:migs_vi_isol_growth_condt](https://w3id.org/mixs/vocab/migs_vi_isol_growth_condt) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lat_lon.md b/mixs6/migs_vi_lat_lon.md new file mode 100644 index 00000000..b0e195f1 --- /dev/null +++ b/mixs6/migs_vi_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: migs_vi_lat_lon + + + + +URI: [mixs.vocab:migs_vi_lat_lon](https://w3id.org/mixs/vocab/migs_vi_lat_lon) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_lib_layout.md b/mixs6/migs_vi_lib_layout.md new file mode 100644 index 00000000..2def1775 --- /dev/null +++ b/mixs6/migs_vi_lib_layout.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_lib_layout + + + + +URI: [mixs.vocab:migs_vi_lib_layout](https://w3id.org/mixs/vocab/migs_vi_lib_layout) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_reads_seqd.md b/mixs6/migs_vi_lib_reads_seqd.md new file mode 100644 index 00000000..8a9dfebe --- /dev/null +++ b/mixs6/migs_vi_lib_reads_seqd.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_lib_reads_seqd + + + + +URI: [mixs.vocab:migs_vi_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_vi_lib_reads_seqd) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_screen.md b/mixs6/migs_vi_lib_screen.md new file mode 100644 index 00000000..fd862f04 --- /dev/null +++ b/mixs6/migs_vi_lib_screen.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_lib_screen + + + + +URI: [mixs.vocab:migs_vi_lib_screen](https://w3id.org/mixs/vocab/migs_vi_lib_screen) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_size.md b/mixs6/migs_vi_lib_size.md new file mode 100644 index 00000000..df2b6dce --- /dev/null +++ b/mixs6/migs_vi_lib_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_lib_size + + + + +URI: [mixs.vocab:migs_vi_lib_size](https://w3id.org/mixs/vocab/migs_vi_lib_size) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_vector.md b/mixs6/migs_vi_lib_vector.md new file mode 100644 index 00000000..24de264c --- /dev/null +++ b/mixs6/migs_vi_lib_vector.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_lib_vector + + + + +URI: [mixs.vocab:migs_vi_lib_vector](https://w3id.org/mixs/vocab/migs_vi_lib_vector) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_nucl_acid_amp.md b/mixs6/migs_vi_nucl_acid_amp.md new file mode 100644 index 00000000..fd54de7e --- /dev/null +++ b/mixs6/migs_vi_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_nucl_acid_amp + + + + +URI: [mixs.vocab:migs_vi_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_vi_nucl_acid_amp) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_nucl_acid_ext.md b/mixs6/migs_vi_nucl_acid_ext.md new file mode 100644 index 00000000..a00e5ede --- /dev/null +++ b/mixs6/migs_vi_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_nucl_acid_ext + + + + +URI: [mixs.vocab:migs_vi_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_vi_nucl_acid_ext) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_num_replicons.md b/mixs6/migs_vi_num_replicons.md new file mode 100644 index 00000000..5e6749b2 --- /dev/null +++ b/mixs6/migs_vi_num_replicons.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_num_replicons + + + + +URI: [mixs.vocab:migs_vi_num_replicons](https://w3id.org/mixs/vocab/migs_vi_num_replicons) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [num_replicons](num_replicons.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_number_contig.md b/mixs6/migs_vi_number_contig.md new file mode 100644 index 00000000..82e79e12 --- /dev/null +++ b/mixs6/migs_vi_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_number_contig + + + + +URI: [mixs.vocab:migs_vi_number_contig](https://w3id.org/mixs/vocab/migs_vi_number_contig) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_pathogenicity.md b/mixs6/migs_vi_pathogenicity.md new file mode 100644 index 00000000..0a9e7b93 --- /dev/null +++ b/mixs6/migs_vi_pathogenicity.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_pathogenicity + + + + +URI: [mixs.vocab:migs_vi_pathogenicity](https://w3id.org/mixs/vocab/migs_vi_pathogenicity) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_project_name.md b/mixs6/migs_vi_project_name.md new file mode 100644 index 00000000..b0315090 --- /dev/null +++ b/mixs6/migs_vi_project_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_project_name + + + + +URI: [mixs.vocab:migs_vi_project_name](https://w3id.org/mixs/vocab/migs_vi_project_name) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_propagation.md b/mixs6/migs_vi_propagation.md new file mode 100644 index 00000000..4ff00178 --- /dev/null +++ b/mixs6/migs_vi_propagation.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_propagation + + + + +URI: [mixs.vocab:migs_vi_propagation](https://w3id.org/mixs/vocab/migs_vi_propagation) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [propagation](propagation.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_ref_biomaterial.md b/mixs6/migs_vi_ref_biomaterial.md new file mode 100644 index 00000000..e19d83fa --- /dev/null +++ b/mixs6/migs_vi_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_ref_biomaterial + + + + +URI: [mixs.vocab:migs_vi_ref_biomaterial](https://w3id.org/mixs/vocab/migs_vi_ref_biomaterial) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_ref_db.md b/mixs6/migs_vi_ref_db.md new file mode 100644 index 00000000..a91a4e21 --- /dev/null +++ b/mixs6/migs_vi_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_ref_db + + + + +URI: [mixs.vocab:migs_vi_ref_db](https://w3id.org/mixs/vocab/migs_vi_ref_db) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_collect_device.md b/mixs6/migs_vi_samp_collect_device.md new file mode 100644 index 00000000..fdc01030 --- /dev/null +++ b/mixs6/migs_vi_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_samp_collect_device + + + + +URI: [mixs.vocab:migs_vi_samp_collect_device](https://w3id.org/mixs/vocab/migs_vi_samp_collect_device) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_mat_process.md b/mixs6/migs_vi_samp_mat_process.md new file mode 100644 index 00000000..d67bdf69 --- /dev/null +++ b/mixs6/migs_vi_samp_mat_process.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_samp_mat_process + + + + +URI: [mixs.vocab:migs_vi_samp_mat_process](https://w3id.org/mixs/vocab/migs_vi_samp_mat_process) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_size.md b/mixs6/migs_vi_samp_size.md new file mode 100644 index 00000000..cc7cc740 --- /dev/null +++ b/mixs6/migs_vi_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_samp_size + + + + +URI: [mixs.vocab:migs_vi_samp_size](https://w3id.org/mixs/vocab/migs_vi_samp_size) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sample_name.md b/mixs6/migs_vi_sample_name.md new file mode 100644 index 00000000..29ac0ecf --- /dev/null +++ b/mixs6/migs_vi_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_sample_name + + + + +URI: [mixs.vocab:migs_vi_sample_name](https://w3id.org/mixs/vocab/migs_vi_sample_name) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_seq_meth.md b/mixs6/migs_vi_seq_meth.md new file mode 100644 index 00000000..2eff2c0e --- /dev/null +++ b/mixs6/migs_vi_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_seq_meth + + + + +URI: [mixs.vocab:migs_vi_seq_meth](https://w3id.org/mixs/vocab/migs_vi_seq_meth) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sim_search_meth.md b/mixs6/migs_vi_sim_search_meth.md new file mode 100644 index 00000000..1ce26ef0 --- /dev/null +++ b/mixs6/migs_vi_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_sim_search_meth + + + + +URI: [mixs.vocab:migs_vi_sim_search_meth](https://w3id.org/mixs/vocab/migs_vi_sim_search_meth) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sop.md b/mixs6/migs_vi_sop.md new file mode 100644 index 00000000..4698f009 --- /dev/null +++ b/mixs6/migs_vi_sop.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_sop + + + + +URI: [mixs.vocab:migs_vi_sop](https://w3id.org/mixs/vocab/migs_vi_sop) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_source_mat_id.md b/mixs6/migs_vi_source_mat_id.md new file mode 100644 index 00000000..473569c4 --- /dev/null +++ b/mixs6/migs_vi_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_source_mat_id + + + + +URI: [mixs.vocab:migs_vi_source_mat_id](https://w3id.org/mixs/vocab/migs_vi_source_mat_id) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_specific_host.md b/mixs6/migs_vi_specific_host.md new file mode 100644 index 00000000..9028a162 --- /dev/null +++ b/mixs6/migs_vi_specific_host.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_specific_host + + + + +URI: [mixs.vocab:migs_vi_specific_host](https://w3id.org/mixs/vocab/migs_vi_specific_host) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_submitted_to_insdc.md b/mixs6/migs_vi_submitted_to_insdc.md new file mode 100644 index 00000000..59d3c3e4 --- /dev/null +++ b/mixs6/migs_vi_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_submitted_to_insdc + + + + +URI: [mixs.vocab:migs_vi_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_vi_submitted_to_insdc) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_subspecf_gen_lin.md b/mixs6/migs_vi_subspecf_gen_lin.md new file mode 100644 index 00000000..c9b3d5ee --- /dev/null +++ b/mixs6/migs_vi_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_subspecf_gen_lin + + + + +URI: [mixs.vocab:migs_vi_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_vi_subspecf_gen_lin) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_tax_class.md b/mixs6/migs_vi_tax_class.md new file mode 100644 index 00000000..0faa9072 --- /dev/null +++ b/mixs6/migs_vi_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: migs_vi_tax_class + + + + +URI: [mixs.vocab:migs_vi_tax_class](https://w3id.org/mixs/vocab/migs_vi_tax_class) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_tax_ident.md b/mixs6/migs_vi_tax_ident.md new file mode 100644 index 00000000..2fc7500b --- /dev/null +++ b/mixs6/migs_vi_tax_ident.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_tax_ident + + + + +URI: [mixs.vocab:migs_vi_tax_ident](https://w3id.org/mixs/vocab/migs_vi_tax_ident) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_url.md b/mixs6/migs_vi_url.md new file mode 100644 index 00000000..dcf986ec --- /dev/null +++ b/mixs6/migs_vi_url.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_url + + + + +URI: [mixs.vocab:migs_vi_url](https://w3id.org/mixs/vocab/migs_vi_url) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/migs_vi_virus_enrich_appr.md b/mixs6/migs_vi_virus_enrich_appr.md new file mode 100644 index 00000000..83390996 --- /dev/null +++ b/mixs6/migs_vi_virus_enrich_appr.md @@ -0,0 +1,47 @@ + +# Slot: migs_vi_virus_enrich_appr + + + + +URI: [mixs.vocab:migs_vi_virus_enrich_appr](https://w3id.org/mixs/vocab/migs_vi_virus_enrich_appr) + + +## Domain and Range + +[MigsVi](MigsVi.md) -> OPT + +## Parents + + * is_a: [virus_enrich_appr](virus_enrich_appr.md) + +## Children + + +## Used by + + * [AirMigsVi](AirMigsVi.md) + * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) + * [Host-associatedMigsVi](Host-associatedMigsVi.md) + * [Human-associatedMigsVi](Human-associatedMigsVi.md) + * [Human-gutMigsVi](Human-gutMigsVi.md) + * [Human-oralMigsVi](Human-oralMigsVi.md) + * [Human-skinMigsVi](Human-skinMigsVi.md) + * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) + * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) + * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) + * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) + * [MigsVi](MigsVi.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) + * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) + * [SedimentMigsVi](SedimentMigsVi.md) + * [SoilMigsVi](SoilMigsVi.md) + * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) + * [WaterMigsVi](WaterMigsVi.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_adapters.md b/mixs6/mimag_adapters.md new file mode 100644 index 00000000..d90e0432 --- /dev/null +++ b/mixs6/mimag_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_adapters + + + + +URI: [mixs.vocab:MIMAG_adapters](https://w3id.org/mixs/vocab/MIMAG_adapters) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_annot.md b/mixs6/mimag_annot.md new file mode 100644 index 00000000..8624758f --- /dev/null +++ b/mixs6/mimag_annot.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_annot + + + + +URI: [mixs.vocab:MIMAG_annot](https://w3id.org/mixs/vocab/MIMAG_annot) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_assembly_name.md b/mixs6/mimag_assembly_name.md new file mode 100644 index 00000000..8edc97de --- /dev/null +++ b/mixs6/mimag_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_assembly_name + + + + +URI: [mixs.vocab:MIMAG_assembly_name](https://w3id.org/mixs/vocab/MIMAG_assembly_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_assembly_qual.md b/mixs6/mimag_assembly_qual.md new file mode 100644 index 00000000..274945a1 --- /dev/null +++ b/mixs6/mimag_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_assembly_qual + + + + +URI: [mixs.vocab:MIMAG_assembly_qual](https://w3id.org/mixs/vocab/MIMAG_assembly_qual) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_assembly_software.md b/mixs6/mimag_assembly_software.md new file mode 100644 index 00000000..2d3f8b61 --- /dev/null +++ b/mixs6/mimag_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_assembly_software + + + + +URI: [mixs.vocab:MIMAG_assembly_software](https://w3id.org/mixs/vocab/MIMAG_assembly_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_bin_param.md b/mixs6/mimag_bin_param.md new file mode 100644 index 00000000..ee267096 --- /dev/null +++ b/mixs6/mimag_bin_param.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_bin_param + + + + +URI: [mixs.vocab:MIMAG_bin_param](https://w3id.org/mixs/vocab/MIMAG_bin_param) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [bin_param](bin_param.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_bin_software.md b/mixs6/mimag_bin_software.md new file mode 100644 index 00000000..d72ad7be --- /dev/null +++ b/mixs6/mimag_bin_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_bin_software + + + + +URI: [mixs.vocab:MIMAG_bin_software](https://w3id.org/mixs/vocab/MIMAG_bin_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [bin_software](bin_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_collection_date.md b/mixs6/mimag_collection_date.md new file mode 100644 index 00000000..e5500089 --- /dev/null +++ b/mixs6/mimag_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_collection_date + + + + +URI: [mixs.vocab:MIMAG_collection_date](https://w3id.org/mixs/vocab/MIMAG_collection_date) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_compl_appr.md b/mixs6/mimag_compl_appr.md new file mode 100644 index 00000000..cdf87307 --- /dev/null +++ b/mixs6/mimag_compl_appr.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_appr + + + + +URI: [mixs.vocab:MIMAG_compl_appr](https://w3id.org/mixs/vocab/MIMAG_compl_appr) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_compl_score.md b/mixs6/mimag_compl_score.md new file mode 100644 index 00000000..6faad65d --- /dev/null +++ b/mixs6/mimag_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_score + + + + +URI: [mixs.vocab:MIMAG_compl_score](https://w3id.org/mixs/vocab/MIMAG_compl_score) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_compl_software.md b/mixs6/mimag_compl_software.md new file mode 100644 index 00000000..4f7ef72b --- /dev/null +++ b/mixs6/mimag_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_compl_software + + + + +URI: [mixs.vocab:MIMAG_compl_software](https://w3id.org/mixs/vocab/MIMAG_compl_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_score.md b/mixs6/mimag_contam_score.md new file mode 100644 index 00000000..f6e043e5 --- /dev/null +++ b/mixs6/mimag_contam_score.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_score + + + + +URI: [mixs.vocab:MIMAG_contam_score](https://w3id.org/mixs/vocab/MIMAG_contam_score) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [contam_score](contam_score.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_screen_input.md b/mixs6/mimag_contam_screen_input.md new file mode 100644 index 00000000..2ae01980 --- /dev/null +++ b/mixs6/mimag_contam_screen_input.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_screen_input + + + + +URI: [mixs.vocab:MIMAG_contam_screen_input](https://w3id.org/mixs/vocab/MIMAG_contam_screen_input) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [contam_screen_input](contam_screen_input.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_contam_screen_param.md b/mixs6/mimag_contam_screen_param.md new file mode 100644 index 00000000..5ff87855 --- /dev/null +++ b/mixs6/mimag_contam_screen_param.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_contam_screen_param + + + + +URI: [mixs.vocab:MIMAG_contam_screen_param](https://w3id.org/mixs/vocab/MIMAG_contam_screen_param) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [contam_screen_param](contam_screen_param.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_decontam_software.md b/mixs6/mimag_decontam_software.md new file mode 100644 index 00000000..b94187ce --- /dev/null +++ b/mixs6/mimag_decontam_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_decontam_software + + + + +URI: [mixs.vocab:MIMAG_decontam_software](https://w3id.org/mixs/vocab/MIMAG_decontam_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [decontam_software](decontam_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_env_broad_scale.md b/mixs6/mimag_env_broad_scale.md new file mode 100644 index 00000000..91939812 --- /dev/null +++ b/mixs6/mimag_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_broad_scale + + + + +URI: [mixs.vocab:MIMAG_env_broad_scale](https://w3id.org/mixs/vocab/MIMAG_env_broad_scale) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_local_scale.md b/mixs6/mimag_env_local_scale.md new file mode 100644 index 00000000..80017ddc --- /dev/null +++ b/mixs6/mimag_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_local_scale + + + + +URI: [mixs.vocab:MIMAG_env_local_scale](https://w3id.org/mixs/vocab/MIMAG_env_local_scale) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_medium.md b/mixs6/mimag_env_medium.md new file mode 100644 index 00000000..13770f6a --- /dev/null +++ b/mixs6/mimag_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_env_medium + + + + +URI: [mixs.vocab:MIMAG_env_medium](https://w3id.org/mixs/vocab/MIMAG_env_medium) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_env_package.md b/mixs6/mimag_env_package.md new file mode 100644 index 00000000..8e7d6506 --- /dev/null +++ b/mixs6/mimag_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_env_package + + + + +URI: [mixs.vocab:MIMAG_env_package](https://w3id.org/mixs/vocab/MIMAG_env_package) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_experimental_factor.md b/mixs6/mimag_experimental_factor.md new file mode 100644 index 00000000..58c230d9 --- /dev/null +++ b/mixs6/mimag_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_experimental_factor + + + + +URI: [mixs.vocab:MIMAG_experimental_factor](https://w3id.org/mixs/vocab/MIMAG_experimental_factor) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_feat_pred.md b/mixs6/mimag_feat_pred.md new file mode 100644 index 00000000..ab41ee9c --- /dev/null +++ b/mixs6/mimag_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_feat_pred + + + + +URI: [mixs.vocab:MIMAG_feat_pred](https://w3id.org/mixs/vocab/MIMAG_feat_pred) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_geo_loc_name.md b/mixs6/mimag_geo_loc_name.md new file mode 100644 index 00000000..690a20c6 --- /dev/null +++ b/mixs6/mimag_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_geo_loc_name + + + + +URI: [mixs.vocab:MIMAG_geo_loc_name](https://w3id.org/mixs/vocab/MIMAG_geo_loc_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_investigation_type.md b/mixs6/mimag_investigation_type.md new file mode 100644 index 00000000..0cb1b3f6 --- /dev/null +++ b/mixs6/mimag_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_investigation_type + + + + +URI: [mixs.vocab:MIMAG_investigation_type](https://w3id.org/mixs/vocab/MIMAG_investigation_type) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_lat_lon.md b/mixs6/mimag_lat_lon.md new file mode 100644 index 00000000..97658751 --- /dev/null +++ b/mixs6/mimag_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIMAG_lat_lon + + + + +URI: [mixs.vocab:MIMAG_lat_lon](https://w3id.org/mixs/vocab/MIMAG_lat_lon) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) diff --git a/mixs6/mimag_lib_layout.md b/mixs6/mimag_lib_layout.md new file mode 100644 index 00000000..44e094cc --- /dev/null +++ b/mixs6/mimag_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_layout + + + + +URI: [mixs.vocab:MIMAG_lib_layout](https://w3id.org/mixs/vocab/MIMAG_lib_layout) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_reads_seqd.md b/mixs6/mimag_lib_reads_seqd.md new file mode 100644 index 00000000..88d873ce --- /dev/null +++ b/mixs6/mimag_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_reads_seqd + + + + +URI: [mixs.vocab:MIMAG_lib_reads_seqd](https://w3id.org/mixs/vocab/MIMAG_lib_reads_seqd) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_screen.md b/mixs6/mimag_lib_screen.md new file mode 100644 index 00000000..4ffa0d3d --- /dev/null +++ b/mixs6/mimag_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_screen + + + + +URI: [mixs.vocab:MIMAG_lib_screen](https://w3id.org/mixs/vocab/MIMAG_lib_screen) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_size.md b/mixs6/mimag_lib_size.md new file mode 100644 index 00000000..1f42fc15 --- /dev/null +++ b/mixs6/mimag_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_size + + + + +URI: [mixs.vocab:MIMAG_lib_size](https://w3id.org/mixs/vocab/MIMAG_lib_size) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_lib_vector.md b/mixs6/mimag_lib_vector.md new file mode 100644 index 00000000..58c1635a --- /dev/null +++ b/mixs6/mimag_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_lib_vector + + + + +URI: [mixs.vocab:MIMAG_lib_vector](https://w3id.org/mixs/vocab/MIMAG_lib_vector) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_mag_cov_software.md b/mixs6/mimag_mag_cov_software.md new file mode 100644 index 00000000..6ddb533a --- /dev/null +++ b/mixs6/mimag_mag_cov_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_mag_cov_software + + + + +URI: [mixs.vocab:MIMAG_mag_cov_software](https://w3id.org/mixs/vocab/MIMAG_mag_cov_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [mag_cov_software](mag_cov_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_mid.md b/mixs6/mimag_mid.md new file mode 100644 index 00000000..4c92bcec --- /dev/null +++ b/mixs6/mimag_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_mid + + + + +URI: [mixs.vocab:MIMAG_mid](https://w3id.org/mixs/vocab/MIMAG_mid) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_nucl_acid_amp.md b/mixs6/mimag_nucl_acid_amp.md new file mode 100644 index 00000000..56cde0a8 --- /dev/null +++ b/mixs6/mimag_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_nucl_acid_amp + + + + +URI: [mixs.vocab:MIMAG_nucl_acid_amp](https://w3id.org/mixs/vocab/MIMAG_nucl_acid_amp) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_nucl_acid_ext.md b/mixs6/mimag_nucl_acid_ext.md new file mode 100644 index 00000000..ef861b55 --- /dev/null +++ b/mixs6/mimag_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_nucl_acid_ext + + + + +URI: [mixs.vocab:MIMAG_nucl_acid_ext](https://w3id.org/mixs/vocab/MIMAG_nucl_acid_ext) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_number_contig.md b/mixs6/mimag_number_contig.md new file mode 100644 index 00000000..fd13378b --- /dev/null +++ b/mixs6/mimag_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_number_contig + + + + +URI: [mixs.vocab:MIMAG_number_contig](https://w3id.org/mixs/vocab/MIMAG_number_contig) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_project_name.md b/mixs6/mimag_project_name.md new file mode 100644 index 00000000..291c914e --- /dev/null +++ b/mixs6/mimag_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_project_name + + + + +URI: [mixs.vocab:MIMAG_project_name](https://w3id.org/mixs/vocab/MIMAG_project_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_reassembly_bin.md b/mixs6/mimag_reassembly_bin.md new file mode 100644 index 00000000..4191fc58 --- /dev/null +++ b/mixs6/mimag_reassembly_bin.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_reassembly_bin + + + + +URI: [mixs.vocab:MIMAG_reassembly_bin](https://w3id.org/mixs/vocab/MIMAG_reassembly_bin) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [reassembly_bin](reassembly_bin.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_ref_biomaterial.md b/mixs6/mimag_ref_biomaterial.md new file mode 100644 index 00000000..0468abf3 --- /dev/null +++ b/mixs6/mimag_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_ref_biomaterial + + + + +URI: [mixs.vocab:MIMAG_ref_biomaterial](https://w3id.org/mixs/vocab/MIMAG_ref_biomaterial) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_ref_db.md b/mixs6/mimag_ref_db.md new file mode 100644 index 00000000..c4c48b1e --- /dev/null +++ b/mixs6/mimag_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_ref_db + + + + +URI: [mixs.vocab:MIMAG_ref_db](https://w3id.org/mixs/vocab/MIMAG_ref_db) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_rel_to_oxygen.md b/mixs6/mimag_rel_to_oxygen.md new file mode 100644 index 00000000..3d4cf051 --- /dev/null +++ b/mixs6/mimag_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_rel_to_oxygen + + + + +URI: [mixs.vocab:MIMAG_rel_to_oxygen](https://w3id.org/mixs/vocab/MIMAG_rel_to_oxygen) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_samp_collect_device.md b/mixs6/mimag_samp_collect_device.md new file mode 100644 index 00000000..ef2d4b48 --- /dev/null +++ b/mixs6/mimag_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_samp_collect_device + + + + +URI: [mixs.vocab:MIMAG_samp_collect_device](https://w3id.org/mixs/vocab/MIMAG_samp_collect_device) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_samp_mat_process.md b/mixs6/mimag_samp_mat_process.md new file mode 100644 index 00000000..a758e129 --- /dev/null +++ b/mixs6/mimag_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_samp_mat_process + + + + +URI: [mixs.vocab:MIMAG_samp_mat_process](https://w3id.org/mixs/vocab/MIMAG_samp_mat_process) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_samp_size.md b/mixs6/mimag_samp_size.md new file mode 100644 index 00000000..2adf058f --- /dev/null +++ b/mixs6/mimag_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_samp_size + + + + +URI: [mixs.vocab:MIMAG_samp_size](https://w3id.org/mixs/vocab/MIMAG_samp_size) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_sample_name.md b/mixs6/mimag_sample_name.md new file mode 100644 index 00000000..a73fa25e --- /dev/null +++ b/mixs6/mimag_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_sample_name + + + + +URI: [mixs.vocab:MIMAG_sample_name](https://w3id.org/mixs/vocab/MIMAG_sample_name) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_seq_meth.md b/mixs6/mimag_seq_meth.md new file mode 100644 index 00000000..ec64f504 --- /dev/null +++ b/mixs6/mimag_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_seq_meth + + + + +URI: [mixs.vocab:MIMAG_seq_meth](https://w3id.org/mixs/vocab/MIMAG_seq_meth) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_sim_search_meth.md b/mixs6/mimag_sim_search_meth.md new file mode 100644 index 00000000..5be7e7fb --- /dev/null +++ b/mixs6/mimag_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_sim_search_meth + + + + +URI: [mixs.vocab:MIMAG_sim_search_meth](https://w3id.org/mixs/vocab/MIMAG_sim_search_meth) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_size_frac.md b/mixs6/mimag_size_frac.md new file mode 100644 index 00000000..0c8fcd9f --- /dev/null +++ b/mixs6/mimag_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_size_frac + + + + +URI: [mixs.vocab:MIMAG_size_frac](https://w3id.org/mixs/vocab/MIMAG_size_frac) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_sop.md b/mixs6/mimag_sop.md new file mode 100644 index 00000000..0ae6cf9f --- /dev/null +++ b/mixs6/mimag_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_sop + + + + +URI: [mixs.vocab:MIMAG_sop](https://w3id.org/mixs/vocab/MIMAG_sop) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_source_mat_id.md b/mixs6/mimag_source_mat_id.md new file mode 100644 index 00000000..790c66f4 --- /dev/null +++ b/mixs6/mimag_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_source_mat_id + + + + +URI: [mixs.vocab:MIMAG_source_mat_id](https://w3id.org/mixs/vocab/MIMAG_source_mat_id) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_submitted_to_insdc.md b/mixs6/mimag_submitted_to_insdc.md new file mode 100644 index 00000000..5836d4df --- /dev/null +++ b/mixs6/mimag_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_submitted_to_insdc + + + + +URI: [mixs.vocab:MIMAG_submitted_to_insdc](https://w3id.org/mixs/vocab/MIMAG_submitted_to_insdc) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_tax_class.md b/mixs6/mimag_tax_class.md new file mode 100644 index 00000000..41614da2 --- /dev/null +++ b/mixs6/mimag_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_tax_class + + + + +URI: [mixs.vocab:MIMAG_tax_class](https://w3id.org/mixs/vocab/MIMAG_tax_class) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_tax_ident.md b/mixs6/mimag_tax_ident.md new file mode 100644 index 00000000..c7c8aafc --- /dev/null +++ b/mixs6/mimag_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_tax_ident + + + + +URI: [mixs.vocab:MIMAG_tax_ident](https://w3id.org/mixs/vocab/MIMAG_tax_ident) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> REQ + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_trna_ext_software.md b/mixs6/mimag_trna_ext_software.md new file mode 100644 index 00000000..0e27d2f6 --- /dev/null +++ b/mixs6/mimag_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_trna_ext_software + + + + +URI: [mixs.vocab:MIMAG_trna_ext_software](https://w3id.org/mixs/vocab/MIMAG_trna_ext_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_trnas.md b/mixs6/mimag_trnas.md new file mode 100644 index 00000000..1a83a531 --- /dev/null +++ b/mixs6/mimag_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_trnas + + + + +URI: [mixs.vocab:MIMAG_trnas](https://w3id.org/mixs/vocab/MIMAG_trnas) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_url.md b/mixs6/mimag_url.md new file mode 100644 index 00000000..6e717ccd --- /dev/null +++ b/mixs6/mimag_url.md @@ -0,0 +1,47 @@ + +# Slot: MIMAG_url + + + + +URI: [mixs.vocab:MIMAG_url](https://w3id.org/mixs/vocab/MIMAG_url) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimag_x_16s_recover.md b/mixs6/mimag_x_16s_recover.md new file mode 100644 index 00000000..59935b76 --- /dev/null +++ b/mixs6/mimag_x_16s_recover.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_x_16s_recover + + + + +URI: [mixs.vocab:MIMAG_x_16s_recover](https://w3id.org/mixs/vocab/MIMAG_x_16s_recover) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover](x_16s_recover.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimag_x_16s_recover_software.md b/mixs6/mimag_x_16s_recover_software.md new file mode 100644 index 00000000..3b488185 --- /dev/null +++ b/mixs6/mimag_x_16s_recover_software.md @@ -0,0 +1,40 @@ + +# Slot: MIMAG_x_16s_recover_software + + + + +URI: [mixs.vocab:MIMAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MIMAG_x_16s_recover_software) + + +## Domain and Range + +[MIMAG](MIMAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover_software](x_16s_recover_software.md) + +## Children + + +## Used by + + * [MIMAG](MIMAG.md) + * [AirMIMAG](AirMIMAG.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SoilMIMAG](SoilMIMAG.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WaterMIMAG](WaterMIMAG.md) diff --git a/mixs6/mimarks_c_biotic_relationship.md b/mixs6/mimarks_c_biotic_relationship.md new file mode 100644 index 00000000..9350b59f --- /dev/null +++ b/mixs6/mimarks_c_biotic_relationship.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_biotic_relationship + + + + +URI: [mixs.vocab:mimarks_c_biotic_relationship](https://w3id.org/mixs/vocab/mimarks_c_biotic_relationship) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_chimera_check.md b/mixs6/mimarks_c_chimera_check.md new file mode 100644 index 00000000..8acfe8fa --- /dev/null +++ b/mixs6/mimarks_c_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_chimera_check + + + + +URI: [mixs.vocab:mimarks_c_chimera_check](https://w3id.org/mixs/vocab/mimarks_c_chimera_check) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_collection_date.md b/mixs6/mimarks_c_collection_date.md new file mode 100644 index 00000000..1d90d71d --- /dev/null +++ b/mixs6/mimarks_c_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_collection_date + + + + +URI: [mixs.vocab:mimarks_c_collection_date](https://w3id.org/mixs/vocab/mimarks_c_collection_date) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_broad_scale.md b/mixs6/mimarks_c_env_broad_scale.md new file mode 100644 index 00000000..5df4a781 --- /dev/null +++ b/mixs6/mimarks_c_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_env_broad_scale + + + + +URI: [mixs.vocab:mimarks_c_env_broad_scale](https://w3id.org/mixs/vocab/mimarks_c_env_broad_scale) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_local_scale.md b/mixs6/mimarks_c_env_local_scale.md new file mode 100644 index 00000000..efa8b90c --- /dev/null +++ b/mixs6/mimarks_c_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_env_local_scale + + + + +URI: [mixs.vocab:mimarks_c_env_local_scale](https://w3id.org/mixs/vocab/mimarks_c_env_local_scale) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_medium.md b/mixs6/mimarks_c_env_medium.md new file mode 100644 index 00000000..1249b0d5 --- /dev/null +++ b/mixs6/mimarks_c_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_env_medium + + + + +URI: [mixs.vocab:mimarks_c_env_medium](https://w3id.org/mixs/vocab/mimarks_c_env_medium) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_package.md b/mixs6/mimarks_c_env_package.md new file mode 100644 index 00000000..ebf7d669 --- /dev/null +++ b/mixs6/mimarks_c_env_package.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_env_package + + + + +URI: [mixs.vocab:mimarks_c_env_package](https://w3id.org/mixs/vocab/mimarks_c_env_package) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_experimental_factor.md b/mixs6/mimarks_c_experimental_factor.md new file mode 100644 index 00000000..f00839f8 --- /dev/null +++ b/mixs6/mimarks_c_experimental_factor.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_experimental_factor + + + + +URI: [mixs.vocab:mimarks_c_experimental_factor](https://w3id.org/mixs/vocab/mimarks_c_experimental_factor) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_extrachrom_elements.md b/mixs6/mimarks_c_extrachrom_elements.md new file mode 100644 index 00000000..6fd2d180 --- /dev/null +++ b/mixs6/mimarks_c_extrachrom_elements.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_extrachrom_elements + + + + +URI: [mixs.vocab:mimarks_c_extrachrom_elements](https://w3id.org/mixs/vocab/mimarks_c_extrachrom_elements) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [extrachrom_elements](extrachrom_elements.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_geo_loc_name.md b/mixs6/mimarks_c_geo_loc_name.md new file mode 100644 index 00000000..bbd3cef2 --- /dev/null +++ b/mixs6/mimarks_c_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_geo_loc_name + + + + +URI: [mixs.vocab:mimarks_c_geo_loc_name](https://w3id.org/mixs/vocab/mimarks_c_geo_loc_name) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_investigation_type.md b/mixs6/mimarks_c_investigation_type.md new file mode 100644 index 00000000..e5f4009c --- /dev/null +++ b/mixs6/mimarks_c_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_investigation_type + + + + +URI: [mixs.vocab:mimarks_c_investigation_type](https://w3id.org/mixs/vocab/mimarks_c_investigation_type) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_isol_growth_condt.md b/mixs6/mimarks_c_isol_growth_condt.md new file mode 100644 index 00000000..32f03ddb --- /dev/null +++ b/mixs6/mimarks_c_isol_growth_condt.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_isol_growth_condt + + + + +URI: [mixs.vocab:mimarks_c_isol_growth_condt](https://w3id.org/mixs/vocab/mimarks_c_isol_growth_condt) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [isol_growth_condt](isol_growth_condt.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_lat_lon.md b/mixs6/mimarks_c_lat_lon.md new file mode 100644 index 00000000..18d53c49 --- /dev/null +++ b/mixs6/mimarks_c_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_c_lat_lon + + + + +URI: [mixs.vocab:mimarks_c_lat_lon](https://w3id.org/mixs/vocab/mimarks_c_lat_lon) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_nucl_acid_amp.md b/mixs6/mimarks_c_nucl_acid_amp.md new file mode 100644 index 00000000..188f89f7 --- /dev/null +++ b/mixs6/mimarks_c_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_nucl_acid_amp + + + + +URI: [mixs.vocab:mimarks_c_nucl_acid_amp](https://w3id.org/mixs/vocab/mimarks_c_nucl_acid_amp) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_nucl_acid_ext.md b/mixs6/mimarks_c_nucl_acid_ext.md new file mode 100644 index 00000000..1a3eee85 --- /dev/null +++ b/mixs6/mimarks_c_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_nucl_acid_ext + + + + +URI: [mixs.vocab:mimarks_c_nucl_acid_ext](https://w3id.org/mixs/vocab/mimarks_c_nucl_acid_ext) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_pcr_cond.md b/mixs6/mimarks_c_pcr_cond.md new file mode 100644 index 00000000..8361cddd --- /dev/null +++ b/mixs6/mimarks_c_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_pcr_cond + + + + +URI: [mixs.vocab:mimarks_c_pcr_cond](https://w3id.org/mixs/vocab/mimarks_c_pcr_cond) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_pcr_primers.md b/mixs6/mimarks_c_pcr_primers.md new file mode 100644 index 00000000..53e87436 --- /dev/null +++ b/mixs6/mimarks_c_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_pcr_primers + + + + +URI: [mixs.vocab:mimarks_c_pcr_primers](https://w3id.org/mixs/vocab/mimarks_c_pcr_primers) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_project_name.md b/mixs6/mimarks_c_project_name.md new file mode 100644 index 00000000..4da8637b --- /dev/null +++ b/mixs6/mimarks_c_project_name.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_project_name + + + + +URI: [mixs.vocab:mimarks_c_project_name](https://w3id.org/mixs/vocab/mimarks_c_project_name) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_rel_to_oxygen.md b/mixs6/mimarks_c_rel_to_oxygen.md new file mode 100644 index 00000000..e1f2cdaa --- /dev/null +++ b/mixs6/mimarks_c_rel_to_oxygen.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_rel_to_oxygen + + + + +URI: [mixs.vocab:mimarks_c_rel_to_oxygen](https://w3id.org/mixs/vocab/mimarks_c_rel_to_oxygen) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_samp_collect_device.md b/mixs6/mimarks_c_samp_collect_device.md new file mode 100644 index 00000000..8c4a28f2 --- /dev/null +++ b/mixs6/mimarks_c_samp_collect_device.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_samp_collect_device + + + + +URI: [mixs.vocab:mimarks_c_samp_collect_device](https://w3id.org/mixs/vocab/mimarks_c_samp_collect_device) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_samp_mat_process.md b/mixs6/mimarks_c_samp_mat_process.md new file mode 100644 index 00000000..7e194cbb --- /dev/null +++ b/mixs6/mimarks_c_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_samp_mat_process + + + + +URI: [mixs.vocab:mimarks_c_samp_mat_process](https://w3id.org/mixs/vocab/mimarks_c_samp_mat_process) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_samp_size.md b/mixs6/mimarks_c_samp_size.md new file mode 100644 index 00000000..b5187114 --- /dev/null +++ b/mixs6/mimarks_c_samp_size.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_samp_size + + + + +URI: [mixs.vocab:mimarks_c_samp_size](https://w3id.org/mixs/vocab/mimarks_c_samp_size) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_sample_name.md b/mixs6/mimarks_c_sample_name.md new file mode 100644 index 00000000..5975c748 --- /dev/null +++ b/mixs6/mimarks_c_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_sample_name + + + + +URI: [mixs.vocab:mimarks_c_sample_name](https://w3id.org/mixs/vocab/mimarks_c_sample_name) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_seq_meth.md b/mixs6/mimarks_c_seq_meth.md new file mode 100644 index 00000000..d823808f --- /dev/null +++ b/mixs6/mimarks_c_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_seq_meth + + + + +URI: [mixs.vocab:mimarks_c_seq_meth](https://w3id.org/mixs/vocab/mimarks_c_seq_meth) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_seq_quality_check.md b/mixs6/mimarks_c_seq_quality_check.md new file mode 100644 index 00000000..da7b6fe9 --- /dev/null +++ b/mixs6/mimarks_c_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_seq_quality_check + + + + +URI: [mixs.vocab:mimarks_c_seq_quality_check](https://w3id.org/mixs/vocab/mimarks_c_seq_quality_check) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_sop.md b/mixs6/mimarks_c_sop.md new file mode 100644 index 00000000..7bc4d927 --- /dev/null +++ b/mixs6/mimarks_c_sop.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_sop + + + + +URI: [mixs.vocab:mimarks_c_sop](https://w3id.org/mixs/vocab/mimarks_c_sop) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_source_mat_id.md b/mixs6/mimarks_c_source_mat_id.md new file mode 100644 index 00000000..3eb109b7 --- /dev/null +++ b/mixs6/mimarks_c_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_source_mat_id + + + + +URI: [mixs.vocab:mimarks_c_source_mat_id](https://w3id.org/mixs/vocab/mimarks_c_source_mat_id) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_submitted_to_insdc.md b/mixs6/mimarks_c_submitted_to_insdc.md new file mode 100644 index 00000000..7275dfed --- /dev/null +++ b/mixs6/mimarks_c_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_submitted_to_insdc + + + + +URI: [mixs.vocab:mimarks_c_submitted_to_insdc](https://w3id.org/mixs/vocab/mimarks_c_submitted_to_insdc) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_subspecf_gen_lin.md b/mixs6/mimarks_c_subspecf_gen_lin.md new file mode 100644 index 00000000..9929caf2 --- /dev/null +++ b/mixs6/mimarks_c_subspecf_gen_lin.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_subspecf_gen_lin + + + + +URI: [mixs.vocab:mimarks_c_subspecf_gen_lin](https://w3id.org/mixs/vocab/mimarks_c_subspecf_gen_lin) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_target_gene.md b/mixs6/mimarks_c_target_gene.md new file mode 100644 index 00000000..77612bff --- /dev/null +++ b/mixs6/mimarks_c_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_c_target_gene + + + + +URI: [mixs.vocab:mimarks_c_target_gene](https://w3id.org/mixs/vocab/mimarks_c_target_gene) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_target_subfragment.md b/mixs6/mimarks_c_target_subfragment.md new file mode 100644 index 00000000..42caae68 --- /dev/null +++ b/mixs6/mimarks_c_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_target_subfragment + + + + +URI: [mixs.vocab:mimarks_c_target_subfragment](https://w3id.org/mixs/vocab/mimarks_c_target_subfragment) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_trophic_level.md b/mixs6/mimarks_c_trophic_level.md new file mode 100644 index 00000000..0932b65e --- /dev/null +++ b/mixs6/mimarks_c_trophic_level.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_trophic_level + + + + +URI: [mixs.vocab:mimarks_c_trophic_level](https://w3id.org/mixs/vocab/mimarks_c_trophic_level) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT + +## Parents + + * is_a: [trophic_level](trophic_level.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_c_url.md b/mixs6/mimarks_c_url.md new file mode 100644 index 00000000..8eab9102 --- /dev/null +++ b/mixs6/mimarks_c_url.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_c_url + + + + +URI: [mixs.vocab:mimarks_c_url](https://w3id.org/mixs/vocab/mimarks_c_url) + + +## Domain and Range + +[MimarksC](MimarksC.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMimarksC](AirMimarksC.md) + * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) + * [Host-associatedMimarksC](Host-associatedMimarksC.md) + * [Human-associatedMimarksC](Human-associatedMimarksC.md) + * [Human-gutMimarksC](Human-gutMimarksC.md) + * [Human-oralMimarksC](Human-oralMimarksC.md) + * [Human-skinMimarksC](Human-skinMimarksC.md) + * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) + * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) + * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) + * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) + * [MimarksC](MimarksC.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) + * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) + * [SedimentMimarksC](SedimentMimarksC.md) + * [SoilMimarksC](SoilMimarksC.md) + * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) + * [WaterMimarksC](WaterMimarksC.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_adapters.md b/mixs6/mimarks_s_adapters.md new file mode 100644 index 00000000..219598d3 --- /dev/null +++ b/mixs6/mimarks_s_adapters.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_adapters + + + + +URI: [mixs.vocab:mimarks_s_adapters](https://w3id.org/mixs/vocab/mimarks_s_adapters) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_assembly_software.md b/mixs6/mimarks_s_assembly_software.md new file mode 100644 index 00000000..7081c1f7 --- /dev/null +++ b/mixs6/mimarks_s_assembly_software.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_assembly_software + + + + +URI: [mixs.vocab:mimarks_s_assembly_software](https://w3id.org/mixs/vocab/mimarks_s_assembly_software) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_chimera_check.md b/mixs6/mimarks_s_chimera_check.md new file mode 100644 index 00000000..c05d04a4 --- /dev/null +++ b/mixs6/mimarks_s_chimera_check.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_chimera_check + + + + +URI: [mixs.vocab:mimarks_s_chimera_check](https://w3id.org/mixs/vocab/mimarks_s_chimera_check) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [chimera_check](chimera_check.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_collection_date.md b/mixs6/mimarks_s_collection_date.md new file mode 100644 index 00000000..e0b78bea --- /dev/null +++ b/mixs6/mimarks_s_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_collection_date + + + + +URI: [mixs.vocab:mimarks_s_collection_date](https://w3id.org/mixs/vocab/mimarks_s_collection_date) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_broad_scale.md b/mixs6/mimarks_s_env_broad_scale.md new file mode 100644 index 00000000..fe42d3e2 --- /dev/null +++ b/mixs6/mimarks_s_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_env_broad_scale + + + + +URI: [mixs.vocab:mimarks_s_env_broad_scale](https://w3id.org/mixs/vocab/mimarks_s_env_broad_scale) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_local_scale.md b/mixs6/mimarks_s_env_local_scale.md new file mode 100644 index 00000000..3d5fec36 --- /dev/null +++ b/mixs6/mimarks_s_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_env_local_scale + + + + +URI: [mixs.vocab:mimarks_s_env_local_scale](https://w3id.org/mixs/vocab/mimarks_s_env_local_scale) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_medium.md b/mixs6/mimarks_s_env_medium.md new file mode 100644 index 00000000..4bb72bb9 --- /dev/null +++ b/mixs6/mimarks_s_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_env_medium + + + + +URI: [mixs.vocab:mimarks_s_env_medium](https://w3id.org/mixs/vocab/mimarks_s_env_medium) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_package.md b/mixs6/mimarks_s_env_package.md new file mode 100644 index 00000000..4b44fb07 --- /dev/null +++ b/mixs6/mimarks_s_env_package.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_env_package + + + + +URI: [mixs.vocab:mimarks_s_env_package](https://w3id.org/mixs/vocab/mimarks_s_env_package) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_experimental_factor.md b/mixs6/mimarks_s_experimental_factor.md new file mode 100644 index 00000000..9dffb071 --- /dev/null +++ b/mixs6/mimarks_s_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_experimental_factor + + + + +URI: [mixs.vocab:mimarks_s_experimental_factor](https://w3id.org/mixs/vocab/mimarks_s_experimental_factor) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_geo_loc_name.md b/mixs6/mimarks_s_geo_loc_name.md new file mode 100644 index 00000000..520ab78c --- /dev/null +++ b/mixs6/mimarks_s_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_geo_loc_name + + + + +URI: [mixs.vocab:mimarks_s_geo_loc_name](https://w3id.org/mixs/vocab/mimarks_s_geo_loc_name) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_investigation_type.md b/mixs6/mimarks_s_investigation_type.md new file mode 100644 index 00000000..64c64c3b --- /dev/null +++ b/mixs6/mimarks_s_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_investigation_type + + + + +URI: [mixs.vocab:mimarks_s_investigation_type](https://w3id.org/mixs/vocab/mimarks_s_investigation_type) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_lat_lon.md b/mixs6/mimarks_s_lat_lon.md new file mode 100644 index 00000000..f0a0748e --- /dev/null +++ b/mixs6/mimarks_s_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: mimarks_s_lat_lon + + + + +URI: [mixs.vocab:mimarks_s_lat_lon](https://w3id.org/mixs/vocab/mimarks_s_lat_lon) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_lib_layout.md b/mixs6/mimarks_s_lib_layout.md new file mode 100644 index 00000000..80c06f0a --- /dev/null +++ b/mixs6/mimarks_s_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_lib_layout + + + + +URI: [mixs.vocab:mimarks_s_lib_layout](https://w3id.org/mixs/vocab/mimarks_s_lib_layout) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_lib_reads_seqd.md b/mixs6/mimarks_s_lib_reads_seqd.md new file mode 100644 index 00000000..3a1e63bd --- /dev/null +++ b/mixs6/mimarks_s_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_lib_reads_seqd + + + + +URI: [mixs.vocab:mimarks_s_lib_reads_seqd](https://w3id.org/mixs/vocab/mimarks_s_lib_reads_seqd) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_lib_screen.md b/mixs6/mimarks_s_lib_screen.md new file mode 100644 index 00000000..2f19a0e1 --- /dev/null +++ b/mixs6/mimarks_s_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_lib_screen + + + + +URI: [mixs.vocab:mimarks_s_lib_screen](https://w3id.org/mixs/vocab/mimarks_s_lib_screen) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_lib_size.md b/mixs6/mimarks_s_lib_size.md new file mode 100644 index 00000000..16dea143 --- /dev/null +++ b/mixs6/mimarks_s_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_lib_size + + + + +URI: [mixs.vocab:mimarks_s_lib_size](https://w3id.org/mixs/vocab/mimarks_s_lib_size) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_lib_vector.md b/mixs6/mimarks_s_lib_vector.md new file mode 100644 index 00000000..d0889f3e --- /dev/null +++ b/mixs6/mimarks_s_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_lib_vector + + + + +URI: [mixs.vocab:mimarks_s_lib_vector](https://w3id.org/mixs/vocab/mimarks_s_lib_vector) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_mid.md b/mixs6/mimarks_s_mid.md new file mode 100644 index 00000000..bdde8ece --- /dev/null +++ b/mixs6/mimarks_s_mid.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_mid + + + + +URI: [mixs.vocab:mimarks_s_mid](https://w3id.org/mixs/vocab/mimarks_s_mid) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_nucl_acid_amp.md b/mixs6/mimarks_s_nucl_acid_amp.md new file mode 100644 index 00000000..968f9206 --- /dev/null +++ b/mixs6/mimarks_s_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_nucl_acid_amp + + + + +URI: [mixs.vocab:mimarks_s_nucl_acid_amp](https://w3id.org/mixs/vocab/mimarks_s_nucl_acid_amp) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_nucl_acid_ext.md b/mixs6/mimarks_s_nucl_acid_ext.md new file mode 100644 index 00000000..6988d9fb --- /dev/null +++ b/mixs6/mimarks_s_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_nucl_acid_ext + + + + +URI: [mixs.vocab:mimarks_s_nucl_acid_ext](https://w3id.org/mixs/vocab/mimarks_s_nucl_acid_ext) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_pcr_cond.md b/mixs6/mimarks_s_pcr_cond.md new file mode 100644 index 00000000..fa49eceb --- /dev/null +++ b/mixs6/mimarks_s_pcr_cond.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_pcr_cond + + + + +URI: [mixs.vocab:mimarks_s_pcr_cond](https://w3id.org/mixs/vocab/mimarks_s_pcr_cond) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_cond](pcr_cond.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_pcr_primers.md b/mixs6/mimarks_s_pcr_primers.md new file mode 100644 index 00000000..c157768c --- /dev/null +++ b/mixs6/mimarks_s_pcr_primers.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_pcr_primers + + + + +URI: [mixs.vocab:mimarks_s_pcr_primers](https://w3id.org/mixs/vocab/mimarks_s_pcr_primers) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pcr_primers](pcr_primers.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_project_name.md b/mixs6/mimarks_s_project_name.md new file mode 100644 index 00000000..ed56a308 --- /dev/null +++ b/mixs6/mimarks_s_project_name.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_project_name + + + + +URI: [mixs.vocab:mimarks_s_project_name](https://w3id.org/mixs/vocab/mimarks_s_project_name) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_rel_to_oxygen.md b/mixs6/mimarks_s_rel_to_oxygen.md new file mode 100644 index 00000000..0256ff8a --- /dev/null +++ b/mixs6/mimarks_s_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_rel_to_oxygen + + + + +URI: [mixs.vocab:mimarks_s_rel_to_oxygen](https://w3id.org/mixs/vocab/mimarks_s_rel_to_oxygen) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_samp_collect_device.md b/mixs6/mimarks_s_samp_collect_device.md new file mode 100644 index 00000000..9c7a0ed6 --- /dev/null +++ b/mixs6/mimarks_s_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_samp_collect_device + + + + +URI: [mixs.vocab:mimarks_s_samp_collect_device](https://w3id.org/mixs/vocab/mimarks_s_samp_collect_device) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_samp_mat_process.md b/mixs6/mimarks_s_samp_mat_process.md new file mode 100644 index 00000000..cb17af05 --- /dev/null +++ b/mixs6/mimarks_s_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_samp_mat_process + + + + +URI: [mixs.vocab:mimarks_s_samp_mat_process](https://w3id.org/mixs/vocab/mimarks_s_samp_mat_process) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_samp_size.md b/mixs6/mimarks_s_samp_size.md new file mode 100644 index 00000000..7b11e673 --- /dev/null +++ b/mixs6/mimarks_s_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_samp_size + + + + +URI: [mixs.vocab:mimarks_s_samp_size](https://w3id.org/mixs/vocab/mimarks_s_samp_size) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_sample_name.md b/mixs6/mimarks_s_sample_name.md new file mode 100644 index 00000000..75b36885 --- /dev/null +++ b/mixs6/mimarks_s_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_sample_name + + + + +URI: [mixs.vocab:mimarks_s_sample_name](https://w3id.org/mixs/vocab/mimarks_s_sample_name) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_seq_meth.md b/mixs6/mimarks_s_seq_meth.md new file mode 100644 index 00000000..ddc6e6f0 --- /dev/null +++ b/mixs6/mimarks_s_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_seq_meth + + + + +URI: [mixs.vocab:mimarks_s_seq_meth](https://w3id.org/mixs/vocab/mimarks_s_seq_meth) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_seq_quality_check.md b/mixs6/mimarks_s_seq_quality_check.md new file mode 100644 index 00000000..30657c3d --- /dev/null +++ b/mixs6/mimarks_s_seq_quality_check.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_seq_quality_check + + + + +URI: [mixs.vocab:mimarks_s_seq_quality_check](https://w3id.org/mixs/vocab/mimarks_s_seq_quality_check) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [seq_quality_check](seq_quality_check.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_size_frac.md b/mixs6/mimarks_s_size_frac.md new file mode 100644 index 00000000..fb33e692 --- /dev/null +++ b/mixs6/mimarks_s_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_size_frac + + + + +URI: [mixs.vocab:mimarks_s_size_frac](https://w3id.org/mixs/vocab/mimarks_s_size_frac) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_sop.md b/mixs6/mimarks_s_sop.md new file mode 100644 index 00000000..8573e491 --- /dev/null +++ b/mixs6/mimarks_s_sop.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_sop + + + + +URI: [mixs.vocab:mimarks_s_sop](https://w3id.org/mixs/vocab/mimarks_s_sop) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_source_mat_id.md b/mixs6/mimarks_s_source_mat_id.md new file mode 100644 index 00000000..7b8dfbd2 --- /dev/null +++ b/mixs6/mimarks_s_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_source_mat_id + + + + +URI: [mixs.vocab:mimarks_s_source_mat_id](https://w3id.org/mixs/vocab/mimarks_s_source_mat_id) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_submitted_to_insdc.md b/mixs6/mimarks_s_submitted_to_insdc.md new file mode 100644 index 00000000..214b9f04 --- /dev/null +++ b/mixs6/mimarks_s_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_submitted_to_insdc + + + + +URI: [mixs.vocab:mimarks_s_submitted_to_insdc](https://w3id.org/mixs/vocab/mimarks_s_submitted_to_insdc) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_target_gene.md b/mixs6/mimarks_s_target_gene.md new file mode 100644 index 00000000..abd724f4 --- /dev/null +++ b/mixs6/mimarks_s_target_gene.md @@ -0,0 +1,40 @@ + +# Slot: mimarks_s_target_gene + + + + +URI: [mixs.vocab:mimarks_s_target_gene](https://w3id.org/mixs/vocab/mimarks_s_target_gene) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [target_gene](target_gene.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_target_subfragment.md b/mixs6/mimarks_s_target_subfragment.md new file mode 100644 index 00000000..3b928359 --- /dev/null +++ b/mixs6/mimarks_s_target_subfragment.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_target_subfragment + + + + +URI: [mixs.vocab:mimarks_s_target_subfragment](https://w3id.org/mixs/vocab/mimarks_s_target_subfragment) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [target_subfragment](target_subfragment.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mimarks_s_url.md b/mixs6/mimarks_s_url.md new file mode 100644 index 00000000..d4157a81 --- /dev/null +++ b/mixs6/mimarks_s_url.md @@ -0,0 +1,47 @@ + +# Slot: mimarks_s_url + + + + +URI: [mixs.vocab:mimarks_s_url](https://w3id.org/mixs/vocab/mimarks_s_url) + + +## Domain and Range + +[MimarksS](MimarksS.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [AirMimarksS](AirMimarksS.md) + * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) + * [Host-associatedMimarksS](Host-associatedMimarksS.md) + * [Human-associatedMimarksS](Human-associatedMimarksS.md) + * [Human-gutMimarksS](Human-gutMimarksS.md) + * [Human-oralMimarksS](Human-oralMimarksS.md) + * [Human-skinMimarksS](Human-skinMimarksS.md) + * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) + * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) + * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) + * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) + * [MimarksS](MimarksS.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) + * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) + * [SedimentMimarksS](SedimentMimarksS.md) + * [SoilMimarksS](SoilMimarksS.md) + * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) + * [WaterMimarksS](WaterMimarksS.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/mineral_nutr_regm.md b/mixs6/mineral_nutr_regm.md index 74fe7773..606e7540 100644 --- a/mixs6/mineral_nutr_regm.md +++ b/mixs6/mineral_nutr_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/misag_adapters.md b/mixs6/misag_adapters.md new file mode 100644 index 00000000..a114706c --- /dev/null +++ b/mixs6/misag_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_adapters + + + + +URI: [mixs.vocab:MISAG_adapters](https://w3id.org/mixs/vocab/MISAG_adapters) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_annot.md b/mixs6/misag_annot.md new file mode 100644 index 00000000..605703b6 --- /dev/null +++ b/mixs6/misag_annot.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_annot + + + + +URI: [mixs.vocab:MISAG_annot](https://w3id.org/mixs/vocab/MISAG_annot) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_assembly_name.md b/mixs6/misag_assembly_name.md new file mode 100644 index 00000000..cec5c3c9 --- /dev/null +++ b/mixs6/misag_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_assembly_name + + + + +URI: [mixs.vocab:MISAG_assembly_name](https://w3id.org/mixs/vocab/MISAG_assembly_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_assembly_qual.md b/mixs6/misag_assembly_qual.md new file mode 100644 index 00000000..3096c276 --- /dev/null +++ b/mixs6/misag_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_assembly_qual + + + + +URI: [mixs.vocab:MISAG_assembly_qual](https://w3id.org/mixs/vocab/MISAG_assembly_qual) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_assembly_software.md b/mixs6/misag_assembly_software.md new file mode 100644 index 00000000..a4b4d6b0 --- /dev/null +++ b/mixs6/misag_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_assembly_software + + + + +URI: [mixs.vocab:MISAG_assembly_software](https://w3id.org/mixs/vocab/MISAG_assembly_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_collection_date.md b/mixs6/misag_collection_date.md new file mode 100644 index 00000000..0d310c2f --- /dev/null +++ b/mixs6/misag_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_collection_date + + + + +URI: [mixs.vocab:MISAG_collection_date](https://w3id.org/mixs/vocab/MISAG_collection_date) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_compl_appr.md b/mixs6/misag_compl_appr.md new file mode 100644 index 00000000..3ed7eb42 --- /dev/null +++ b/mixs6/misag_compl_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_appr + + + + +URI: [mixs.vocab:MISAG_compl_appr](https://w3id.org/mixs/vocab/MISAG_compl_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_compl_score.md b/mixs6/misag_compl_score.md new file mode 100644 index 00000000..6eb075c3 --- /dev/null +++ b/mixs6/misag_compl_score.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_score + + + + +URI: [mixs.vocab:MISAG_compl_score](https://w3id.org/mixs/vocab/MISAG_compl_score) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_compl_software.md b/mixs6/misag_compl_software.md new file mode 100644 index 00000000..8a733c86 --- /dev/null +++ b/mixs6/misag_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_compl_software + + + + +URI: [mixs.vocab:MISAG_compl_software](https://w3id.org/mixs/vocab/MISAG_compl_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_score.md b/mixs6/misag_contam_score.md new file mode 100644 index 00000000..1b54e765 --- /dev/null +++ b/mixs6/misag_contam_score.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_score + + + + +URI: [mixs.vocab:MISAG_contam_score](https://w3id.org/mixs/vocab/MISAG_contam_score) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [contam_score](contam_score.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_screen_input.md b/mixs6/misag_contam_screen_input.md new file mode 100644 index 00000000..d881d54f --- /dev/null +++ b/mixs6/misag_contam_screen_input.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_screen_input + + + + +URI: [mixs.vocab:MISAG_contam_screen_input](https://w3id.org/mixs/vocab/MISAG_contam_screen_input) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [contam_screen_input](contam_screen_input.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_contam_screen_param.md b/mixs6/misag_contam_screen_param.md new file mode 100644 index 00000000..458fcaa0 --- /dev/null +++ b/mixs6/misag_contam_screen_param.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_contam_screen_param + + + + +URI: [mixs.vocab:MISAG_contam_screen_param](https://w3id.org/mixs/vocab/MISAG_contam_screen_param) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [contam_screen_param](contam_screen_param.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_decontam_software.md b/mixs6/misag_decontam_software.md new file mode 100644 index 00000000..f2b95321 --- /dev/null +++ b/mixs6/misag_decontam_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_decontam_software + + + + +URI: [mixs.vocab:MISAG_decontam_software](https://w3id.org/mixs/vocab/MISAG_decontam_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [decontam_software](decontam_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_env_broad_scale.md b/mixs6/misag_env_broad_scale.md new file mode 100644 index 00000000..8cb25b24 --- /dev/null +++ b/mixs6/misag_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_broad_scale + + + + +URI: [mixs.vocab:MISAG_env_broad_scale](https://w3id.org/mixs/vocab/MISAG_env_broad_scale) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_local_scale.md b/mixs6/misag_env_local_scale.md new file mode 100644 index 00000000..205dd0be --- /dev/null +++ b/mixs6/misag_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_local_scale + + + + +URI: [mixs.vocab:MISAG_env_local_scale](https://w3id.org/mixs/vocab/MISAG_env_local_scale) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_medium.md b/mixs6/misag_env_medium.md new file mode 100644 index 00000000..2a43dec0 --- /dev/null +++ b/mixs6/misag_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_env_medium + + + + +URI: [mixs.vocab:MISAG_env_medium](https://w3id.org/mixs/vocab/MISAG_env_medium) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_env_package.md b/mixs6/misag_env_package.md new file mode 100644 index 00000000..438c6411 --- /dev/null +++ b/mixs6/misag_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_env_package + + + + +URI: [mixs.vocab:MISAG_env_package](https://w3id.org/mixs/vocab/MISAG_env_package) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_experimental_factor.md b/mixs6/misag_experimental_factor.md new file mode 100644 index 00000000..2f381967 --- /dev/null +++ b/mixs6/misag_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_experimental_factor + + + + +URI: [mixs.vocab:MISAG_experimental_factor](https://w3id.org/mixs/vocab/MISAG_experimental_factor) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_feat_pred.md b/mixs6/misag_feat_pred.md new file mode 100644 index 00000000..c263d715 --- /dev/null +++ b/mixs6/misag_feat_pred.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_feat_pred + + + + +URI: [mixs.vocab:MISAG_feat_pred](https://w3id.org/mixs/vocab/MISAG_feat_pred) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_geo_loc_name.md b/mixs6/misag_geo_loc_name.md new file mode 100644 index 00000000..48afa724 --- /dev/null +++ b/mixs6/misag_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_geo_loc_name + + + + +URI: [mixs.vocab:MISAG_geo_loc_name](https://w3id.org/mixs/vocab/MISAG_geo_loc_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_investigation_type.md b/mixs6/misag_investigation_type.md new file mode 100644 index 00000000..a06228f2 --- /dev/null +++ b/mixs6/misag_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_investigation_type + + + + +URI: [mixs.vocab:MISAG_investigation_type](https://w3id.org/mixs/vocab/MISAG_investigation_type) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_lat_lon.md b/mixs6/misag_lat_lon.md new file mode 100644 index 00000000..0d425b05 --- /dev/null +++ b/mixs6/misag_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MISAG_lat_lon + + + + +URI: [mixs.vocab:MISAG_lat_lon](https://w3id.org/mixs/vocab/MISAG_lat_lon) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) diff --git a/mixs6/misag_lib_layout.md b/mixs6/misag_lib_layout.md new file mode 100644 index 00000000..96ba5f9d --- /dev/null +++ b/mixs6/misag_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_layout + + + + +URI: [mixs.vocab:MISAG_lib_layout](https://w3id.org/mixs/vocab/MISAG_lib_layout) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_reads_seqd.md b/mixs6/misag_lib_reads_seqd.md new file mode 100644 index 00000000..2ee70bb6 --- /dev/null +++ b/mixs6/misag_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_reads_seqd + + + + +URI: [mixs.vocab:MISAG_lib_reads_seqd](https://w3id.org/mixs/vocab/MISAG_lib_reads_seqd) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_screen.md b/mixs6/misag_lib_screen.md new file mode 100644 index 00000000..9b65f378 --- /dev/null +++ b/mixs6/misag_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_screen + + + + +URI: [mixs.vocab:MISAG_lib_screen](https://w3id.org/mixs/vocab/MISAG_lib_screen) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_size.md b/mixs6/misag_lib_size.md new file mode 100644 index 00000000..93f242bc --- /dev/null +++ b/mixs6/misag_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_size + + + + +URI: [mixs.vocab:MISAG_lib_size](https://w3id.org/mixs/vocab/MISAG_lib_size) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_lib_vector.md b/mixs6/misag_lib_vector.md new file mode 100644 index 00000000..273f09f4 --- /dev/null +++ b/mixs6/misag_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_lib_vector + + + + +URI: [mixs.vocab:MISAG_lib_vector](https://w3id.org/mixs/vocab/MISAG_lib_vector) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_mid.md b/mixs6/misag_mid.md new file mode 100644 index 00000000..e279d26c --- /dev/null +++ b/mixs6/misag_mid.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_mid + + + + +URI: [mixs.vocab:MISAG_mid](https://w3id.org/mixs/vocab/MISAG_mid) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_nucl_acid_amp.md b/mixs6/misag_nucl_acid_amp.md new file mode 100644 index 00000000..c1ff35b3 --- /dev/null +++ b/mixs6/misag_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_nucl_acid_amp + + + + +URI: [mixs.vocab:MISAG_nucl_acid_amp](https://w3id.org/mixs/vocab/MISAG_nucl_acid_amp) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_nucl_acid_ext.md b/mixs6/misag_nucl_acid_ext.md new file mode 100644 index 00000000..cc15c052 --- /dev/null +++ b/mixs6/misag_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_nucl_acid_ext + + + + +URI: [mixs.vocab:MISAG_nucl_acid_ext](https://w3id.org/mixs/vocab/MISAG_nucl_acid_ext) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_number_contig.md b/mixs6/misag_number_contig.md new file mode 100644 index 00000000..2389dc85 --- /dev/null +++ b/mixs6/misag_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_number_contig + + + + +URI: [mixs.vocab:MISAG_number_contig](https://w3id.org/mixs/vocab/MISAG_number_contig) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_project_name.md b/mixs6/misag_project_name.md new file mode 100644 index 00000000..943c0c55 --- /dev/null +++ b/mixs6/misag_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_project_name + + + + +URI: [mixs.vocab:MISAG_project_name](https://w3id.org/mixs/vocab/MISAG_project_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_ref_biomaterial.md b/mixs6/misag_ref_biomaterial.md new file mode 100644 index 00000000..6bb610b2 --- /dev/null +++ b/mixs6/misag_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_ref_biomaterial + + + + +URI: [mixs.vocab:MISAG_ref_biomaterial](https://w3id.org/mixs/vocab/MISAG_ref_biomaterial) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_ref_db.md b/mixs6/misag_ref_db.md new file mode 100644 index 00000000..d0448aec --- /dev/null +++ b/mixs6/misag_ref_db.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_ref_db + + + + +URI: [mixs.vocab:MISAG_ref_db](https://w3id.org/mixs/vocab/MISAG_ref_db) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_rel_to_oxygen.md b/mixs6/misag_rel_to_oxygen.md new file mode 100644 index 00000000..63343978 --- /dev/null +++ b/mixs6/misag_rel_to_oxygen.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_rel_to_oxygen + + + + +URI: [mixs.vocab:MISAG_rel_to_oxygen](https://w3id.org/mixs/vocab/MISAG_rel_to_oxygen) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT + +## Parents + + * is_a: [rel_to_oxygen](rel_to_oxygen.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_samp_collect_device.md b/mixs6/misag_samp_collect_device.md new file mode 100644 index 00000000..55e704ea --- /dev/null +++ b/mixs6/misag_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_samp_collect_device + + + + +URI: [mixs.vocab:MISAG_samp_collect_device](https://w3id.org/mixs/vocab/MISAG_samp_collect_device) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_samp_mat_process.md b/mixs6/misag_samp_mat_process.md new file mode 100644 index 00000000..f32b89e8 --- /dev/null +++ b/mixs6/misag_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_samp_mat_process + + + + +URI: [mixs.vocab:MISAG_samp_mat_process](https://w3id.org/mixs/vocab/MISAG_samp_mat_process) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_samp_size.md b/mixs6/misag_samp_size.md new file mode 100644 index 00000000..942a6bc7 --- /dev/null +++ b/mixs6/misag_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_samp_size + + + + +URI: [mixs.vocab:MISAG_samp_size](https://w3id.org/mixs/vocab/MISAG_samp_size) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_sample_name.md b/mixs6/misag_sample_name.md new file mode 100644 index 00000000..de41f168 --- /dev/null +++ b/mixs6/misag_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sample_name + + + + +URI: [mixs.vocab:MISAG_sample_name](https://w3id.org/mixs/vocab/MISAG_sample_name) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_seq_meth.md b/mixs6/misag_seq_meth.md new file mode 100644 index 00000000..2b28e8e6 --- /dev/null +++ b/mixs6/misag_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_seq_meth + + + + +URI: [mixs.vocab:MISAG_seq_meth](https://w3id.org/mixs/vocab/MISAG_seq_meth) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_sim_search_meth.md b/mixs6/misag_sim_search_meth.md new file mode 100644 index 00000000..0f30eb12 --- /dev/null +++ b/mixs6/misag_sim_search_meth.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sim_search_meth + + + + +URI: [mixs.vocab:MISAG_sim_search_meth](https://w3id.org/mixs/vocab/MISAG_sim_search_meth) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_single_cell_lysis_appr.md b/mixs6/misag_single_cell_lysis_appr.md new file mode 100644 index 00000000..ad7a24d0 --- /dev/null +++ b/mixs6/misag_single_cell_lysis_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_single_cell_lysis_appr + + + + +URI: [mixs.vocab:MISAG_single_cell_lysis_appr](https://w3id.org/mixs/vocab/MISAG_single_cell_lysis_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [single_cell_lysis_appr](single_cell_lysis_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_single_cell_lysis_prot.md b/mixs6/misag_single_cell_lysis_prot.md new file mode 100644 index 00000000..da94e88a --- /dev/null +++ b/mixs6/misag_single_cell_lysis_prot.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_single_cell_lysis_prot + + + + +URI: [mixs.vocab:MISAG_single_cell_lysis_prot](https://w3id.org/mixs/vocab/MISAG_single_cell_lysis_prot) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [single_cell_lysis_prot](single_cell_lysis_prot.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_size_frac.md b/mixs6/misag_size_frac.md new file mode 100644 index 00000000..a1faa0c5 --- /dev/null +++ b/mixs6/misag_size_frac.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_size_frac + + + + +URI: [mixs.vocab:MISAG_size_frac](https://w3id.org/mixs/vocab/MISAG_size_frac) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_sop.md b/mixs6/misag_sop.md new file mode 100644 index 00000000..efdc3ebc --- /dev/null +++ b/mixs6/misag_sop.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_sop + + + + +URI: [mixs.vocab:MISAG_sop](https://w3id.org/mixs/vocab/MISAG_sop) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_sort_tech.md b/mixs6/misag_sort_tech.md new file mode 100644 index 00000000..96540572 --- /dev/null +++ b/mixs6/misag_sort_tech.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_sort_tech + + + + +URI: [mixs.vocab:MISAG_sort_tech](https://w3id.org/mixs/vocab/MISAG_sort_tech) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [sort_tech](sort_tech.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_source_mat_id.md b/mixs6/misag_source_mat_id.md new file mode 100644 index 00000000..4c673c81 --- /dev/null +++ b/mixs6/misag_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_source_mat_id + + + + +URI: [mixs.vocab:MISAG_source_mat_id](https://w3id.org/mixs/vocab/MISAG_source_mat_id) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_submitted_to_insdc.md b/mixs6/misag_submitted_to_insdc.md new file mode 100644 index 00000000..31906e60 --- /dev/null +++ b/mixs6/misag_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_submitted_to_insdc + + + + +URI: [mixs.vocab:MISAG_submitted_to_insdc](https://w3id.org/mixs/vocab/MISAG_submitted_to_insdc) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_tax_class.md b/mixs6/misag_tax_class.md new file mode 100644 index 00000000..edc6dff0 --- /dev/null +++ b/mixs6/misag_tax_class.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_tax_class + + + + +URI: [mixs.vocab:MISAG_tax_class](https://w3id.org/mixs/vocab/MISAG_tax_class) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_tax_ident.md b/mixs6/misag_tax_ident.md new file mode 100644 index 00000000..55fa12df --- /dev/null +++ b/mixs6/misag_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_tax_ident + + + + +URI: [mixs.vocab:MISAG_tax_ident](https://w3id.org/mixs/vocab/MISAG_tax_ident) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_trna_ext_software.md b/mixs6/misag_trna_ext_software.md new file mode 100644 index 00000000..9a0e5cc8 --- /dev/null +++ b/mixs6/misag_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_trna_ext_software + + + + +URI: [mixs.vocab:MISAG_trna_ext_software](https://w3id.org/mixs/vocab/MISAG_trna_ext_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_trnas.md b/mixs6/misag_trnas.md new file mode 100644 index 00000000..13c4ca45 --- /dev/null +++ b/mixs6/misag_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_trnas + + + + +URI: [mixs.vocab:MISAG_trnas](https://w3id.org/mixs/vocab/MISAG_trnas) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_url.md b/mixs6/misag_url.md new file mode 100644 index 00000000..f032f1fb --- /dev/null +++ b/mixs6/misag_url.md @@ -0,0 +1,47 @@ + +# Slot: MISAG_url + + + + +URI: [mixs.vocab:MISAG_url](https://w3id.org/mixs/vocab/MISAG_url) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/misag_wga_amp_appr.md b/mixs6/misag_wga_amp_appr.md new file mode 100644 index 00000000..053f81e9 --- /dev/null +++ b/mixs6/misag_wga_amp_appr.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_wga_amp_appr + + + + +URI: [mixs.vocab:MISAG_wga_amp_appr](https://w3id.org/mixs/vocab/MISAG_wga_amp_appr) + + +## Domain and Range + +[MISAG](MISAG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [wga_amp_appr](wga_amp_appr.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_wga_amp_kit.md b/mixs6/misag_wga_amp_kit.md new file mode 100644 index 00000000..7e76763c --- /dev/null +++ b/mixs6/misag_wga_amp_kit.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_wga_amp_kit + + + + +URI: [mixs.vocab:MISAG_wga_amp_kit](https://w3id.org/mixs/vocab/MISAG_wga_amp_kit) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_kit](wga_amp_kit.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_x_16s_recover.md b/mixs6/misag_x_16s_recover.md new file mode 100644 index 00000000..d867584d --- /dev/null +++ b/mixs6/misag_x_16s_recover.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_x_16s_recover + + + + +URI: [mixs.vocab:MISAG_x_16s_recover](https://w3id.org/mixs/vocab/MISAG_x_16s_recover) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover](x_16s_recover.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misag_x_16s_recover_software.md b/mixs6/misag_x_16s_recover_software.md new file mode 100644 index 00000000..f9658c21 --- /dev/null +++ b/mixs6/misag_x_16s_recover_software.md @@ -0,0 +1,40 @@ + +# Slot: MISAG_x_16s_recover_software + + + + +URI: [mixs.vocab:MISAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MISAG_x_16s_recover_software) + + +## Domain and Range + +[MISAG](MISAG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [x_16s_recover_software](x_16s_recover_software.md) + +## Children + + +## Used by + + * [MISAG](MISAG.md) + * [AirMISAG](AirMISAG.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SoilMISAG](SoilMISAG.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WaterMISAG](WaterMISAG.md) diff --git a/mixs6/misc_param.md b/mixs6/misc_param.md index 03a18be2..dcaed98d 100644 --- a/mixs6/misc_param.md +++ b/mixs6/misc_param.md @@ -21,197 +21,197 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/miuvig_adapters.md b/mixs6/miuvig_adapters.md new file mode 100644 index 00000000..e15f4bb3 --- /dev/null +++ b/mixs6/miuvig_adapters.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_adapters + + + + +URI: [mixs.vocab:MIUVIG_adapters](https://w3id.org/mixs/vocab/MIUVIG_adapters) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [adapters](adapters.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_annot.md b/mixs6/miuvig_annot.md new file mode 100644 index 00000000..5eeab41a --- /dev/null +++ b/mixs6/miuvig_annot.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_annot + + + + +URI: [mixs.vocab:MIUVIG_annot](https://w3id.org/mixs/vocab/MIUVIG_annot) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [annot](annot.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_assembly_name.md b/mixs6/miuvig_assembly_name.md new file mode 100644 index 00000000..7d398981 --- /dev/null +++ b/mixs6/miuvig_assembly_name.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_assembly_name + + + + +URI: [mixs.vocab:MIUVIG_assembly_name](https://w3id.org/mixs/vocab/MIUVIG_assembly_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [assembly_name](assembly_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_assembly_qual.md b/mixs6/miuvig_assembly_qual.md new file mode 100644 index 00000000..515a782f --- /dev/null +++ b/mixs6/miuvig_assembly_qual.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_assembly_qual + + + + +URI: [mixs.vocab:MIUVIG_assembly_qual](https://w3id.org/mixs/vocab/MIUVIG_assembly_qual) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [assembly_qual](assembly_qual.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_assembly_software.md b/mixs6/miuvig_assembly_software.md new file mode 100644 index 00000000..91e41a50 --- /dev/null +++ b/mixs6/miuvig_assembly_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_assembly_software + + + + +URI: [mixs.vocab:MIUVIG_assembly_software](https://w3id.org/mixs/vocab/MIUVIG_assembly_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [assembly_software](assembly_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_bin_param.md b/mixs6/miuvig_bin_param.md new file mode 100644 index 00000000..9e9cad62 --- /dev/null +++ b/mixs6/miuvig_bin_param.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_bin_param + + + + +URI: [mixs.vocab:MIUVIG_bin_param](https://w3id.org/mixs/vocab/MIUVIG_bin_param) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [bin_param](bin_param.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_bin_software.md b/mixs6/miuvig_bin_software.md new file mode 100644 index 00000000..3acea16e --- /dev/null +++ b/mixs6/miuvig_bin_software.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_bin_software + + + + +URI: [mixs.vocab:MIUVIG_bin_software](https://w3id.org/mixs/vocab/MIUVIG_bin_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [bin_software](bin_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_biotic_relationship.md b/mixs6/miuvig_biotic_relationship.md new file mode 100644 index 00000000..ba1d68ed --- /dev/null +++ b/mixs6/miuvig_biotic_relationship.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_biotic_relationship + + + + +URI: [mixs.vocab:MIUVIG_biotic_relationship](https://w3id.org/mixs/vocab/MIUVIG_biotic_relationship) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [biotic_relationship](biotic_relationship.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_collection_date.md b/mixs6/miuvig_collection_date.md new file mode 100644 index 00000000..a8744090 --- /dev/null +++ b/mixs6/miuvig_collection_date.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_collection_date + + + + +URI: [mixs.vocab:MIUVIG_collection_date](https://w3id.org/mixs/vocab/MIUVIG_collection_date) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [collection_date](collection_date.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_compl_appr.md b/mixs6/miuvig_compl_appr.md new file mode 100644 index 00000000..165316b6 --- /dev/null +++ b/mixs6/miuvig_compl_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_compl_appr + + + + +URI: [mixs.vocab:MIUVIG_compl_appr](https://w3id.org/mixs/vocab/MIUVIG_compl_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [compl_appr](compl_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_compl_score.md b/mixs6/miuvig_compl_score.md new file mode 100644 index 00000000..ed398660 --- /dev/null +++ b/mixs6/miuvig_compl_score.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_compl_score + + + + +URI: [mixs.vocab:MIUVIG_compl_score](https://w3id.org/mixs/vocab/MIUVIG_compl_score) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [compl_score](compl_score.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_compl_software.md b/mixs6/miuvig_compl_software.md new file mode 100644 index 00000000..c5273c3b --- /dev/null +++ b/mixs6/miuvig_compl_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_compl_software + + + + +URI: [mixs.vocab:MIUVIG_compl_software](https://w3id.org/mixs/vocab/MIUVIG_compl_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [compl_software](compl_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_detec_type.md b/mixs6/miuvig_detec_type.md new file mode 100644 index 00000000..7098fffd --- /dev/null +++ b/mixs6/miuvig_detec_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_detec_type + + + + +URI: [mixs.vocab:MIUVIG_detec_type](https://w3id.org/mixs/vocab/MIUVIG_detec_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [detec_type](detec_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_env_broad_scale.md b/mixs6/miuvig_env_broad_scale.md new file mode 100644 index 00000000..0db123de --- /dev/null +++ b/mixs6/miuvig_env_broad_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_broad_scale + + + + +URI: [mixs.vocab:MIUVIG_env_broad_scale](https://w3id.org/mixs/vocab/MIUVIG_env_broad_scale) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_broad_scale](env_broad_scale.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_local_scale.md b/mixs6/miuvig_env_local_scale.md new file mode 100644 index 00000000..f27eac13 --- /dev/null +++ b/mixs6/miuvig_env_local_scale.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_local_scale + + + + +URI: [mixs.vocab:MIUVIG_env_local_scale](https://w3id.org/mixs/vocab/MIUVIG_env_local_scale) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_local_scale](env_local_scale.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_medium.md b/mixs6/miuvig_env_medium.md new file mode 100644 index 00000000..b58ac09a --- /dev/null +++ b/mixs6/miuvig_env_medium.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_env_medium + + + + +URI: [mixs.vocab:MIUVIG_env_medium](https://w3id.org/mixs/vocab/MIUVIG_env_medium) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [env_medium](env_medium.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_env_package.md b/mixs6/miuvig_env_package.md new file mode 100644 index 00000000..ab3fcefc --- /dev/null +++ b/mixs6/miuvig_env_package.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_env_package + + + + +URI: [mixs.vocab:MIUVIG_env_package](https://w3id.org/mixs/vocab/MIUVIG_env_package) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [env_package](env_package.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_estimated_size.md b/mixs6/miuvig_estimated_size.md new file mode 100644 index 00000000..f1d7ffd3 --- /dev/null +++ b/mixs6/miuvig_estimated_size.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_estimated_size + + + + +URI: [mixs.vocab:MIUVIG_estimated_size](https://w3id.org/mixs/vocab/MIUVIG_estimated_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [estimated_size](estimated_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_experimental_factor.md b/mixs6/miuvig_experimental_factor.md new file mode 100644 index 00000000..6d32d32e --- /dev/null +++ b/mixs6/miuvig_experimental_factor.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_experimental_factor + + + + +URI: [mixs.vocab:MIUVIG_experimental_factor](https://w3id.org/mixs/vocab/MIUVIG_experimental_factor) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [experimental_factor](experimental_factor.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_feat_pred.md b/mixs6/miuvig_feat_pred.md new file mode 100644 index 00000000..74b50c64 --- /dev/null +++ b/mixs6/miuvig_feat_pred.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_feat_pred + + + + +URI: [mixs.vocab:MIUVIG_feat_pred](https://w3id.org/mixs/vocab/MIUVIG_feat_pred) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [feat_pred](feat_pred.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_geo_loc_name.md b/mixs6/miuvig_geo_loc_name.md new file mode 100644 index 00000000..db0ca0f9 --- /dev/null +++ b/mixs6/miuvig_geo_loc_name.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_geo_loc_name + + + + +URI: [mixs.vocab:MIUVIG_geo_loc_name](https://w3id.org/mixs/vocab/MIUVIG_geo_loc_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [geo_loc_name](geo_loc_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_host_pred_appr.md b/mixs6/miuvig_host_pred_appr.md new file mode 100644 index 00000000..51f76cc6 --- /dev/null +++ b/mixs6/miuvig_host_pred_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_host_pred_appr + + + + +URI: [mixs.vocab:MIUVIG_host_pred_appr](https://w3id.org/mixs/vocab/MIUVIG_host_pred_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [host_pred_appr](host_pred_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_host_pred_est_acc.md b/mixs6/miuvig_host_pred_est_acc.md new file mode 100644 index 00000000..0d66a240 --- /dev/null +++ b/mixs6/miuvig_host_pred_est_acc.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_host_pred_est_acc + + + + +URI: [mixs.vocab:MIUVIG_host_pred_est_acc](https://w3id.org/mixs/vocab/MIUVIG_host_pred_est_acc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_pred_est_acc](host_pred_est_acc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_host_spec_range.md b/mixs6/miuvig_host_spec_range.md new file mode 100644 index 00000000..16c57982 --- /dev/null +++ b/mixs6/miuvig_host_spec_range.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_host_spec_range + + + + +URI: [mixs.vocab:MIUVIG_host_spec_range](https://w3id.org/mixs/vocab/MIUVIG_host_spec_range) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [host_spec_range](host_spec_range.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_investigation_type.md b/mixs6/miuvig_investigation_type.md new file mode 100644 index 00000000..47fab6bc --- /dev/null +++ b/mixs6/miuvig_investigation_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_investigation_type + + + + +URI: [mixs.vocab:MIUVIG_investigation_type](https://w3id.org/mixs/vocab/MIUVIG_investigation_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [investigation_type](investigation_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_lat_lon.md b/mixs6/miuvig_lat_lon.md new file mode 100644 index 00000000..5e10ade0 --- /dev/null +++ b/mixs6/miuvig_lat_lon.md @@ -0,0 +1,23 @@ + +# Slot: MIUVIG_lat_lon + + + + +URI: [mixs.vocab:MIUVIG_lat_lon](https://w3id.org/mixs/vocab/MIUVIG_lat_lon) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [lat_lon](lat_lon.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) diff --git a/mixs6/miuvig_lib_layout.md b/mixs6/miuvig_lib_layout.md new file mode 100644 index 00000000..c586c195 --- /dev/null +++ b/mixs6/miuvig_lib_layout.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_layout + + + + +URI: [mixs.vocab:MIUVIG_lib_layout](https://w3id.org/mixs/vocab/MIUVIG_lib_layout) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [lib_layout](lib_layout.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_reads_seqd.md b/mixs6/miuvig_lib_reads_seqd.md new file mode 100644 index 00000000..dd73845c --- /dev/null +++ b/mixs6/miuvig_lib_reads_seqd.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_reads_seqd + + + + +URI: [mixs.vocab:MIUVIG_lib_reads_seqd](https://w3id.org/mixs/vocab/MIUVIG_lib_reads_seqd) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_reads_seqd](lib_reads_seqd.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_screen.md b/mixs6/miuvig_lib_screen.md new file mode 100644 index 00000000..b165ba37 --- /dev/null +++ b/mixs6/miuvig_lib_screen.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_screen + + + + +URI: [mixs.vocab:MIUVIG_lib_screen](https://w3id.org/mixs/vocab/MIUVIG_lib_screen) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_screen](lib_screen.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_size.md b/mixs6/miuvig_lib_size.md new file mode 100644 index 00000000..d90a7681 --- /dev/null +++ b/mixs6/miuvig_lib_size.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_size + + + + +URI: [mixs.vocab:MIUVIG_lib_size](https://w3id.org/mixs/vocab/MIUVIG_lib_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_size](lib_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_lib_vector.md b/mixs6/miuvig_lib_vector.md new file mode 100644 index 00000000..784f3acc --- /dev/null +++ b/mixs6/miuvig_lib_vector.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_lib_vector + + + + +URI: [mixs.vocab:MIUVIG_lib_vector](https://w3id.org/mixs/vocab/MIUVIG_lib_vector) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [lib_vector](lib_vector.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_mag_cov_software.md b/mixs6/miuvig_mag_cov_software.md new file mode 100644 index 00000000..a3014ec6 --- /dev/null +++ b/mixs6/miuvig_mag_cov_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_mag_cov_software + + + + +URI: [mixs.vocab:MIUVIG_mag_cov_software](https://w3id.org/mixs/vocab/MIUVIG_mag_cov_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [mag_cov_software](mag_cov_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_mid.md b/mixs6/miuvig_mid.md new file mode 100644 index 00000000..7706eee3 --- /dev/null +++ b/mixs6/miuvig_mid.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_mid + + + + +URI: [mixs.vocab:MIUVIG_mid](https://w3id.org/mixs/vocab/MIUVIG_mid) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [mid](mid.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_nucl_acid_amp.md b/mixs6/miuvig_nucl_acid_amp.md new file mode 100644 index 00000000..c1a844bd --- /dev/null +++ b/mixs6/miuvig_nucl_acid_amp.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_nucl_acid_amp + + + + +URI: [mixs.vocab:MIUVIG_nucl_acid_amp](https://w3id.org/mixs/vocab/MIUVIG_nucl_acid_amp) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_amp](nucl_acid_amp.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_nucl_acid_ext.md b/mixs6/miuvig_nucl_acid_ext.md new file mode 100644 index 00000000..8ac66447 --- /dev/null +++ b/mixs6/miuvig_nucl_acid_ext.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_nucl_acid_ext + + + + +URI: [mixs.vocab:MIUVIG_nucl_acid_ext](https://w3id.org/mixs/vocab/MIUVIG_nucl_acid_ext) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucl_acid_ext](nucl_acid_ext.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_number_contig.md b/mixs6/miuvig_number_contig.md new file mode 100644 index 00000000..65153efb --- /dev/null +++ b/mixs6/miuvig_number_contig.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_number_contig + + + + +URI: [mixs.vocab:MIUVIG_number_contig](https://w3id.org/mixs/vocab/MIUVIG_number_contig) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [number_contig](number_contig.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pathogenicity.md b/mixs6/miuvig_pathogenicity.md new file mode 100644 index 00000000..a8513c3d --- /dev/null +++ b/mixs6/miuvig_pathogenicity.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pathogenicity + + + + +URI: [mixs.vocab:MIUVIG_pathogenicity](https://w3id.org/mixs/vocab/MIUVIG_pathogenicity) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [pathogenicity](pathogenicity.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pred_genome_struc.md b/mixs6/miuvig_pred_genome_struc.md new file mode 100644 index 00000000..e65cacfe --- /dev/null +++ b/mixs6/miuvig_pred_genome_struc.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pred_genome_struc + + + + +URI: [mixs.vocab:MIUVIG_pred_genome_struc](https://w3id.org/mixs/vocab/MIUVIG_pred_genome_struc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [pred_genome_struc](pred_genome_struc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_pred_genome_type.md b/mixs6/miuvig_pred_genome_type.md new file mode 100644 index 00000000..92bb1df7 --- /dev/null +++ b/mixs6/miuvig_pred_genome_type.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_pred_genome_type + + + + +URI: [mixs.vocab:MIUVIG_pred_genome_type](https://w3id.org/mixs/vocab/MIUVIG_pred_genome_type) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [pred_genome_type](pred_genome_type.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_project_name.md b/mixs6/miuvig_project_name.md new file mode 100644 index 00000000..fdde3b1e --- /dev/null +++ b/mixs6/miuvig_project_name.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_project_name + + + + +URI: [mixs.vocab:MIUVIG_project_name](https://w3id.org/mixs/vocab/MIUVIG_project_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [project_name](project_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_reassembly_bin.md b/mixs6/miuvig_reassembly_bin.md new file mode 100644 index 00000000..b22bac5c --- /dev/null +++ b/mixs6/miuvig_reassembly_bin.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_reassembly_bin + + + + +URI: [mixs.vocab:MIUVIG_reassembly_bin](https://w3id.org/mixs/vocab/MIUVIG_reassembly_bin) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [reassembly_bin](reassembly_bin.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_ref_biomaterial.md b/mixs6/miuvig_ref_biomaterial.md new file mode 100644 index 00000000..a31d3e4d --- /dev/null +++ b/mixs6/miuvig_ref_biomaterial.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_ref_biomaterial + + + + +URI: [mixs.vocab:MIUVIG_ref_biomaterial](https://w3id.org/mixs/vocab/MIUVIG_ref_biomaterial) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_biomaterial](ref_biomaterial.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_ref_db.md b/mixs6/miuvig_ref_db.md new file mode 100644 index 00000000..45160b73 --- /dev/null +++ b/mixs6/miuvig_ref_db.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_ref_db + + + + +URI: [mixs.vocab:MIUVIG_ref_db](https://w3id.org/mixs/vocab/MIUVIG_ref_db) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [ref_db](ref_db.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_collect_device.md b/mixs6/miuvig_samp_collect_device.md new file mode 100644 index 00000000..c0fef2c1 --- /dev/null +++ b/mixs6/miuvig_samp_collect_device.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_samp_collect_device + + + + +URI: [mixs.vocab:MIUVIG_samp_collect_device](https://w3id.org/mixs/vocab/MIUVIG_samp_collect_device) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_collect_device](samp_collect_device.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_mat_process.md b/mixs6/miuvig_samp_mat_process.md new file mode 100644 index 00000000..60f5db1b --- /dev/null +++ b/mixs6/miuvig_samp_mat_process.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_samp_mat_process + + + + +URI: [mixs.vocab:MIUVIG_samp_mat_process](https://w3id.org/mixs/vocab/MIUVIG_samp_mat_process) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [samp_mat_process](samp_mat_process.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_size.md b/mixs6/miuvig_samp_size.md new file mode 100644 index 00000000..eca8e8fa --- /dev/null +++ b/mixs6/miuvig_samp_size.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_samp_size + + + + +URI: [mixs.vocab:MIUVIG_samp_size](https://w3id.org/mixs/vocab/MIUVIG_samp_size) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [QuantityValue](QuantityValue.md) + +## Parents + + * is_a: [samp_size](samp_size.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sample_name.md b/mixs6/miuvig_sample_name.md new file mode 100644 index 00000000..b1f4ac41 --- /dev/null +++ b/mixs6/miuvig_sample_name.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_sample_name + + + + +URI: [mixs.vocab:MIUVIG_sample_name](https://w3id.org/mixs/vocab/MIUVIG_sample_name) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_name](sample_name.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_seq_meth.md b/mixs6/miuvig_seq_meth.md new file mode 100644 index 00000000..00687d2f --- /dev/null +++ b/mixs6/miuvig_seq_meth.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_seq_meth + + + + +URI: [mixs.vocab:MIUVIG_seq_meth](https://w3id.org/mixs/vocab/MIUVIG_seq_meth) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [seq_meth](seq_meth.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_sim_search_meth.md b/mixs6/miuvig_sim_search_meth.md new file mode 100644 index 00000000..67926fe9 --- /dev/null +++ b/mixs6/miuvig_sim_search_meth.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sim_search_meth + + + + +URI: [mixs.vocab:MIUVIG_sim_search_meth](https://w3id.org/mixs/vocab/MIUVIG_sim_search_meth) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sim_search_meth](sim_search_meth.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_single_cell_lysis_appr.md b/mixs6/miuvig_single_cell_lysis_appr.md new file mode 100644 index 00000000..da873597 --- /dev/null +++ b/mixs6/miuvig_single_cell_lysis_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_single_cell_lysis_appr + + + + +URI: [mixs.vocab:MIUVIG_single_cell_lysis_appr](https://w3id.org/mixs/vocab/MIUVIG_single_cell_lysis_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [single_cell_lysis_appr](single_cell_lysis_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_single_cell_lysis_prot.md b/mixs6/miuvig_single_cell_lysis_prot.md new file mode 100644 index 00000000..2445d9aa --- /dev/null +++ b/mixs6/miuvig_single_cell_lysis_prot.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_single_cell_lysis_prot + + + + +URI: [mixs.vocab:MIUVIG_single_cell_lysis_prot](https://w3id.org/mixs/vocab/MIUVIG_single_cell_lysis_prot) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [single_cell_lysis_prot](single_cell_lysis_prot.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_size_frac.md b/mixs6/miuvig_size_frac.md new file mode 100644 index 00000000..509e9bc0 --- /dev/null +++ b/mixs6/miuvig_size_frac.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_size_frac + + + + +URI: [mixs.vocab:MIUVIG_size_frac](https://w3id.org/mixs/vocab/MIUVIG_size_frac) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [size_frac](size_frac.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sop.md b/mixs6/miuvig_sop.md new file mode 100644 index 00000000..3289ec69 --- /dev/null +++ b/mixs6/miuvig_sop.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sop + + + + +URI: [mixs.vocab:MIUVIG_sop](https://w3id.org/mixs/vocab/MIUVIG_sop) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sop](sop.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_sort_tech.md b/mixs6/miuvig_sort_tech.md new file mode 100644 index 00000000..6d6a6e28 --- /dev/null +++ b/mixs6/miuvig_sort_tech.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sort_tech + + + + +URI: [mixs.vocab:MIUVIG_sort_tech](https://w3id.org/mixs/vocab/MIUVIG_sort_tech) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [sort_tech](sort_tech.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_source_mat_id.md b/mixs6/miuvig_source_mat_id.md new file mode 100644 index 00000000..5be280f7 --- /dev/null +++ b/mixs6/miuvig_source_mat_id.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_source_mat_id + + + + +URI: [mixs.vocab:MIUVIG_source_mat_id](https://w3id.org/mixs/vocab/MIUVIG_source_mat_id) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [source_mat_id](source_mat_id.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_source_uvig.md b/mixs6/miuvig_source_uvig.md new file mode 100644 index 00000000..8f4e0d1c --- /dev/null +++ b/mixs6/miuvig_source_uvig.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_source_uvig + + + + +URI: [mixs.vocab:MIUVIG_source_uvig](https://w3id.org/mixs/vocab/MIUVIG_source_uvig) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [source_uvig](source_uvig.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_specific_host.md b/mixs6/miuvig_specific_host.md new file mode 100644 index 00000000..554e8924 --- /dev/null +++ b/mixs6/miuvig_specific_host.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_specific_host + + + + +URI: [mixs.vocab:MIUVIG_specific_host](https://w3id.org/mixs/vocab/MIUVIG_specific_host) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [specific_host](specific_host.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_submitted_to_insdc.md b/mixs6/miuvig_submitted_to_insdc.md new file mode 100644 index 00000000..235fc6a0 --- /dev/null +++ b/mixs6/miuvig_submitted_to_insdc.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_submitted_to_insdc + + + + +URI: [mixs.vocab:MIUVIG_submitted_to_insdc](https://w3id.org/mixs/vocab/MIUVIG_submitted_to_insdc) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [submitted_to_insdc](submitted_to_insdc.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_tax_class.md b/mixs6/miuvig_tax_class.md new file mode 100644 index 00000000..816b70b0 --- /dev/null +++ b/mixs6/miuvig_tax_class.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_tax_class + + + + +URI: [mixs.vocab:MIUVIG_tax_class](https://w3id.org/mixs/vocab/MIUVIG_tax_class) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [tax_class](tax_class.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_tax_ident.md b/mixs6/miuvig_tax_ident.md new file mode 100644 index 00000000..14c3f884 --- /dev/null +++ b/mixs6/miuvig_tax_ident.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_tax_ident + + + + +URI: [mixs.vocab:MIUVIG_tax_ident](https://w3id.org/mixs/vocab/MIUVIG_tax_ident) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT + +## Parents + + * is_a: [tax_ident](tax_ident.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_trna_ext_software.md b/mixs6/miuvig_trna_ext_software.md new file mode 100644 index 00000000..95f2b597 --- /dev/null +++ b/mixs6/miuvig_trna_ext_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_trna_ext_software + + + + +URI: [mixs.vocab:MIUVIG_trna_ext_software](https://w3id.org/mixs/vocab/MIUVIG_trna_ext_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trna_ext_software](trna_ext_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_trnas.md b/mixs6/miuvig_trnas.md new file mode 100644 index 00000000..4ec928f5 --- /dev/null +++ b/mixs6/miuvig_trnas.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_trnas + + + + +URI: [mixs.vocab:MIUVIG_trnas](https://w3id.org/mixs/vocab/MIUVIG_trnas) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [trnas](trnas.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_url.md b/mixs6/miuvig_url.md new file mode 100644 index 00000000..9219ddb4 --- /dev/null +++ b/mixs6/miuvig_url.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_url + + + + +URI: [mixs.vocab:MIUVIG_url](https://w3id.org/mixs/vocab/MIUVIG_url) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [url](url.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_vir_ident_software.md b/mixs6/miuvig_vir_ident_software.md new file mode 100644 index 00000000..64c4c086 --- /dev/null +++ b/mixs6/miuvig_vir_ident_software.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_vir_ident_software + + + + +URI: [mixs.vocab:MIUVIG_vir_ident_software](https://w3id.org/mixs/vocab/MIUVIG_vir_ident_software) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) + +## Parents + + * is_a: [vir_ident_software](vir_ident_software.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_virus_enrich_appr.md b/mixs6/miuvig_virus_enrich_appr.md new file mode 100644 index 00000000..4d9e6441 --- /dev/null +++ b/mixs6/miuvig_virus_enrich_appr.md @@ -0,0 +1,40 @@ + +# Slot: MIUVIG_virus_enrich_appr + + + + +URI: [mixs.vocab:MIUVIG_virus_enrich_appr](https://w3id.org/mixs/vocab/MIUVIG_virus_enrich_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> REQ + +## Parents + + * is_a: [virus_enrich_appr](virus_enrich_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) diff --git a/mixs6/miuvig_votu_class_appr.md b/mixs6/miuvig_votu_class_appr.md new file mode 100644 index 00000000..b68330ad --- /dev/null +++ b/mixs6/miuvig_votu_class_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_class_appr + + + + +URI: [mixs.vocab:MIUVIG_votu_class_appr](https://w3id.org/mixs/vocab/MIUVIG_votu_class_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_class_appr](votu_class_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_votu_db.md b/mixs6/miuvig_votu_db.md new file mode 100644 index 00000000..5c4c96c1 --- /dev/null +++ b/mixs6/miuvig_votu_db.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_db + + + + +URI: [mixs.vocab:MIUVIG_votu_db](https://w3id.org/mixs/vocab/MIUVIG_votu_db) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_db](votu_db.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_votu_seq_comp_appr.md b/mixs6/miuvig_votu_seq_comp_appr.md new file mode 100644 index 00000000..71f7abde --- /dev/null +++ b/mixs6/miuvig_votu_seq_comp_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_votu_seq_comp_appr + + + + +URI: [mixs.vocab:MIUVIG_votu_seq_comp_appr](https://w3id.org/mixs/vocab/MIUVIG_votu_seq_comp_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [votu_seq_comp_appr](votu_seq_comp_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_wga_amp_appr.md b/mixs6/miuvig_wga_amp_appr.md new file mode 100644 index 00000000..1710900f --- /dev/null +++ b/mixs6/miuvig_wga_amp_appr.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_wga_amp_appr + + + + +URI: [mixs.vocab:MIUVIG_wga_amp_appr](https://w3id.org/mixs/vocab/MIUVIG_wga_amp_appr) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_appr](wga_amp_appr.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_wga_amp_kit.md b/mixs6/miuvig_wga_amp_kit.md new file mode 100644 index 00000000..b19690ac --- /dev/null +++ b/mixs6/miuvig_wga_amp_kit.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_wga_amp_kit + + + + +URI: [mixs.vocab:MIUVIG_wga_amp_kit](https://w3id.org/mixs/vocab/MIUVIG_wga_amp_kit) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [wga_amp_kit](wga_amp_kit.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/n_alkanes.md b/mixs6/n_alkanes.md index fe45fdb9..9808f2bc 100644 --- a/mixs6/n_alkanes.md +++ b/mixs6/n_alkanes.md @@ -21,41 +21,41 @@ None -> OPT [String](types/String.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/nitrate.md b/mixs6/nitrate.md index 5294fc32..95ce10f2 100644 --- a/mixs6/nitrate.md +++ b/mixs6/nitrate.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/nitrite.md b/mixs6/nitrite.md index 4b8270fb..973719d7 100644 --- a/mixs6/nitrite.md +++ b/mixs6/nitrite.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/nitro.md b/mixs6/nitro.md index ae6b4849..0f77f2a4 100644 --- a/mixs6/nitro.md +++ b/mixs6/nitro.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/non_mineral_nutr_regm.md b/mixs6/non_mineral_nutr_regm.md index b703354c..c328660e 100644 --- a/mixs6/non_mineral_nutr_regm.md +++ b/mixs6/non_mineral_nutr_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/nose_mouth_teeth_throat_disord.md b/mixs6/nose_mouth_teeth_throat_disord.md index f489788f..2b3adc0b 100644 --- a/mixs6/nose_mouth_teeth_throat_disord.md +++ b/mixs6/nose_mouth_teeth_throat_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) ## Other properties diff --git a/mixs6/nose_throat_disord.md b/mixs6/nose_throat_disord.md index 8f34c848..994c51a1 100644 --- a/mixs6/nose_throat_disord.md +++ b/mixs6/nose_throat_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/nucl_acid_amp.md b/mixs6/nucl_acid_amp.md index 00d60643..b0d9531a 100644 --- a/mixs6/nucl_acid_amp.md +++ b/mixs6/nucl_acid_amp.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞nucl_acid_amp](me_nucl_acid_amp.md) - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) - * [migs_org➞nucl_acid_amp](migs_org_nucl_acid_amp.md) - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) - * [mimag➞nucl_acid_amp](mimag_nucl_acid_amp.md) - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) - * [misag➞nucl_acid_amp](misag_nucl_acid_amp.md) - * [miuvig➞nucl_acid_amp](miuvig_nucl_acid_amp.md) + * [ME➞nucl_acid_amp](ME_nucl_acid_amp.md) + * [MIGS bacteria➞nucl_acid_amp](MIGS_bacteria_nucl_acid_amp.md) + * [MIGS eukaryote➞nucl_acid_amp](MIGS_eukaryote_nucl_acid_amp.md) + * [MIGS org➞nucl_acid_amp](MIGS_org_nucl_acid_amp.md) + * [MIGS plant➞nucl_acid_amp](MIGS_plant_nucl_acid_amp.md) + * [MIGS virus➞nucl_acid_amp](MIGS_virus_nucl_acid_amp.md) + * [MIMAG➞nucl_acid_amp](MIMAG_nucl_acid_amp.md) + * [MIMARKS specimen➞nucl_acid_amp](MIMARKS_specimen_nucl_acid_amp.md) + * [MIMARKS survey➞nucl_acid_amp](MIMARKS_survey_nucl_acid_amp.md) + * [MISAG➞nucl_acid_amp](MISAG_nucl_acid_amp.md) + * [MIUVIG➞nucl_acid_amp](MIUVIG_nucl_acid_amp.md) ## Used by diff --git a/mixs6/nucl_acid_ext.md b/mixs6/nucl_acid_ext.md index b49b4624..00180d9c 100644 --- a/mixs6/nucl_acid_ext.md +++ b/mixs6/nucl_acid_ext.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞nucl_acid_ext](me_nucl_acid_ext.md) - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) - * [migs_org➞nucl_acid_ext](migs_org_nucl_acid_ext.md) - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) - * [mimag➞nucl_acid_ext](mimag_nucl_acid_ext.md) - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) - * [misag➞nucl_acid_ext](misag_nucl_acid_ext.md) - * [miuvig➞nucl_acid_ext](miuvig_nucl_acid_ext.md) + * [ME➞nucl_acid_ext](ME_nucl_acid_ext.md) + * [MIGS bacteria➞nucl_acid_ext](MIGS_bacteria_nucl_acid_ext.md) + * [MIGS eukaryote➞nucl_acid_ext](MIGS_eukaryote_nucl_acid_ext.md) + * [MIGS org➞nucl_acid_ext](MIGS_org_nucl_acid_ext.md) + * [MIGS plant➞nucl_acid_ext](MIGS_plant_nucl_acid_ext.md) + * [MIGS virus➞nucl_acid_ext](MIGS_virus_nucl_acid_ext.md) + * [MIMAG➞nucl_acid_ext](MIMAG_nucl_acid_ext.md) + * [MIMARKS specimen➞nucl_acid_ext](MIMARKS_specimen_nucl_acid_ext.md) + * [MIMARKS survey➞nucl_acid_ext](MIMARKS_survey_nucl_acid_ext.md) + * [MISAG➞nucl_acid_ext](MISAG_nucl_acid_ext.md) + * [MIUVIG➞nucl_acid_ext](MIUVIG_nucl_acid_ext.md) ## Used by diff --git a/mixs6/num_replicons.md b/mixs6/num_replicons.md index 35ba25c8..4331e28f 100644 --- a/mixs6/num_replicons.md +++ b/mixs6/num_replicons.md @@ -17,9 +17,9 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) + * [MIGS bacteria➞num_replicons](MIGS_bacteria_num_replicons.md) + * [MIGS eukaryote➞num_replicons](MIGS_eukaryote_num_replicons.md) + * [MIGS virus➞num_replicons](MIGS_virus_num_replicons.md) ## Used by diff --git a/mixs6/number_contig.md b/mixs6/number_contig.md index bbbef608..f1cf1324 100644 --- a/mixs6/number_contig.md +++ b/mixs6/number_contig.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞number_contig](me_number_contig.md) - * [migs_ba➞number_contig](migs_ba_number_contig.md) - * [migs_eu➞number_contig](migs_eu_number_contig.md) - * [migs_org➞number_contig](migs_org_number_contig.md) - * [migs_pl➞number_contig](migs_pl_number_contig.md) - * [migs_vi➞number_contig](migs_vi_number_contig.md) - * [mimag➞number_contig](mimag_number_contig.md) - * [misag➞number_contig](misag_number_contig.md) - * [miuvig➞number_contig](miuvig_number_contig.md) + * [ME➞number_contig](ME_number_contig.md) + * [MIGS bacteria➞number_contig](MIGS_bacteria_number_contig.md) + * [MIGS eukaryote➞number_contig](MIGS_eukaryote_number_contig.md) + * [MIGS org➞number_contig](MIGS_org_number_contig.md) + * [MIGS plant➞number_contig](MIGS_plant_number_contig.md) + * [MIGS virus➞number_contig](MIGS_virus_number_contig.md) + * [MIMAG➞number_contig](MIMAG_number_contig.md) + * [MISAG➞number_contig](MISAG_number_contig.md) + * [MIUVIG➞number_contig](MIUVIG_number_contig.md) ## Used by diff --git a/mixs6/number_pets.md b/mixs6/number_pets.md index c4df6476..8bfe99d4 100644 --- a/mixs6/number_pets.md +++ b/mixs6/number_pets.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/number_plants.md b/mixs6/number_plants.md index 9700fafa..e83bda15 100644 --- a/mixs6/number_plants.md +++ b/mixs6/number_plants.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/number_resident.md b/mixs6/number_resident.md index 91b2876e..dcd222b8 100644 --- a/mixs6/number_resident.md +++ b/mixs6/number_resident.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/occup_density_samp.md b/mixs6/occup_density_samp.md index 9f21d64b..d6b4e88c 100644 --- a/mixs6/occup_density_samp.md +++ b/mixs6/occup_density_samp.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/occup_document.md b/mixs6/occup_document.md index 40548460..6fb56e74 100644 --- a/mixs6/occup_document.md +++ b/mixs6/occup_document.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/occup_samp.md b/mixs6/occup_samp.md index a1743786..94c16be0 100644 --- a/mixs6/occup_samp.md +++ b/mixs6/occup_samp.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/org_carb.md b/mixs6/org_carb.md index 363eaa9c..3ddc21ea 100644 --- a/mixs6/org_carb.md +++ b/mixs6/org_carb.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/org_matter.md b/mixs6/org_matter.md index acbf7cf4..f9ecd874 100644 --- a/mixs6/org_matter.md +++ b/mixs6/org_matter.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/org_nitro.md b/mixs6/org_nitro.md index 9ac7700b..8e786400 100644 --- a/mixs6/org_nitro.md +++ b/mixs6/org_nitro.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/org_particles.md b/mixs6/org_particles.md index 8be37984..c1febbcd 100644 --- a/mixs6/org_particles.md +++ b/mixs6/org_particles.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/organism_count.md b/mixs6/organism_count.md index 50cdcbfb..411f4277 100644 --- a/mixs6/organism_count.md +++ b/mixs6/organism_count.md @@ -21,197 +21,197 @@ None -> OPT ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/organism_count_qpcr_info.md b/mixs6/organism_count_qpcr_info.md index 3969c83d..930d3f80 100644 --- a/mixs6/organism_count_qpcr_info.md +++ b/mixs6/organism_count_qpcr_info.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/owc_tvdss.md b/mixs6/owc_tvdss.md index 95d4d1e0..1f464f29 100644 --- a/mixs6/owc_tvdss.md +++ b/mixs6/owc_tvdss.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/oxy_stat_samp.md b/mixs6/oxy_stat_samp.md index e4d6aa26..f7c12893 100644 --- a/mixs6/oxy_stat_samp.md +++ b/mixs6/oxy_stat_samp.md @@ -21,185 +21,185 @@ None -> OPT ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/oxygen.md b/mixs6/oxygen.md index 925ab518..bd5ca5fd 100644 --- a/mixs6/oxygen.md +++ b/mixs6/oxygen.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/part_org_carb.md b/mixs6/part_org_carb.md index ff9307ed..c828044a 100644 --- a/mixs6/part_org_carb.md +++ b/mixs6/part_org_carb.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/part_org_nitro.md b/mixs6/part_org_nitro.md index 3782755d..cde8f82a 100644 --- a/mixs6/part_org_nitro.md +++ b/mixs6/part_org_nitro.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/particle_class.md b/mixs6/particle_class.md index 3192bef6..ce3b5732 100644 --- a/mixs6/particle_class.md +++ b/mixs6/particle_class.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) ## Other properties diff --git a/mixs6/pathogenicity.md b/mixs6/pathogenicity.md index b277a4b7..8b6748c0 100644 --- a/mixs6/pathogenicity.md +++ b/mixs6/pathogenicity.md @@ -17,10 +17,10 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) - * [miuvig➞pathogenicity](miuvig_pathogenicity.md) + * [MIGS bacteria➞pathogenicity](MIGS_bacteria_pathogenicity.md) + * [MIGS eukaryote➞pathogenicity](MIGS_eukaryote_pathogenicity.md) + * [MIGS virus➞pathogenicity](MIGS_virus_pathogenicity.md) + * [MIUVIG➞pathogenicity](MIUVIG_pathogenicity.md) ## Used by diff --git a/mixs6/pcr_cond.md b/mixs6/pcr_cond.md index 28aed573..89b637b6 100644 --- a/mixs6/pcr_cond.md +++ b/mixs6/pcr_cond.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) + * [MIMARKS specimen➞pcr_cond](MIMARKS_specimen_pcr_cond.md) + * [MIMARKS survey➞pcr_cond](MIMARKS_survey_pcr_cond.md) ## Used by diff --git a/mixs6/pcr_primers.md b/mixs6/pcr_primers.md index df23eee3..e3806479 100644 --- a/mixs6/pcr_primers.md +++ b/mixs6/pcr_primers.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) + * [MIMARKS specimen➞pcr_primers](MIMARKS_specimen_pcr_primers.md) + * [MIMARKS survey➞pcr_primers](MIMARKS_survey_pcr_primers.md) ## Used by diff --git a/mixs6/permeability.md b/mixs6/permeability.md index 590c17c2..a5b76ced 100644 --- a/mixs6/permeability.md +++ b/mixs6/permeability.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/perturbation.md b/mixs6/perturbation.md index b53feaf9..23cec6be 100644 --- a/mixs6/perturbation.md +++ b/mixs6/perturbation.md @@ -21,161 +21,161 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/pesticide_regm.md b/mixs6/pesticide_regm.md index 05c8b2e4..88a03381 100644 --- a/mixs6/pesticide_regm.md +++ b/mixs6/pesticide_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/pet_farm_animal.md b/mixs6/pet_farm_animal.md index 90f7bfd0..ce73318a 100644 --- a/mixs6/pet_farm_animal.md +++ b/mixs6/pet_farm_animal.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/petroleum_hydrocarb.md b/mixs6/petroleum_hydrocarb.md index 81c49fc8..308274a9 100644 --- a/mixs6/petroleum_hydrocarb.md +++ b/mixs6/petroleum_hydrocarb.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/ph.md b/mixs6/ph.md index cb1e4755..20b75298 100644 --- a/mixs6/ph.md +++ b/mixs6/ph.md @@ -21,101 +21,101 @@ None -> OPT [Double](types/Double.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/ph_meth.md b/mixs6/ph_meth.md index 54d63510..565af776 100644 --- a/mixs6/ph_meth.md +++ b/mixs6/ph_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/ph_regm.md b/mixs6/ph_regm.md index 828e21cb..d6b8be04 100644 --- a/mixs6/ph_regm.md +++ b/mixs6/ph_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/phaeopigments.md b/mixs6/phaeopigments.md index 868a5581..31c2ae2b 100644 --- a/mixs6/phaeopigments.md +++ b/mixs6/phaeopigments.md @@ -21,41 +21,41 @@ None -> OPT [String](types/String.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/phosphate.md b/mixs6/phosphate.md index 1aa68564..fbf309a6 100644 --- a/mixs6/phosphate.md +++ b/mixs6/phosphate.md @@ -21,65 +21,65 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/phosplipid_fatt_acid.md b/mixs6/phosplipid_fatt_acid.md index 9843e722..95d796aa 100644 --- a/mixs6/phosplipid_fatt_acid.md +++ b/mixs6/phosplipid_fatt_acid.md @@ -21,53 +21,53 @@ None -> OPT [String](types/String.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/photon_flux.md b/mixs6/photon_flux.md index 3f18247f..2a6b1729 100644 --- a/mixs6/photon_flux.md +++ b/mixs6/photon_flux.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/plant_growth_med.md b/mixs6/plant_growth_med.md index 958733c5..95729514 100644 --- a/mixs6/plant_growth_med.md +++ b/mixs6/plant_growth_med.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/plant_product.md b/mixs6/plant_product.md index 625a85bf..90ad01e0 100644 --- a/mixs6/plant_product.md +++ b/mixs6/plant_product.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/plant_sex.md b/mixs6/plant_sex.md index b49c67a4..af3f4182 100644 --- a/mixs6/plant_sex.md +++ b/mixs6/plant_sex.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/plant_struc.md b/mixs6/plant_struc.md index 13195696..d40d7b2e 100644 --- a/mixs6/plant_struc.md +++ b/mixs6/plant_struc.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/ploidy.md b/mixs6/ploidy.md index 853e5d03..6fa85340 100644 --- a/mixs6/ploidy.md +++ b/mixs6/ploidy.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [migs_eu➞ploidy](migs_eu_ploidy.md) + * [MIGS eukaryote➞ploidy](MIGS_eukaryote_ploidy.md) ## Used by diff --git a/mixs6/pollutants.md b/mixs6/pollutants.md index cda94787..420ae44b 100644 --- a/mixs6/pollutants.md +++ b/mixs6/pollutants.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/pool_dna_extracts.md b/mixs6/pool_dna_extracts.md index 271b6e7d..ba6196af 100644 --- a/mixs6/pool_dna_extracts.md +++ b/mixs6/pool_dna_extracts.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/porosity.md b/mixs6/porosity.md index 894d5057..8834ba44 100644 --- a/mixs6/porosity.md +++ b/mixs6/porosity.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) ## Other properties diff --git a/mixs6/potassium.md b/mixs6/potassium.md index e4b5249f..f709fb5f 100644 --- a/mixs6/potassium.md +++ b/mixs6/potassium.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/pour_point.md b/mixs6/pour_point.md index 32f0c656..d6f9b157 100644 --- a/mixs6/pour_point.md +++ b/mixs6/pour_point.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/pre_treatment.md b/mixs6/pre_treatment.md index 22e5b57a..afaad096 100644 --- a/mixs6/pre_treatment.md +++ b/mixs6/pre_treatment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/pred_genome_struc.md b/mixs6/pred_genome_struc.md index 7cabd459..5f0c4c06 100644 --- a/mixs6/pred_genome_struc.md +++ b/mixs6/pred_genome_struc.md @@ -17,7 +17,7 @@ None -> OPT ## Children - * [miuvig➞pred_genome_struc](miuvig_pred_genome_struc.md) + * [MIUVIG➞pred_genome_struc](MIUVIG_pred_genome_struc.md) ## Used by diff --git a/mixs6/pred_genome_type.md b/mixs6/pred_genome_type.md index cca7ecda..2ea16948 100644 --- a/mixs6/pred_genome_type.md +++ b/mixs6/pred_genome_type.md @@ -17,7 +17,7 @@ None -> OPT ## Children - * [miuvig➞pred_genome_type](miuvig_pred_genome_type.md) + * [MIUVIG➞pred_genome_type](MIUVIG_pred_genome_type.md) ## Used by diff --git a/mixs6/pregnancy.md b/mixs6/pregnancy.md index 1ae70257..b148c082 100644 --- a/mixs6/pregnancy.md +++ b/mixs6/pregnancy.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/pres_animal.md b/mixs6/pres_animal.md index 3fb3fff5..1dd6f1e0 100644 --- a/mixs6/pres_animal.md +++ b/mixs6/pres_animal.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/pressure.md b/mixs6/pressure.md index f50109f9..52c21352 100644 --- a/mixs6/pressure.md +++ b/mixs6/pressure.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/previous_land_use.md b/mixs6/previous_land_use.md index d8ba829b..b91b670f 100644 --- a/mixs6/previous_land_use.md +++ b/mixs6/previous_land_use.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/previous_land_use_meth.md b/mixs6/previous_land_use_meth.md index 7b0fa348..d4ec556e 100644 --- a/mixs6/previous_land_use_meth.md +++ b/mixs6/previous_land_use_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/primary_prod.md b/mixs6/primary_prod.md index 1777c31f..dcbdf807 100644 --- a/mixs6/primary_prod.md +++ b/mixs6/primary_prod.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/primary_treatment.md b/mixs6/primary_treatment.md index fd505f46..d3fc4261 100644 --- a/mixs6/primary_treatment.md +++ b/mixs6/primary_treatment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/prod_rate.md b/mixs6/prod_rate.md index 10096100..0afab620 100644 --- a/mixs6/prod_rate.md +++ b/mixs6/prod_rate.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/prod_start_date.md b/mixs6/prod_start_date.md index ca0c9434..ea26e784 100644 --- a/mixs6/prod_start_date.md +++ b/mixs6/prod_start_date.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/profile_position.md b/mixs6/profile_position.md index 4af8338c..d092e510 100644 --- a/mixs6/profile_position.md +++ b/mixs6/profile_position.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/project_name.md b/mixs6/project_name.md index 5646099e..b09dcb56 100644 --- a/mixs6/project_name.md +++ b/mixs6/project_name.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞project_name](me_project_name.md) - * [migs_ba➞project_name](migs_ba_project_name.md) - * [migs_eu➞project_name](migs_eu_project_name.md) - * [migs_org➞project_name](migs_org_project_name.md) - * [migs_pl➞project_name](migs_pl_project_name.md) - * [migs_vi➞project_name](migs_vi_project_name.md) - * [mimag➞project_name](mimag_project_name.md) - * [mimarks_c➞project_name](mimarks_c_project_name.md) - * [mimarks_s➞project_name](mimarks_s_project_name.md) - * [misag➞project_name](misag_project_name.md) - * [miuvig➞project_name](miuvig_project_name.md) + * [ME➞project_name](ME_project_name.md) + * [MIGS bacteria➞project_name](MIGS_bacteria_project_name.md) + * [MIGS eukaryote➞project_name](MIGS_eukaryote_project_name.md) + * [MIGS org➞project_name](MIGS_org_project_name.md) + * [MIGS plant➞project_name](MIGS_plant_project_name.md) + * [MIGS virus➞project_name](MIGS_virus_project_name.md) + * [MIMAG➞project_name](MIMAG_project_name.md) + * [MIMARKS specimen➞project_name](MIMARKS_specimen_project_name.md) + * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) + * [MISAG➞project_name](MISAG_project_name.md) + * [MIUVIG➞project_name](MIUVIG_project_name.md) ## Used by diff --git a/mixs6/propagation.md b/mixs6/propagation.md index 07b0e37e..6c5918da 100644 --- a/mixs6/propagation.md +++ b/mixs6/propagation.md @@ -17,9 +17,9 @@ None -> OPT [String](types/String.md) ## Children - * [migs_eu➞propagation](migs_eu_propagation.md) - * [migs_pl➞propagation](migs_pl_propagation.md) - * [migs_vi➞propagation](migs_vi_propagation.md) + * [MIGS eukaryote➞propagation](MIGS_eukaryote_propagation.md) + * [MIGS plant➞propagation](MIGS_plant_propagation.md) + * [MIGS virus➞propagation](MIGS_virus_propagation.md) ## Used by diff --git a/mixs6/pulmonary_disord.md b/mixs6/pulmonary_disord.md index 7c59f603..ff8a8cd7 100644 --- a/mixs6/pulmonary_disord.md +++ b/mixs6/pulmonary_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/quad_pos.md b/mixs6/quad_pos.md index 0453166d..81a77ced 100644 --- a/mixs6/quad_pos.md +++ b/mixs6/quad_pos.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/quantityValue__has_numeric_value.md b/mixs6/quantityValue__has_numeric_value.md new file mode 100644 index 00000000..e6e8c1df --- /dev/null +++ b/mixs6/quantityValue__has_numeric_value.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_numeric_value + + + + +URI: [mixs.vocab:quantityValue__has_numeric_value](https://w3id.org/mixs/vocab/quantityValue__has_numeric_value) + + +## Domain and Range + +None -> OPT [Double](types/Double.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/quantityValue__has_raw_value.md b/mixs6/quantityValue__has_raw_value.md new file mode 100644 index 00000000..978be9b3 --- /dev/null +++ b/mixs6/quantityValue__has_raw_value.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_raw_value + + + + +URI: [mixs.vocab:quantityValue__has_raw_value](https://w3id.org/mixs/vocab/quantityValue__has_raw_value) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/quantityValue__has_unit.md b/mixs6/quantityValue__has_unit.md new file mode 100644 index 00000000..edcf5854 --- /dev/null +++ b/mixs6/quantityValue__has_unit.md @@ -0,0 +1,22 @@ + +# Slot: quantityValue__has_unit + + +Example "m" + +URI: [mixs.vocab:quantityValue__has_unit](https://w3id.org/mixs/vocab/quantityValue__has_unit) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + +## Children + + +## Used by + + * [QuantityValue](QuantityValue.md) diff --git a/mixs6/radiation_regm.md b/mixs6/radiation_regm.md index a8188981..7b7d4567 100644 --- a/mixs6/radiation_regm.md +++ b/mixs6/radiation_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/rainfall_regm.md b/mixs6/rainfall_regm.md index 0d96d066..0379b700 100644 --- a/mixs6/rainfall_regm.md +++ b/mixs6/rainfall_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/reactor_type.md b/mixs6/reactor_type.md index bc4d59f8..5f00dd4e 100644 --- a/mixs6/reactor_type.md +++ b/mixs6/reactor_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/reassembly_bin.md b/mixs6/reassembly_bin.md index 09474c6f..c94a38bd 100644 --- a/mixs6/reassembly_bin.md +++ b/mixs6/reassembly_bin.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞reassembly_bin](mimag_reassembly_bin.md) - * [miuvig➞reassembly_bin](miuvig_reassembly_bin.md) + * [MIMAG➞reassembly_bin](MIMAG_reassembly_bin.md) + * [MIUVIG➞reassembly_bin](MIUVIG_reassembly_bin.md) ## Used by diff --git a/mixs6/redox_potential.md b/mixs6/redox_potential.md index 3202d774..36615afe 100644 --- a/mixs6/redox_potential.md +++ b/mixs6/redox_potential.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/ref_biomaterial.md b/mixs6/ref_biomaterial.md index 0fd61e7b..1c8ebcb2 100644 --- a/mixs6/ref_biomaterial.md +++ b/mixs6/ref_biomaterial.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞ref_biomaterial](me_ref_biomaterial.md) - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) - * [migs_org➞ref_biomaterial](migs_org_ref_biomaterial.md) - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) - * [mimag➞ref_biomaterial](mimag_ref_biomaterial.md) - * [misag➞ref_biomaterial](misag_ref_biomaterial.md) - * [miuvig➞ref_biomaterial](miuvig_ref_biomaterial.md) + * [ME➞ref_biomaterial](ME_ref_biomaterial.md) + * [MIGS bacteria➞ref_biomaterial](MIGS_bacteria_ref_biomaterial.md) + * [MIGS eukaryote➞ref_biomaterial](MIGS_eukaryote_ref_biomaterial.md) + * [MIGS org➞ref_biomaterial](MIGS_org_ref_biomaterial.md) + * [MIGS plant➞ref_biomaterial](MIGS_plant_ref_biomaterial.md) + * [MIGS virus➞ref_biomaterial](MIGS_virus_ref_biomaterial.md) + * [MIMAG➞ref_biomaterial](MIMAG_ref_biomaterial.md) + * [MISAG➞ref_biomaterial](MISAG_ref_biomaterial.md) + * [MIUVIG➞ref_biomaterial](MIUVIG_ref_biomaterial.md) ## Used by diff --git a/mixs6/ref_db.md b/mixs6/ref_db.md index 88ca55a1..a7830813 100644 --- a/mixs6/ref_db.md +++ b/mixs6/ref_db.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞ref_db](me_ref_db.md) - * [migs_ba➞ref_db](migs_ba_ref_db.md) - * [migs_eu➞ref_db](migs_eu_ref_db.md) - * [migs_org➞ref_db](migs_org_ref_db.md) - * [migs_pl➞ref_db](migs_pl_ref_db.md) - * [migs_vi➞ref_db](migs_vi_ref_db.md) - * [mimag➞ref_db](mimag_ref_db.md) - * [misag➞ref_db](misag_ref_db.md) - * [miuvig➞ref_db](miuvig_ref_db.md) + * [ME➞ref_db](ME_ref_db.md) + * [MIGS bacteria➞ref_db](MIGS_bacteria_ref_db.md) + * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) + * [MIGS org➞ref_db](MIGS_org_ref_db.md) + * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) + * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) + * [MIMAG➞ref_db](MIMAG_ref_db.md) + * [MISAG➞ref_db](MISAG_ref_db.md) + * [MIUVIG➞ref_db](MIUVIG_ref_db.md) ## Used by diff --git a/mixs6/rel_air_humidity.md b/mixs6/rel_air_humidity.md index 02f129ef..ef7307f2 100644 --- a/mixs6/rel_air_humidity.md +++ b/mixs6/rel_air_humidity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/rel_humidity_out.md b/mixs6/rel_humidity_out.md index c42e7033..6d715107 100644 --- a/mixs6/rel_humidity_out.md +++ b/mixs6/rel_humidity_out.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/rel_samp_loc.md b/mixs6/rel_samp_loc.md index ee0b20b7..a5d7f3e5 100644 --- a/mixs6/rel_samp_loc.md +++ b/mixs6/rel_samp_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/rel_to_oxygen.md b/mixs6/rel_to_oxygen.md index 689c6d7c..8af98c6c 100644 --- a/mixs6/rel_to_oxygen.md +++ b/mixs6/rel_to_oxygen.md @@ -17,12 +17,12 @@ None -> OPT ## Children - * [me➞rel_to_oxygen](me_rel_to_oxygen.md) - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) - * [mimag➞rel_to_oxygen](mimag_rel_to_oxygen.md) - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) - * [misag➞rel_to_oxygen](misag_rel_to_oxygen.md) + * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) + * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) + * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) + * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) + * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) + * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) ## Used by diff --git a/mixs6/reservoir.md b/mixs6/reservoir.md index 4a283f36..1a2754ba 100644 --- a/mixs6/reservoir.md +++ b/mixs6/reservoir.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/resins_pc.md b/mixs6/resins_pc.md index 04b1a07a..48d36240 100644 --- a/mixs6/resins_pc.md +++ b/mixs6/resins_pc.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/resp_part_matter.md b/mixs6/resp_part_matter.md index 93161b5a..18ab9c0f 100644 --- a/mixs6/resp_part_matter.md +++ b/mixs6/resp_part_matter.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/room_air_exch_rate.md b/mixs6/room_air_exch_rate.md index 975ab88a..21cbce51 100644 --- a/mixs6/room_air_exch_rate.md +++ b/mixs6/room_air_exch_rate.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_architec_element.md b/mixs6/room_architec_element.md index dfa6caf5..8fc56935 100644 --- a/mixs6/room_architec_element.md +++ b/mixs6/room_architec_element.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_condt.md b/mixs6/room_condt.md index cfff06fb..2a1393f6 100644 --- a/mixs6/room_condt.md +++ b/mixs6/room_condt.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_connected.md b/mixs6/room_connected.md index 1424b527..f39788e4 100644 --- a/mixs6/room_connected.md +++ b/mixs6/room_connected.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_count.md b/mixs6/room_count.md index 1de37476..3cdb20f8 100644 --- a/mixs6/room_count.md +++ b/mixs6/room_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_dim.md b/mixs6/room_dim.md index 7ced664d..1cba763b 100644 --- a/mixs6/room_dim.md +++ b/mixs6/room_dim.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_door_dist.md b/mixs6/room_door_dist.md index 8d4f36fa..206ca8cc 100644 --- a/mixs6/room_door_dist.md +++ b/mixs6/room_door_dist.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_door_share.md b/mixs6/room_door_share.md index 4bc1e713..22b0da5d 100644 --- a/mixs6/room_door_share.md +++ b/mixs6/room_door_share.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_hallway.md b/mixs6/room_hallway.md index f2a23571..60fc8f2f 100644 --- a/mixs6/room_hallway.md +++ b/mixs6/room_hallway.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_loc.md b/mixs6/room_loc.md index 2b3784a1..720b0887 100644 --- a/mixs6/room_loc.md +++ b/mixs6/room_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_moist_damage_hist.md b/mixs6/room_moist_damage_hist.md index c5a5953f..1f7f12d9 100644 --- a/mixs6/room_moist_damage_hist.md +++ b/mixs6/room_moist_damage_hist.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_net_area.md b/mixs6/room_net_area.md index dbaa11b4..bce188ad 100644 --- a/mixs6/room_net_area.md +++ b/mixs6/room_net_area.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_occup.md b/mixs6/room_occup.md index 16a26a99..5ef9a1dc 100644 --- a/mixs6/room_occup.md +++ b/mixs6/room_occup.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_samp_pos.md b/mixs6/room_samp_pos.md index f2f2039c..7003f8f1 100644 --- a/mixs6/room_samp_pos.md +++ b/mixs6/room_samp_pos.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_type.md b/mixs6/room_type.md index 31daca4d..ea4b27bf 100644 --- a/mixs6/room_type.md +++ b/mixs6/room_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_vol.md b/mixs6/room_vol.md index 4663e653..6392d5da 100644 --- a/mixs6/room_vol.md +++ b/mixs6/room_vol.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_wall_share.md b/mixs6/room_wall_share.md index 6a251043..68063d5a 100644 --- a/mixs6/room_wall_share.md +++ b/mixs6/room_wall_share.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/room_window_count.md b/mixs6/room_window_count.md index 111ac2db..2a13261c 100644 --- a/mixs6/room_window_count.md +++ b/mixs6/room_window_count.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/root_cond.md b/mixs6/root_cond.md index ce56ec62..3165d47a 100644 --- a/mixs6/root_cond.md +++ b/mixs6/root_cond.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_carbon.md b/mixs6/root_med_carbon.md index 35d0c799..fa4cba0c 100644 --- a/mixs6/root_med_carbon.md +++ b/mixs6/root_med_carbon.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_macronutr.md b/mixs6/root_med_macronutr.md index 957c9d89..1e1f5ba2 100644 --- a/mixs6/root_med_macronutr.md +++ b/mixs6/root_med_macronutr.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_micronutr.md b/mixs6/root_med_micronutr.md index 3a2aca8c..da50d0f6 100644 --- a/mixs6/root_med_micronutr.md +++ b/mixs6/root_med_micronutr.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_ph.md b/mixs6/root_med_ph.md index 6afbdd2d..b1bb72c4 100644 --- a/mixs6/root_med_ph.md +++ b/mixs6/root_med_ph.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_regl.md b/mixs6/root_med_regl.md index 2d927495..731214dc 100644 --- a/mixs6/root_med_regl.md +++ b/mixs6/root_med_regl.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_solid.md b/mixs6/root_med_solid.md index 67ce74d3..f1b76d25 100644 --- a/mixs6/root_med_solid.md +++ b/mixs6/root_med_solid.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/root_med_suppl.md b/mixs6/root_med_suppl.md index 6c57ad83..d7c075b1 100644 --- a/mixs6/root_med_suppl.md +++ b/mixs6/root_med_suppl.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/salinity.md b/mixs6/salinity.md index ba3905b4..bf562fb4 100644 --- a/mixs6/salinity.md +++ b/mixs6/salinity.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/salinity_meth.md b/mixs6/salinity_meth.md index 0176960e..80937d28 100644 --- a/mixs6/salinity_meth.md +++ b/mixs6/salinity_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/salt_regm.md b/mixs6/salt_regm.md index e0f9c9f1..364b9e3a 100644 --- a/mixs6/salt_regm.md +++ b/mixs6/salt_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/samp_capt_status.md b/mixs6/samp_capt_status.md index 881385b1..048e6c70 100644 --- a/mixs6/samp_capt_status.md +++ b/mixs6/samp_capt_status.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/samp_collect_device.md b/mixs6/samp_collect_device.md index f3f98719..59a21dcd 100644 --- a/mixs6/samp_collect_device.md +++ b/mixs6/samp_collect_device.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞samp_collect_device](me_samp_collect_device.md) - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) - * [migs_org➞samp_collect_device](migs_org_samp_collect_device.md) - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) - * [mimag➞samp_collect_device](mimag_samp_collect_device.md) - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) - * [misag➞samp_collect_device](misag_samp_collect_device.md) - * [miuvig➞samp_collect_device](miuvig_samp_collect_device.md) + * [ME➞samp_collect_device](ME_samp_collect_device.md) + * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) + * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) + * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) + * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) + * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) + * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) + * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) + * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) + * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) + * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) ## Used by diff --git a/mixs6/samp_collection_point.md b/mixs6/samp_collection_point.md index 8eb85a36..2373015e 100644 --- a/mixs6/samp_collection_point.md +++ b/mixs6/samp_collection_point.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_dis_stage.md b/mixs6/samp_dis_stage.md index c86d8255..4640e0c7 100644 --- a/mixs6/samp_dis_stage.md +++ b/mixs6/samp_dis_stage.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/samp_floor.md b/mixs6/samp_floor.md index 46cf32c1..b485db6e 100644 --- a/mixs6/samp_floor.md +++ b/mixs6/samp_floor.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/samp_loc_corr_rate.md b/mixs6/samp_loc_corr_rate.md index 3e1ce93f..2afdd3c6 100644 --- a/mixs6/samp_loc_corr_rate.md +++ b/mixs6/samp_loc_corr_rate.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_mat_process.md b/mixs6/samp_mat_process.md index 9d7dc8f7..20839dcd 100644 --- a/mixs6/samp_mat_process.md +++ b/mixs6/samp_mat_process.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞samp_mat_process](me_samp_mat_process.md) - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) - * [migs_org➞samp_mat_process](migs_org_samp_mat_process.md) - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) - * [mimag➞samp_mat_process](mimag_samp_mat_process.md) - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) - * [misag➞samp_mat_process](misag_samp_mat_process.md) - * [miuvig➞samp_mat_process](miuvig_samp_mat_process.md) + * [ME➞samp_mat_process](ME_samp_mat_process.md) + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) ## Used by diff --git a/mixs6/samp_md.md b/mixs6/samp_md.md index 206adb58..cf96da84 100644 --- a/mixs6/samp_md.md +++ b/mixs6/samp_md.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/samp_preserv.md b/mixs6/samp_preserv.md index 4af0496f..d615e0f4 100644 --- a/mixs6/samp_preserv.md +++ b/mixs6/samp_preserv.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_room_id.md b/mixs6/samp_room_id.md index 8a47e40f..36741ba1 100644 --- a/mixs6/samp_room_id.md +++ b/mixs6/samp_room_id.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/samp_salinity.md b/mixs6/samp_salinity.md index 792a9a14..f34a059d 100644 --- a/mixs6/samp_salinity.md +++ b/mixs6/samp_salinity.md @@ -21,137 +21,137 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/samp_size.md b/mixs6/samp_size.md index bd390b51..5b96b2b9 100644 --- a/mixs6/samp_size.md +++ b/mixs6/samp_size.md @@ -17,17 +17,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Children - * [me➞samp_size](me_samp_size.md) - * [migs_ba➞samp_size](migs_ba_samp_size.md) - * [migs_eu➞samp_size](migs_eu_samp_size.md) - * [migs_org➞samp_size](migs_org_samp_size.md) - * [migs_pl➞samp_size](migs_pl_samp_size.md) - * [migs_vi➞samp_size](migs_vi_samp_size.md) - * [mimag➞samp_size](mimag_samp_size.md) - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) - * [misag➞samp_size](misag_samp_size.md) - * [miuvig➞samp_size](miuvig_samp_size.md) + * [ME➞samp_size](ME_samp_size.md) + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) + * [MIGS org➞samp_size](MIGS_org_samp_size.md) + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) + * [MIMAG➞samp_size](MIMAG_samp_size.md) + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) + * [MISAG➞samp_size](MISAG_samp_size.md) + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) ## Used by diff --git a/mixs6/samp_sort_meth.md b/mixs6/samp_sort_meth.md index 004d852a..6620affd 100644 --- a/mixs6/samp_sort_meth.md +++ b/mixs6/samp_sort_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/samp_store_dur.md b/mixs6/samp_store_dur.md index 7535d16d..c271c9e5 100644 --- a/mixs6/samp_store_dur.md +++ b/mixs6/samp_store_dur.md @@ -21,185 +21,185 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/samp_store_loc.md b/mixs6/samp_store_loc.md index 2ba8cda8..5a72cfc6 100644 --- a/mixs6/samp_store_loc.md +++ b/mixs6/samp_store_loc.md @@ -21,185 +21,185 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/samp_store_temp.md b/mixs6/samp_store_temp.md index e9af5a45..fb973fcd 100644 --- a/mixs6/samp_store_temp.md +++ b/mixs6/samp_store_temp.md @@ -21,185 +21,185 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/samp_subtype.md b/mixs6/samp_subtype.md index 9c8baebf..8fa07c34 100644 --- a/mixs6/samp_subtype.md +++ b/mixs6/samp_subtype.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_time_out.md b/mixs6/samp_time_out.md index 476a879c..978123de 100644 --- a/mixs6/samp_time_out.md +++ b/mixs6/samp_time_out.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/samp_transport_cond.md b/mixs6/samp_transport_cond.md index fc356d57..196bd163 100644 --- a/mixs6/samp_transport_cond.md +++ b/mixs6/samp_transport_cond.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_tvdss.md b/mixs6/samp_tvdss.md index b5796c80..63700453 100644 --- a/mixs6/samp_tvdss.md +++ b/mixs6/samp_tvdss.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/samp_type.md b/mixs6/samp_type.md index 8a4f67da..3e9c36c2 100644 --- a/mixs6/samp_type.md +++ b/mixs6/samp_type.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/samp_vol_we_dna_ext.md b/mixs6/samp_vol_we_dna_ext.md index 684a23ca..7ba4dd0c 100644 --- a/mixs6/samp_vol_we_dna_ext.md +++ b/mixs6/samp_vol_we_dna_ext.md @@ -21,197 +21,197 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/samp_weather.md b/mixs6/samp_weather.md index 159a6454..70b4aa0b 100644 --- a/mixs6/samp_weather.md +++ b/mixs6/samp_weather.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/samp_well_name.md b/mixs6/samp_well_name.md index d9d76e6f..dceffe3a 100644 --- a/mixs6/samp_well_name.md +++ b/mixs6/samp_well_name.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/sample_name.md b/mixs6/sample_name.md index fa336154..32b6604f 100644 --- a/mixs6/sample_name.md +++ b/mixs6/sample_name.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞sample_name](me_sample_name.md) - * [migs_ba➞sample_name](migs_ba_sample_name.md) - * [migs_eu➞sample_name](migs_eu_sample_name.md) - * [migs_org➞sample_name](migs_org_sample_name.md) - * [migs_pl➞sample_name](migs_pl_sample_name.md) - * [migs_vi➞sample_name](migs_vi_sample_name.md) - * [mimag➞sample_name](mimag_sample_name.md) - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) - * [misag➞sample_name](misag_sample_name.md) - * [miuvig➞sample_name](miuvig_sample_name.md) + * [ME➞sample_name](ME_sample_name.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) + * [MISAG➞sample_name](MISAG_sample_name.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) ## Used by diff --git a/mixs6/saturates_pc.md b/mixs6/saturates_pc.md index 4694e2ab..b1167a1b 100644 --- a/mixs6/saturates_pc.md +++ b/mixs6/saturates_pc.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/season.md b/mixs6/season.md index 6d1ddbef..112d24de 100644 --- a/mixs6/season.md +++ b/mixs6/season.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/season_environment.md b/mixs6/season_environment.md index 012d4f20..57e167b2 100644 --- a/mixs6/season_environment.md +++ b/mixs6/season_environment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/season_precpt.md b/mixs6/season_precpt.md index 53b4bd4d..3e4ceee4 100644 --- a/mixs6/season_precpt.md +++ b/mixs6/season_precpt.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/season_temp.md b/mixs6/season_temp.md index e5279f06..fc126b77 100644 --- a/mixs6/season_temp.md +++ b/mixs6/season_temp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/season_use.md b/mixs6/season_use.md index a29f954b..76a0ba97 100644 --- a/mixs6/season_use.md +++ b/mixs6/season_use.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/secondary_treatment.md b/mixs6/secondary_treatment.md index e1ea5fc4..1e3529ba 100644 --- a/mixs6/secondary_treatment.md +++ b/mixs6/secondary_treatment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/sediment_type.md b/mixs6/sediment_type.md index 57eba3fe..f7ef1fac 100644 --- a/mixs6/sediment_type.md +++ b/mixs6/sediment_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) ## Other properties diff --git a/mixs6/seq_meth.md b/mixs6/seq_meth.md index 369317d4..7be0dd84 100644 --- a/mixs6/seq_meth.md +++ b/mixs6/seq_meth.md @@ -17,17 +17,17 @@ None -> OPT ## Children - * [me➞seq_meth](me_seq_meth.md) - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) - * [migs_org➞seq_meth](migs_org_seq_meth.md) - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) - * [mimag➞seq_meth](mimag_seq_meth.md) - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) - * [misag➞seq_meth](misag_seq_meth.md) - * [miuvig➞seq_meth](miuvig_seq_meth.md) + * [ME➞seq_meth](ME_seq_meth.md) + * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) + * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) + * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) + * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) + * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) + * [MIMAG➞seq_meth](MIMAG_seq_meth.md) + * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) + * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) + * [MISAG➞seq_meth](MISAG_seq_meth.md) + * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) ## Used by diff --git a/mixs6/seq_quality_check.md b/mixs6/seq_quality_check.md index 4531334e..f2c2bb8e 100644 --- a/mixs6/seq_quality_check.md +++ b/mixs6/seq_quality_check.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) + * [MIMARKS specimen➞seq_quality_check](MIMARKS_specimen_seq_quality_check.md) + * [MIMARKS survey➞seq_quality_check](MIMARKS_survey_seq_quality_check.md) ## Used by diff --git a/mixs6/sewage_type.md b/mixs6/sewage_type.md index 899b2ea2..4fbaf3b3 100644 --- a/mixs6/sewage_type.md +++ b/mixs6/sewage_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/sexual_act.md b/mixs6/sexual_act.md index c2db90cf..cb551f0f 100644 --- a/mixs6/sexual_act.md +++ b/mixs6/sexual_act.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/shading_device_cond.md b/mixs6/shading_device_cond.md index 1f9431d0..f7e00f98 100644 --- a/mixs6/shading_device_cond.md +++ b/mixs6/shading_device_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/shading_device_loc.md b/mixs6/shading_device_loc.md index 684cb04f..775e4cb4 100644 --- a/mixs6/shading_device_loc.md +++ b/mixs6/shading_device_loc.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/shading_device_mat.md b/mixs6/shading_device_mat.md index a523c6a7..9d5065b6 100644 --- a/mixs6/shading_device_mat.md +++ b/mixs6/shading_device_mat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/shading_device_type.md b/mixs6/shading_device_type.md index 65f64e8d..625cc43c 100644 --- a/mixs6/shading_device_type.md +++ b/mixs6/shading_device_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/shading_device_water_mold.md b/mixs6/shading_device_water_mold.md index b70560d5..3b041c4f 100644 --- a/mixs6/shading_device_water_mold.md +++ b/mixs6/shading_device_water_mold.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/sieving.md b/mixs6/sieving.md index dae90345..2796bbbe 100644 --- a/mixs6/sieving.md +++ b/mixs6/sieving.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/silicate.md b/mixs6/silicate.md index 7a7208de..e6feef8e 100644 --- a/mixs6/silicate.md +++ b/mixs6/silicate.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/sim_search_meth.md b/mixs6/sim_search_meth.md index 741cf252..5301445d 100644 --- a/mixs6/sim_search_meth.md +++ b/mixs6/sim_search_meth.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞sim_search_meth](me_sim_search_meth.md) - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) - * [migs_org➞sim_search_meth](migs_org_sim_search_meth.md) - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) - * [mimag➞sim_search_meth](mimag_sim_search_meth.md) - * [misag➞sim_search_meth](misag_sim_search_meth.md) - * [miuvig➞sim_search_meth](miuvig_sim_search_meth.md) + * [ME➞sim_search_meth](ME_sim_search_meth.md) + * [MIGS bacteria➞sim_search_meth](MIGS_bacteria_sim_search_meth.md) + * [MIGS eukaryote➞sim_search_meth](MIGS_eukaryote_sim_search_meth.md) + * [MIGS org➞sim_search_meth](MIGS_org_sim_search_meth.md) + * [MIGS plant➞sim_search_meth](MIGS_plant_sim_search_meth.md) + * [MIGS virus➞sim_search_meth](MIGS_virus_sim_search_meth.md) + * [MIMAG➞sim_search_meth](MIMAG_sim_search_meth.md) + * [MISAG➞sim_search_meth](MISAG_sim_search_meth.md) + * [MIUVIG➞sim_search_meth](MIUVIG_sim_search_meth.md) ## Used by diff --git a/mixs6/single_cell_lysis_appr.md b/mixs6/single_cell_lysis_appr.md index 4462fd34..f7b73f8c 100644 --- a/mixs6/single_cell_lysis_appr.md +++ b/mixs6/single_cell_lysis_appr.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [misag➞single_cell_lysis_appr](misag_single_cell_lysis_appr.md) - * [miuvig➞single_cell_lysis_appr](miuvig_single_cell_lysis_appr.md) + * [MISAG➞single_cell_lysis_appr](MISAG_single_cell_lysis_appr.md) + * [MIUVIG➞single_cell_lysis_appr](MIUVIG_single_cell_lysis_appr.md) ## Used by diff --git a/mixs6/single_cell_lysis_prot.md b/mixs6/single_cell_lysis_prot.md index a7bbc9c6..118970f4 100644 --- a/mixs6/single_cell_lysis_prot.md +++ b/mixs6/single_cell_lysis_prot.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [misag➞single_cell_lysis_prot](misag_single_cell_lysis_prot.md) - * [miuvig➞single_cell_lysis_prot](miuvig_single_cell_lysis_prot.md) + * [MISAG➞single_cell_lysis_prot](MISAG_single_cell_lysis_prot.md) + * [MIUVIG➞single_cell_lysis_prot](MIUVIG_single_cell_lysis_prot.md) ## Used by diff --git a/mixs6/size_frac.md b/mixs6/size_frac.md index 7dd3c8cd..a2b9dcb9 100644 --- a/mixs6/size_frac.md +++ b/mixs6/size_frac.md @@ -17,11 +17,11 @@ None -> OPT [String](types/String.md) ## Children - * [me➞size_frac](me_size_frac.md) - * [mimag➞size_frac](mimag_size_frac.md) - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) - * [misag➞size_frac](misag_size_frac.md) - * [miuvig➞size_frac](miuvig_size_frac.md) + * [ME➞size_frac](ME_size_frac.md) + * [MIMAG➞size_frac](MIMAG_size_frac.md) + * [MIMARKS specimen➞size_frac](MIMARKS_specimen_size_frac.md) + * [MISAG➞size_frac](MISAG_size_frac.md) + * [MIUVIG➞size_frac](MIUVIG_size_frac.md) ## Used by diff --git a/mixs6/size_frac_low.md b/mixs6/size_frac_low.md index e2e3c833..00adda41 100644 --- a/mixs6/size_frac_low.md +++ b/mixs6/size_frac_low.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/size_frac_up.md b/mixs6/size_frac_up.md index 69efe33f..3fce79c0 100644 --- a/mixs6/size_frac_up.md +++ b/mixs6/size_frac_up.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/slope_aspect.md b/mixs6/slope_aspect.md index 43d68877..5a4ae480 100644 --- a/mixs6/slope_aspect.md +++ b/mixs6/slope_aspect.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/slope_gradient.md b/mixs6/slope_gradient.md index 21ca0a3e..9ba5f8ff 100644 --- a/mixs6/slope_gradient.md +++ b/mixs6/slope_gradient.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/sludge_retent_time.md b/mixs6/sludge_retent_time.md index 616cb0ca..199985fb 100644 --- a/mixs6/sludge_retent_time.md +++ b/mixs6/sludge_retent_time.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/smoker.md b/mixs6/smoker.md index a7732ae2..272e6702 100644 --- a/mixs6/smoker.md +++ b/mixs6/smoker.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/sodium.md b/mixs6/sodium.md index 751948b1..7424e3b3 100644 --- a/mixs6/sodium.md +++ b/mixs6/sodium.md @@ -21,89 +21,89 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/soil_type.md b/mixs6/soil_type.md index 672119ae..7f90cf82 100644 --- a/mixs6/soil_type.md +++ b/mixs6/soil_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/soil_type_meth.md b/mixs6/soil_type_meth.md index c7c6f633..1aa0c6ea 100644 --- a/mixs6/soil_type_meth.md +++ b/mixs6/soil_type_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/solar_irradiance.md b/mixs6/solar_irradiance.md index 4bfcb31c..d6312ed6 100644 --- a/mixs6/solar_irradiance.md +++ b/mixs6/solar_irradiance.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/soluble_inorg_mat.md b/mixs6/soluble_inorg_mat.md index 8499cd26..bd7abeaa 100644 --- a/mixs6/soluble_inorg_mat.md +++ b/mixs6/soluble_inorg_mat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/soluble_org_mat.md b/mixs6/soluble_org_mat.md index 6d80cc6e..1f01e446 100644 --- a/mixs6/soluble_org_mat.md +++ b/mixs6/soluble_org_mat.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/soluble_react_phosp.md b/mixs6/soluble_react_phosp.md index 865148b0..e0b0a190 100644 --- a/mixs6/soluble_react_phosp.md +++ b/mixs6/soluble_react_phosp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/sop.md b/mixs6/sop.md index 4f6400cf..c19dd16c 100644 --- a/mixs6/sop.md +++ b/mixs6/sop.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞sop](me_sop.md) - * [migs_ba➞sop](migs_ba_sop.md) - * [migs_eu➞sop](migs_eu_sop.md) - * [migs_org➞sop](migs_org_sop.md) - * [migs_pl➞sop](migs_pl_sop.md) - * [migs_vi➞sop](migs_vi_sop.md) - * [mimag➞sop](mimag_sop.md) - * [mimarks_c➞sop](mimarks_c_sop.md) - * [mimarks_s➞sop](mimarks_s_sop.md) - * [misag➞sop](misag_sop.md) - * [miuvig➞sop](miuvig_sop.md) + * [ME➞sop](ME_sop.md) + * [MIGS bacteria➞sop](MIGS_bacteria_sop.md) + * [MIGS eukaryote➞sop](MIGS_eukaryote_sop.md) + * [MIGS org➞sop](MIGS_org_sop.md) + * [MIGS plant➞sop](MIGS_plant_sop.md) + * [MIGS virus➞sop](MIGS_virus_sop.md) + * [MIMAG➞sop](MIMAG_sop.md) + * [MIMARKS specimen➞sop](MIMARKS_specimen_sop.md) + * [MIMARKS survey➞sop](MIMARKS_survey_sop.md) + * [MISAG➞sop](MISAG_sop.md) + * [MIUVIG➞sop](MIUVIG_sop.md) ## Used by diff --git a/mixs6/sort_tech.md b/mixs6/sort_tech.md index 8804b9f8..9741f208 100644 --- a/mixs6/sort_tech.md +++ b/mixs6/sort_tech.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [misag➞sort_tech](misag_sort_tech.md) - * [miuvig➞sort_tech](miuvig_sort_tech.md) + * [MISAG➞sort_tech](MISAG_sort_tech.md) + * [MIUVIG➞sort_tech](MIUVIG_sort_tech.md) ## Used by diff --git a/mixs6/source_mat_id.md b/mixs6/source_mat_id.md index d7dad879..6b478f3d 100644 --- a/mixs6/source_mat_id.md +++ b/mixs6/source_mat_id.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞source_mat_id](me_source_mat_id.md) - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) - * [migs_org➞source_mat_id](migs_org_source_mat_id.md) - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) - * [mimag➞source_mat_id](mimag_source_mat_id.md) - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) - * [misag➞source_mat_id](misag_source_mat_id.md) - * [miuvig➞source_mat_id](miuvig_source_mat_id.md) + * [ME➞source_mat_id](ME_source_mat_id.md) + * [MIGS bacteria➞source_mat_id](MIGS_bacteria_source_mat_id.md) + * [MIGS eukaryote➞source_mat_id](MIGS_eukaryote_source_mat_id.md) + * [MIGS org➞source_mat_id](MIGS_org_source_mat_id.md) + * [MIGS plant➞source_mat_id](MIGS_plant_source_mat_id.md) + * [MIGS virus➞source_mat_id](MIGS_virus_source_mat_id.md) + * [MIMAG➞source_mat_id](MIMAG_source_mat_id.md) + * [MIMARKS specimen➞source_mat_id](MIMARKS_specimen_source_mat_id.md) + * [MIMARKS survey➞source_mat_id](MIMARKS_survey_source_mat_id.md) + * [MISAG➞source_mat_id](MISAG_source_mat_id.md) + * [MIUVIG➞source_mat_id](MIUVIG_source_mat_id.md) ## Used by diff --git a/mixs6/source_uvig.md b/mixs6/source_uvig.md index b2d4ffc1..3bedba26 100644 --- a/mixs6/source_uvig.md +++ b/mixs6/source_uvig.md @@ -17,7 +17,7 @@ None -> OPT ## Children - * [miuvig➞source_uvig](miuvig_source_uvig.md) + * [MIUVIG➞source_uvig](MIUVIG_source_uvig.md) ## Used by diff --git a/mixs6/space_typ_state.md b/mixs6/space_typ_state.md index 88faee27..29f2f90b 100644 --- a/mixs6/space_typ_state.md +++ b/mixs6/space_typ_state.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/special_diet.md b/mixs6/special_diet.md index 89bef30a..2cce5583 100644 --- a/mixs6/special_diet.md +++ b/mixs6/special_diet.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) ## Other properties diff --git a/mixs6/specific.md b/mixs6/specific.md index 2d860090..06e4395b 100644 --- a/mixs6/specific.md +++ b/mixs6/specific.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/specific_host.md b/mixs6/specific_host.md index 8cc9dd09..5d081f02 100644 --- a/mixs6/specific_host.md +++ b/mixs6/specific_host.md @@ -17,11 +17,11 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞specific_host](migs_ba_specific_host.md) - * [migs_eu➞specific_host](migs_eu_specific_host.md) - * [migs_pl➞specific_host](migs_pl_specific_host.md) - * [migs_vi➞specific_host](migs_vi_specific_host.md) - * [miuvig➞specific_host](miuvig_specific_host.md) + * [MIGS bacteria➞specific_host](MIGS_bacteria_specific_host.md) + * [MIGS eukaryote➞specific_host](MIGS_eukaryote_specific_host.md) + * [MIGS plant➞specific_host](MIGS_plant_specific_host.md) + * [MIGS virus➞specific_host](MIGS_virus_specific_host.md) + * [MIUVIG➞specific_host](MIUVIG_specific_host.md) ## Used by diff --git a/mixs6/specific_humidity.md b/mixs6/specific_humidity.md index 2d5fa209..baa932bc 100644 --- a/mixs6/specific_humidity.md +++ b/mixs6/specific_humidity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/sr_dep_env.md b/mixs6/sr_dep_env.md index e07282fd..900b1f61 100644 --- a/mixs6/sr_dep_env.md +++ b/mixs6/sr_dep_env.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/sr_geol_age.md b/mixs6/sr_geol_age.md index aff7e4fa..7018fac5 100644 --- a/mixs6/sr_geol_age.md +++ b/mixs6/sr_geol_age.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/sr_kerog_type.md b/mixs6/sr_kerog_type.md index b1ab2783..0723754e 100644 --- a/mixs6/sr_kerog_type.md +++ b/mixs6/sr_kerog_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/sr_lithology.md b/mixs6/sr_lithology.md index e21f1d23..110f5f4c 100644 --- a/mixs6/sr_lithology.md +++ b/mixs6/sr_lithology.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) ## Other properties diff --git a/mixs6/standing_water_regm.md b/mixs6/standing_water_regm.md index 43ebb4c8..dc3f0f73 100644 --- a/mixs6/standing_water_regm.md +++ b/mixs6/standing_water_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/store_cond.md b/mixs6/store_cond.md index a2440559..d05a7fec 100644 --- a/mixs6/store_cond.md +++ b/mixs6/store_cond.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/study_complt_stat.md b/mixs6/study_complt_stat.md index ee18ece4..5e43b5aa 100644 --- a/mixs6/study_complt_stat.md +++ b/mixs6/study_complt_stat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/submitted_to_insdc.md b/mixs6/submitted_to_insdc.md index cf65f882..0af177a4 100644 --- a/mixs6/submitted_to_insdc.md +++ b/mixs6/submitted_to_insdc.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞submitted_to_insdc](me_submitted_to_insdc.md) - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) - * [migs_org➞submitted_to_insdc](migs_org_submitted_to_insdc.md) - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) - * [mimag➞submitted_to_insdc](mimag_submitted_to_insdc.md) - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) - * [misag➞submitted_to_insdc](misag_submitted_to_insdc.md) - * [miuvig➞submitted_to_insdc](miuvig_submitted_to_insdc.md) + * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) + * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) + * [MIGS eukaryote➞submitted_to_insdc](MIGS_eukaryote_submitted_to_insdc.md) + * [MIGS org➞submitted_to_insdc](MIGS_org_submitted_to_insdc.md) + * [MIGS plant➞submitted_to_insdc](MIGS_plant_submitted_to_insdc.md) + * [MIGS virus➞submitted_to_insdc](MIGS_virus_submitted_to_insdc.md) + * [MIMAG➞submitted_to_insdc](MIMAG_submitted_to_insdc.md) + * [MIMARKS specimen➞submitted_to_insdc](MIMARKS_specimen_submitted_to_insdc.md) + * [MIMARKS survey➞submitted_to_insdc](MIMARKS_survey_submitted_to_insdc.md) + * [MISAG➞submitted_to_insdc](MISAG_submitted_to_insdc.md) + * [MIUVIG➞submitted_to_insdc](MIUVIG_submitted_to_insdc.md) ## Used by diff --git a/mixs6/subspecf_gen_lin.md b/mixs6/subspecf_gen_lin.md index eba108cb..9c5bed12 100644 --- a/mixs6/subspecf_gen_lin.md +++ b/mixs6/subspecf_gen_lin.md @@ -17,12 +17,12 @@ None -> OPT [String](types/String.md) ## Children - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) - * [migs_org➞subspecf_gen_lin](migs_org_subspecf_gen_lin.md) - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) + * [MIGS bacteria➞subspecf_gen_lin](MIGS_bacteria_subspecf_gen_lin.md) + * [MIGS eukaryote➞subspecf_gen_lin](MIGS_eukaryote_subspecf_gen_lin.md) + * [MIGS org➞subspecf_gen_lin](MIGS_org_subspecf_gen_lin.md) + * [MIGS plant➞subspecf_gen_lin](MIGS_plant_subspecf_gen_lin.md) + * [MIGS virus➞subspecf_gen_lin](MIGS_virus_subspecf_gen_lin.md) + * [MIMARKS survey➞subspecf_gen_lin](MIMARKS_survey_subspecf_gen_lin.md) ## Used by diff --git a/mixs6/substructure_type.md b/mixs6/substructure_type.md index 21139c53..d9e921eb 100644 --- a/mixs6/substructure_type.md +++ b/mixs6/substructure_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/sulfate.md b/mixs6/sulfate.md index 582d1d90..d9c88fcf 100644 --- a/mixs6/sulfate.md +++ b/mixs6/sulfate.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/sulfate_fw.md b/mixs6/sulfate_fw.md index e6b4afb1..d3f9a9f3 100644 --- a/mixs6/sulfate_fw.md +++ b/mixs6/sulfate_fw.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/sulfide.md b/mixs6/sulfide.md index d73fe895..f9b7c045 100644 --- a/mixs6/sulfide.md +++ b/mixs6/sulfide.md @@ -21,77 +21,77 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/surf_air_cont.md b/mixs6/surf_air_cont.md index 77192770..d159879b 100644 --- a/mixs6/surf_air_cont.md +++ b/mixs6/surf_air_cont.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/surf_humidity.md b/mixs6/surf_humidity.md index c700404e..72af3ddb 100644 --- a/mixs6/surf_humidity.md +++ b/mixs6/surf_humidity.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/surf_material.md b/mixs6/surf_material.md index ed72044b..f0a9765e 100644 --- a/mixs6/surf_material.md +++ b/mixs6/surf_material.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/surf_moisture.md b/mixs6/surf_moisture.md index 1d0f6d00..d0f15547 100644 --- a/mixs6/surf_moisture.md +++ b/mixs6/surf_moisture.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/surf_moisture_ph.md b/mixs6/surf_moisture_ph.md index 300f4fa4..f152361c 100644 --- a/mixs6/surf_moisture_ph.md +++ b/mixs6/surf_moisture_ph.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/surf_temp.md b/mixs6/surf_temp.md index f8c67ef2..77e15c5c 100644 --- a/mixs6/surf_temp.md +++ b/mixs6/surf_temp.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/suspend_part_matter.md b/mixs6/suspend_part_matter.md index a149ccb9..6a1ccefc 100644 --- a/mixs6/suspend_part_matter.md +++ b/mixs6/suspend_part_matter.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/suspend_solids.md b/mixs6/suspend_solids.md index 1b3206b3..b9a2f92a 100644 --- a/mixs6/suspend_solids.md +++ b/mixs6/suspend_solids.md @@ -21,41 +21,41 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/tan.md b/mixs6/tan.md index c5975086..b6919f17 100644 --- a/mixs6/tan.md +++ b/mixs6/tan.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/target_gene.md b/mixs6/target_gene.md index c3c9906f..dc6ffb23 100644 --- a/mixs6/target_gene.md +++ b/mixs6/target_gene.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) + * [MIMARKS specimen➞target_gene](MIMARKS_specimen_target_gene.md) + * [MIMARKS survey➞target_gene](MIMARKS_survey_target_gene.md) ## Used by diff --git a/mixs6/target_subfragment.md b/mixs6/target_subfragment.md index f2a5a97f..c73ae294 100644 --- a/mixs6/target_subfragment.md +++ b/mixs6/target_subfragment.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) + * [MIMARKS specimen➞target_subfragment](MIMARKS_specimen_target_subfragment.md) + * [MIMARKS survey➞target_subfragment](MIMARKS_survey_target_subfragment.md) ## Used by diff --git a/mixs6/tax_class.md b/mixs6/tax_class.md index 7c862b71..b1e17209 100644 --- a/mixs6/tax_class.md +++ b/mixs6/tax_class.md @@ -17,15 +17,15 @@ None -> OPT [String](types/String.md) ## Children - * [me➞tax_class](me_tax_class.md) - * [migs_ba➞tax_class](migs_ba_tax_class.md) - * [migs_eu➞tax_class](migs_eu_tax_class.md) - * [migs_org➞tax_class](migs_org_tax_class.md) - * [migs_pl➞tax_class](migs_pl_tax_class.md) - * [migs_vi➞tax_class](migs_vi_tax_class.md) - * [mimag➞tax_class](mimag_tax_class.md) - * [misag➞tax_class](misag_tax_class.md) - * [miuvig➞tax_class](miuvig_tax_class.md) + * [ME➞tax_class](ME_tax_class.md) + * [MIGS bacteria➞tax_class](MIGS_bacteria_tax_class.md) + * [MIGS eukaryote➞tax_class](MIGS_eukaryote_tax_class.md) + * [MIGS org➞tax_class](MIGS_org_tax_class.md) + * [MIGS plant➞tax_class](MIGS_plant_tax_class.md) + * [MIGS virus➞tax_class](MIGS_virus_tax_class.md) + * [MIMAG➞tax_class](MIMAG_tax_class.md) + * [MISAG➞tax_class](MISAG_tax_class.md) + * [MIUVIG➞tax_class](MIUVIG_tax_class.md) ## Used by diff --git a/mixs6/tax_ident.md b/mixs6/tax_ident.md index e5cf175f..3acadeab 100644 --- a/mixs6/tax_ident.md +++ b/mixs6/tax_ident.md @@ -17,14 +17,14 @@ None -> OPT ## Children - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) - * [migs_org➞tax_ident](migs_org_tax_ident.md) - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) - * [mimag➞tax_ident](mimag_tax_ident.md) - * [misag➞tax_ident](misag_tax_ident.md) - * [miuvig➞tax_ident](miuvig_tax_ident.md) + * [MIGS bacteria➞tax_ident](MIGS_bacteria_tax_ident.md) + * [MIGS eukaryote➞tax_ident](MIGS_eukaryote_tax_ident.md) + * [MIGS org➞tax_ident](MIGS_org_tax_ident.md) + * [MIGS plant➞tax_ident](MIGS_plant_tax_ident.md) + * [MIGS virus➞tax_ident](MIGS_virus_tax_ident.md) + * [MIMAG➞tax_ident](MIMAG_tax_ident.md) + * [MISAG➞tax_ident](MISAG_tax_ident.md) + * [MIUVIG➞tax_ident](MIUVIG_tax_ident.md) ## Used by diff --git a/mixs6/temp.md b/mixs6/temp.md index 371f6e50..78abba69 100644 --- a/mixs6/temp.md +++ b/mixs6/temp.md @@ -21,185 +21,185 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [Host-associated](Host-associated.md) - * [Host-associatedMe](Host-associatedMe.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Host-associatedMigsOrg](Host-associatedMigsOrg.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Host-associatedMimag](Host-associatedMimag.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Host-associatedMisag](Host-associatedMisag.md) - * [Host-associatedMiuvig](Host-associatedMiuvig.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) * [Human-gut](Human-gut.md) - * [Human-gutMe](Human-gutMe.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-gutMigsOrg](Human-gutMigsOrg.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-gutMimag](Human-gutMimag.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-gutMisag](Human-gutMisag.md) - * [Human-gutMiuvig](Human-gutMiuvig.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/temp_out.md b/mixs6/temp_out.md index 2d8298b9..6b0be9aa 100644 --- a/mixs6/temp_out.md +++ b/mixs6/temp_out.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/tertiary_treatment.md b/mixs6/tertiary_treatment.md index d17d162d..0ee67ab2 100644 --- a/mixs6/tertiary_treatment.md +++ b/mixs6/tertiary_treatment.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/texture.md b/mixs6/texture.md index 6fdd69cf..e2e8a57c 100644 --- a/mixs6/texture.md +++ b/mixs6/texture.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/texture_meth.md b/mixs6/texture_meth.md index 9903f4f8..f4385b50 100644 --- a/mixs6/texture_meth.md +++ b/mixs6/texture_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/tidal_stage.md b/mixs6/tidal_stage.md index 1c0e07dc..2ef5392e 100644 --- a/mixs6/tidal_stage.md +++ b/mixs6/tidal_stage.md @@ -21,29 +21,29 @@ None -> OPT ## Used by * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tillage.md b/mixs6/tillage.md index 45daa747..ad68fb6b 100644 --- a/mixs6/tillage.md +++ b/mixs6/tillage.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/time_last_toothbrush.md b/mixs6/time_last_toothbrush.md index 89db40f0..4a51578e 100644 --- a/mixs6/time_last_toothbrush.md +++ b/mixs6/time_last_toothbrush.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-oral](Human-oral.md) - * [Human-oralMe](Human-oralMe.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-oralMigsOrg](Human-oralMigsOrg.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-oralMimag](Human-oralMimag.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-oralMisag](Human-oralMisag.md) - * [Human-oralMiuvig](Human-oralMiuvig.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) ## Other properties diff --git a/mixs6/time_since_last_wash.md b/mixs6/time_since_last_wash.md index d0634785..2eccd0a6 100644 --- a/mixs6/time_since_last_wash.md +++ b/mixs6/time_since_last_wash.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-skin](Human-skin.md) - * [Human-skinMe](Human-skinMe.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-skinMigsOrg](Human-skinMigsOrg.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-skinMimag](Human-skinMimag.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-skinMisag](Human-skinMisag.md) - * [Human-skinMiuvig](Human-skinMiuvig.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) ## Other properties diff --git a/mixs6/tiss_cult_growth_med.md b/mixs6/tiss_cult_growth_med.md index 857a908e..8d8b4f0c 100644 --- a/mixs6/tiss_cult_growth_med.md +++ b/mixs6/tiss_cult_growth_med.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/toluene.md b/mixs6/toluene.md index 997a3cf5..6f7872d7 100644 --- a/mixs6/toluene.md +++ b/mixs6/toluene.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/tot_carb.md b/mixs6/tot_carb.md index 20e3cf32..2f65eaeb 100644 --- a/mixs6/tot_carb.md +++ b/mixs6/tot_carb.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) ## Other properties diff --git a/mixs6/tot_depth_water_col.md b/mixs6/tot_depth_water_col.md index df45c1d9..4e52d339 100644 --- a/mixs6/tot_depth_water_col.md +++ b/mixs6/tot_depth_water_col.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_diss_nitro.md b/mixs6/tot_diss_nitro.md index 8300503f..73776c12 100644 --- a/mixs6/tot_diss_nitro.md +++ b/mixs6/tot_diss_nitro.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_inorg_nitro.md b/mixs6/tot_inorg_nitro.md index fdfb23f9..d3363acf 100644 --- a/mixs6/tot_inorg_nitro.md +++ b/mixs6/tot_inorg_nitro.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_iron.md b/mixs6/tot_iron.md index 11156c61..8bb56327 100644 --- a/mixs6/tot_iron.md +++ b/mixs6/tot_iron.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/tot_nitro.md b/mixs6/tot_nitro.md index 884d3649..185f88f2 100644 --- a/mixs6/tot_nitro.md +++ b/mixs6/tot_nitro.md @@ -21,53 +21,53 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_nitro_content.md b/mixs6/tot_nitro_content.md index 71c210c1..d77995ba 100644 --- a/mixs6/tot_nitro_content.md +++ b/mixs6/tot_nitro_content.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/tot_nitro_content_meth.md b/mixs6/tot_nitro_content_meth.md index c6b97597..ed4cf0ba 100644 --- a/mixs6/tot_nitro_content_meth.md +++ b/mixs6/tot_nitro_content_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/tot_org_c_meth.md b/mixs6/tot_org_c_meth.md index a16da9d8..958a9978 100644 --- a/mixs6/tot_org_c_meth.md +++ b/mixs6/tot_org_c_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/tot_org_carb.md b/mixs6/tot_org_carb.md index 3e42f25f..c3731ea2 100644 --- a/mixs6/tot_org_carb.md +++ b/mixs6/tot_org_carb.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/tot_part_carb.md b/mixs6/tot_part_carb.md index 240cf5f7..04dad259 100644 --- a/mixs6/tot_part_carb.md +++ b/mixs6/tot_part_carb.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_phosp.md b/mixs6/tot_phosp.md index 848ab347..508bc87b 100644 --- a/mixs6/tot_phosp.md +++ b/mixs6/tot_phosp.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tot_phosphate.md b/mixs6/tot_phosphate.md index 7b9836ab..6a5a2efa 100644 --- a/mixs6/tot_phosphate.md +++ b/mixs6/tot_phosphate.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/tot_sulfur.md b/mixs6/tot_sulfur.md index 8bbd4698..6c69aaec 100644 --- a/mixs6/tot_sulfur.md +++ b/mixs6/tot_sulfur.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/train_line.md b/mixs6/train_line.md index 1774bab1..963b9eed 100644 --- a/mixs6/train_line.md +++ b/mixs6/train_line.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/train_stat_loc.md b/mixs6/train_stat_loc.md index 939233ac..91b0eefe 100644 --- a/mixs6/train_stat_loc.md +++ b/mixs6/train_stat_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/train_stop_loc.md b/mixs6/train_stop_loc.md index a4cff1b8..47505a00 100644 --- a/mixs6/train_stop_loc.md +++ b/mixs6/train_stop_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/travel_out_six_month.md b/mixs6/travel_out_six_month.md index aa1d0be1..44d419bd 100644 --- a/mixs6/travel_out_six_month.md +++ b/mixs6/travel_out_six_month.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/trna_ext_software.md b/mixs6/trna_ext_software.md index 1942d7df..3fa8bd25 100644 --- a/mixs6/trna_ext_software.md +++ b/mixs6/trna_ext_software.md @@ -17,9 +17,9 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞trna_ext_software](mimag_trna_ext_software.md) - * [misag➞trna_ext_software](misag_trna_ext_software.md) - * [miuvig➞trna_ext_software](miuvig_trna_ext_software.md) + * [MIMAG➞trna_ext_software](MIMAG_trna_ext_software.md) + * [MISAG➞trna_ext_software](MISAG_trna_ext_software.md) + * [MIUVIG➞trna_ext_software](MIUVIG_trna_ext_software.md) ## Used by diff --git a/mixs6/trnas.md b/mixs6/trnas.md index d0cc9724..19b856fc 100644 --- a/mixs6/trnas.md +++ b/mixs6/trnas.md @@ -17,9 +17,9 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞trnas](mimag_trnas.md) - * [misag➞trnas](misag_trnas.md) - * [miuvig➞trnas](miuvig_trnas.md) + * [MIMAG➞trnas](MIMAG_trnas.md) + * [MISAG➞trnas](MISAG_trnas.md) + * [MIUVIG➞trnas](MIUVIG_trnas.md) ## Used by diff --git a/mixs6/trophic_level.md b/mixs6/trophic_level.md index 19702600..40a22648 100644 --- a/mixs6/trophic_level.md +++ b/mixs6/trophic_level.md @@ -17,9 +17,9 @@ None -> OPT ## Children - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) + * [MIGS bacteria➞trophic_level](MIGS_bacteria_trophic_level.md) + * [MIGS eukaryote➞trophic_level](MIGS_eukaryote_trophic_level.md) + * [MIMARKS survey➞trophic_level](MIMARKS_survey_trophic_level.md) ## Used by diff --git a/mixs6/turbidity.md b/mixs6/turbidity.md index 435c99c2..147ae0e9 100644 --- a/mixs6/turbidity.md +++ b/mixs6/turbidity.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/tvdss_of_hcr_pressure.md b/mixs6/tvdss_of_hcr_pressure.md index 92e7d0b7..5ae80280 100644 --- a/mixs6/tvdss_of_hcr_pressure.md +++ b/mixs6/tvdss_of_hcr_pressure.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/tvdss_of_hcr_temp.md b/mixs6/tvdss_of_hcr_temp.md index 37cfc857..7e1f7576 100644 --- a/mixs6/tvdss_of_hcr_temp.md +++ b/mixs6/tvdss_of_hcr_temp.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/twin_sibling.md b/mixs6/twin_sibling.md index 9d7e99d2..c811dd55 100644 --- a/mixs6/twin_sibling.md +++ b/mixs6/twin_sibling.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/typ_occup_density.md b/mixs6/typ_occup_density.md index 77d128a4..341eab2f 100644 --- a/mixs6/typ_occup_density.md +++ b/mixs6/typ_occup_density.md @@ -21,17 +21,17 @@ None -> OPT [Double](types/Double.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/urine_collect_meth.md b/mixs6/urine_collect_meth.md index 9983fbcb..0f9527c6 100644 --- a/mixs6/urine_collect_meth.md +++ b/mixs6/urine_collect_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/url.md b/mixs6/url.md index 6b71dc6b..2343a57b 100644 --- a/mixs6/url.md +++ b/mixs6/url.md @@ -17,17 +17,17 @@ None -> OPT [String](types/String.md) ## Children - * [me➞url](me_url.md) - * [migs_ba➞url](migs_ba_url.md) - * [migs_eu➞url](migs_eu_url.md) - * [migs_org➞url](migs_org_url.md) - * [migs_pl➞url](migs_pl_url.md) - * [migs_vi➞url](migs_vi_url.md) - * [mimag➞url](mimag_url.md) - * [mimarks_c➞url](mimarks_c_url.md) - * [mimarks_s➞url](mimarks_s_url.md) - * [misag➞url](misag_url.md) - * [miuvig➞url](miuvig_url.md) + * [ME➞url](ME_url.md) + * [MIGS bacteria➞url](MIGS_bacteria_url.md) + * [MIGS eukaryote➞url](MIGS_eukaryote_url.md) + * [MIGS org➞url](MIGS_org_url.md) + * [MIGS plant➞url](MIGS_plant_url.md) + * [MIGS virus➞url](MIGS_virus_url.md) + * [MIMAG➞url](MIMAG_url.md) + * [MIMARKS specimen➞url](MIMARKS_specimen_url.md) + * [MIMARKS survey➞url](MIMARKS_survey_url.md) + * [MISAG➞url](MISAG_url.md) + * [MIUVIG➞url](MIUVIG_url.md) ## Used by diff --git a/mixs6/urogenit_disord.md b/mixs6/urogenit_disord.md index f970859c..6d2a8c04 100644 --- a/mixs6/urogenit_disord.md +++ b/mixs6/urogenit_disord.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-vaginal](Human-vaginal.md) - * [Human-vaginalMe](Human-vaginalMe.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [Human-vaginalMigsOrg](Human-vaginalMigsOrg.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [Human-vaginalMimag](Human-vaginalMimag.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [Human-vaginalMisag](Human-vaginalMisag.md) - * [Human-vaginalMiuvig](Human-vaginalMiuvig.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) ## Other properties diff --git a/mixs6/urogenit_tract_disor.md b/mixs6/urogenit_tract_disor.md index 4e8637ef..78282de7 100644 --- a/mixs6/urogenit_tract_disor.md +++ b/mixs6/urogenit_tract_disor.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/ventilation_rate.md b/mixs6/ventilation_rate.md index 2254e025..8acfdf75 100644 --- a/mixs6/ventilation_rate.md +++ b/mixs6/ventilation_rate.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/ventilation_type.md b/mixs6/ventilation_type.md index 45386e92..bd95ac2b 100644 --- a/mixs6/ventilation_type.md +++ b/mixs6/ventilation_type.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/vfa.md b/mixs6/vfa.md index 6e5c71d8..a9693b86 100644 --- a/mixs6/vfa.md +++ b/mixs6/vfa.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/vfa_fw.md b/mixs6/vfa_fw.md index d9e6691f..d09d63d7 100644 --- a/mixs6/vfa_fw.md +++ b/mixs6/vfa_fw.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/vir_ident_software.md b/mixs6/vir_ident_software.md index 218bd29f..e671405a 100644 --- a/mixs6/vir_ident_software.md +++ b/mixs6/vir_ident_software.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞vir_ident_software](miuvig_vir_ident_software.md) + * [MIUVIG➞vir_ident_software](MIUVIG_vir_ident_software.md) ## Used by diff --git a/mixs6/virus_enrich_appr.md b/mixs6/virus_enrich_appr.md index f59db6e3..a329a501 100644 --- a/mixs6/virus_enrich_appr.md +++ b/mixs6/virus_enrich_appr.md @@ -17,8 +17,8 @@ None -> OPT ## Children - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) - * [miuvig➞virus_enrich_appr](miuvig_virus_enrich_appr.md) + * [MIGS virus➞virus_enrich_appr](MIGS_virus_virus_enrich_appr.md) + * [MIUVIG➞virus_enrich_appr](MIUVIG_virus_enrich_appr.md) ## Used by diff --git a/mixs6/vis_media.md b/mixs6/vis_media.md index c17a1e9f..0ba412bb 100644 --- a/mixs6/vis_media.md +++ b/mixs6/vis_media.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/viscosity.md b/mixs6/viscosity.md index 853feb60..a2990aa2 100644 --- a/mixs6/viscosity.md +++ b/mixs6/viscosity.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/volatile_org_comp.md b/mixs6/volatile_org_comp.md index f0273bfd..4727a549 100644 --- a/mixs6/volatile_org_comp.md +++ b/mixs6/volatile_org_comp.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/votu_class_appr.md b/mixs6/votu_class_appr.md index 29913ae5..28e37396 100644 --- a/mixs6/votu_class_appr.md +++ b/mixs6/votu_class_appr.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞votu_class_appr](miuvig_votu_class_appr.md) + * [MIUVIG➞votu_class_appr](MIUVIG_votu_class_appr.md) ## Used by diff --git a/mixs6/votu_db.md b/mixs6/votu_db.md index 54ae02ba..2214a7aa 100644 --- a/mixs6/votu_db.md +++ b/mixs6/votu_db.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞votu_db](miuvig_votu_db.md) + * [MIUVIG➞votu_db](MIUVIG_votu_db.md) ## Used by diff --git a/mixs6/votu_seq_comp_appr.md b/mixs6/votu_seq_comp_appr.md index e57af414..a9722ddf 100644 --- a/mixs6/votu_seq_comp_appr.md +++ b/mixs6/votu_seq_comp_appr.md @@ -17,7 +17,7 @@ None -> OPT [String](types/String.md) ## Children - * [miuvig➞votu_seq_comp_appr](miuvig_votu_seq_comp_appr.md) + * [MIUVIG➞votu_seq_comp_appr](MIUVIG_votu_seq_comp_appr.md) ## Used by diff --git a/mixs6/wall_area.md b/mixs6/wall_area.md index 1663f1cb..bbed36c8 100644 --- a/mixs6/wall_area.md +++ b/mixs6/wall_area.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_const_type.md b/mixs6/wall_const_type.md index ff7f2f8d..6f1932ce 100644 --- a/mixs6/wall_const_type.md +++ b/mixs6/wall_const_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_finish_mat.md b/mixs6/wall_finish_mat.md index 1d795065..55660d4f 100644 --- a/mixs6/wall_finish_mat.md +++ b/mixs6/wall_finish_mat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_height.md b/mixs6/wall_height.md index fe489ce3..8454c5d2 100644 --- a/mixs6/wall_height.md +++ b/mixs6/wall_height.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_loc.md b/mixs6/wall_loc.md index f4e384cb..f8be255b 100644 --- a/mixs6/wall_loc.md +++ b/mixs6/wall_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_surf_treatment.md b/mixs6/wall_surf_treatment.md index 29854833..cec0595e 100644 --- a/mixs6/wall_surf_treatment.md +++ b/mixs6/wall_surf_treatment.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_texture.md b/mixs6/wall_texture.md index 87c9d56b..47707aab 100644 --- a/mixs6/wall_texture.md +++ b/mixs6/wall_texture.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_thermal_mass.md b/mixs6/wall_thermal_mass.md index 952b1a3c..99c976d1 100644 --- a/mixs6/wall_thermal_mass.md +++ b/mixs6/wall_thermal_mass.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wall_water_mold.md b/mixs6/wall_water_mold.md index a54cda50..2d16e352 100644 --- a/mixs6/wall_water_mold.md +++ b/mixs6/wall_water_mold.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/wastewater_type.md b/mixs6/wastewater_type.md index cf4c7f2c..956a1c0a 100644 --- a/mixs6/wastewater_type.md +++ b/mixs6/wastewater_type.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [WastewaterSludge](WastewaterSludge.md) - * [WastewaterSludgeMe](WastewaterSludgeMe.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WastewaterSludgeMigsOrg](WastewaterSludgeMigsOrg.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WastewaterSludgeMimag](WastewaterSludgeMimag.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WastewaterSludgeMisag](WastewaterSludgeMisag.md) - * [WastewaterSludgeMiuvig](WastewaterSludgeMiuvig.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) ## Other properties diff --git a/mixs6/water_content.md b/mixs6/water_content.md index ff89bd39..e17ebbff 100644 --- a/mixs6/water_content.md +++ b/mixs6/water_content.md @@ -21,41 +21,41 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - * [MicrobialMatBiofilmMe](MicrobialMatBiofilmMe.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MicrobialMatBiofilmMigsOrg](MicrobialMatBiofilmMigsOrg.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MicrobialMatBiofilmMimag](MicrobialMatBiofilmMimag.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MicrobialMatBiofilmMisag](MicrobialMatBiofilmMisag.md) - * [MicrobialMatBiofilmMiuvig](MicrobialMatBiofilmMiuvig.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MicrobialMatBiofilmMIMAG](MicrobialMatBiofilmMIMAG.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MicrobialMatBiofilmMISAG](MicrobialMatBiofilmMISAG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) * [Sediment](Sediment.md) - * [SedimentMe](SedimentMe.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SedimentMigsOrg](SedimentMigsOrg.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SedimentMimag](SedimentMimag.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SedimentMisag](SedimentMisag.md) - * [SedimentMiuvig](SedimentMiuvig.md) + * [SedimentME](SedimentME.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SedimentMIMAG](SedimentMIMAG.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SedimentMISAG](SedimentMISAG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/water_content_soil_meth.md b/mixs6/water_content_soil_meth.md index 19052919..863b650f 100644 --- a/mixs6/water_content_soil_meth.md +++ b/mixs6/water_content_soil_meth.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Soil](Soil.md) - * [SoilMe](SoilMe.md) - * [SoilMigsBa](SoilMigsBa.md) - * [SoilMigsEu](SoilMigsEu.md) - * [SoilMigsOrg](SoilMigsOrg.md) - * [SoilMigsPl](SoilMigsPl.md) - * [SoilMigsVi](SoilMigsVi.md) - * [SoilMimag](SoilMimag.md) - * [SoilMimarksC](SoilMimarksC.md) - * [SoilMimarksS](SoilMimarksS.md) - * [SoilMisag](SoilMisag.md) - * [SoilMiuvig](SoilMiuvig.md) + * [SoilME](SoilME.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [SoilMIMAG](SoilMIMAG.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [SoilMISAG](SoilMISAG.md) + * [SoilMIUVIG](SoilMIUVIG.md) ## Other properties diff --git a/mixs6/water_current.md b/mixs6/water_current.md index 370b63d7..fa1f3f42 100644 --- a/mixs6/water_current.md +++ b/mixs6/water_current.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMe](MiscellaneousNaturalOrArtificialEnvironmentMe.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsOrg](MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimag](MiscellaneousNaturalOrArtificialEnvironmentMimag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMisag](MiscellaneousNaturalOrArtificialEnvironmentMisag.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMiuvig](MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMAG](MiscellaneousNaturalOrArtificialEnvironmentMIMAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMISAG](MiscellaneousNaturalOrArtificialEnvironmentMISAG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) * [Water](Water.md) - * [WaterMe](WaterMe.md) - * [WaterMigsBa](WaterMigsBa.md) - * [WaterMigsEu](WaterMigsEu.md) - * [WaterMigsOrg](WaterMigsOrg.md) - * [WaterMigsPl](WaterMigsPl.md) - * [WaterMigsVi](WaterMigsVi.md) - * [WaterMimag](WaterMimag.md) - * [WaterMimarksC](WaterMimarksC.md) - * [WaterMimarksS](WaterMimarksS.md) - * [WaterMisag](WaterMisag.md) - * [WaterMiuvig](WaterMiuvig.md) + * [WaterME](WaterME.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) + * [WaterMIMAG](WaterMIMAG.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) + * [WaterMISAG](WaterMISAG.md) + * [WaterMIUVIG](WaterMIUVIG.md) ## Other properties diff --git a/mixs6/water_cut.md b/mixs6/water_cut.md index 83013323..1121ced7 100644 --- a/mixs6/water_cut.md +++ b/mixs6/water_cut.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/water_feat_size.md b/mixs6/water_feat_size.md index ae2cf4f0..b10d0e42 100644 --- a/mixs6/water_feat_size.md +++ b/mixs6/water_feat_size.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/water_feat_type.md b/mixs6/water_feat_type.md index 2dd2a699..ff83901a 100644 --- a/mixs6/water_feat_type.md +++ b/mixs6/water_feat_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/water_production_rate.md b/mixs6/water_production_rate.md index de178af3..2cb74c9f 100644 --- a/mixs6/water_production_rate.md +++ b/mixs6/water_production_rate.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/water_temp_regm.md b/mixs6/water_temp_regm.md index 0cc55c5a..fd7380bc 100644 --- a/mixs6/water_temp_regm.md +++ b/mixs6/water_temp_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/watering_regm.md b/mixs6/watering_regm.md index c9db20cf..c08950ca 100644 --- a/mixs6/watering_regm.md +++ b/mixs6/watering_regm.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Plant-associated](Plant-associated.md) - * [Plant-associatedMe](Plant-associatedMe.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [Plant-associatedMigsOrg](Plant-associatedMigsOrg.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [Plant-associatedMimag](Plant-associatedMimag.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [Plant-associatedMisag](Plant-associatedMisag.md) - * [Plant-associatedMiuvig](Plant-associatedMiuvig.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/weekday.md b/mixs6/weekday.md index c60c7720..ab9c321a 100644 --- a/mixs6/weekday.md +++ b/mixs6/weekday.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/weight_loss_3_month.md b/mixs6/weight_loss_3_month.md index 51d4263c..6d9b7a1f 100644 --- a/mixs6/weight_loss_3_month.md +++ b/mixs6/weight_loss_3_month.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Human-associated](Human-associated.md) - * [Human-associatedMe](Human-associatedMe.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-associatedMigsOrg](Human-associatedMigsOrg.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-associatedMimag](Human-associatedMimag.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-associatedMisag](Human-associatedMisag.md) - * [Human-associatedMiuvig](Human-associatedMiuvig.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) ## Other properties diff --git a/mixs6/wga_amp_appr.md b/mixs6/wga_amp_appr.md index 7f9264d8..a4221ed0 100644 --- a/mixs6/wga_amp_appr.md +++ b/mixs6/wga_amp_appr.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [misag➞wga_amp_appr](misag_wga_amp_appr.md) - * [miuvig➞wga_amp_appr](miuvig_wga_amp_appr.md) + * [MISAG➞wga_amp_appr](MISAG_wga_amp_appr.md) + * [MIUVIG➞wga_amp_appr](MIUVIG_wga_amp_appr.md) ## Used by diff --git a/mixs6/wga_amp_kit.md b/mixs6/wga_amp_kit.md index 3aae5df4..0e884c5a 100644 --- a/mixs6/wga_amp_kit.md +++ b/mixs6/wga_amp_kit.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [misag➞wga_amp_kit](misag_wga_amp_kit.md) - * [miuvig➞wga_amp_kit](miuvig_wga_amp_kit.md) + * [MISAG➞wga_amp_kit](MISAG_wga_amp_kit.md) + * [MIUVIG➞wga_amp_kit](MIUVIG_wga_amp_kit.md) ## Used by diff --git a/mixs6/win.md b/mixs6/win.md index 797260ea..c00146ce 100644 --- a/mixs6/win.md +++ b/mixs6/win.md @@ -21,29 +21,29 @@ None -> OPT [String](types/String.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/mixs6/wind_direction.md b/mixs6/wind_direction.md index b9e9ddac..df73e5dc 100644 --- a/mixs6/wind_direction.md +++ b/mixs6/wind_direction.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/wind_speed.md b/mixs6/wind_speed.md index fd08e0e5..581d846f 100644 --- a/mixs6/wind_speed.md +++ b/mixs6/wind_speed.md @@ -21,17 +21,17 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [Air](Air.md) - * [AirMe](AirMe.md) - * [AirMigsBa](AirMigsBa.md) - * [AirMigsEu](AirMigsEu.md) - * [AirMigsOrg](AirMigsOrg.md) - * [AirMigsPl](AirMigsPl.md) - * [AirMigsVi](AirMigsVi.md) - * [AirMimag](AirMimag.md) - * [AirMimarksC](AirMimarksC.md) - * [AirMimarksS](AirMimarksS.md) - * [AirMisag](AirMisag.md) - * [AirMiuvig](AirMiuvig.md) + * [AirME](AirME.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [AirMIMAG](AirMIMAG.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [AirMISAG](AirMISAG.md) + * [AirMIUVIG](AirMIUVIG.md) ## Other properties diff --git a/mixs6/window_cond.md b/mixs6/window_cond.md index 6d12942a..8a54cbfc 100644 --- a/mixs6/window_cond.md +++ b/mixs6/window_cond.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_cover.md b/mixs6/window_cover.md index ecc8031a..87696bf4 100644 --- a/mixs6/window_cover.md +++ b/mixs6/window_cover.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_horiz_pos.md b/mixs6/window_horiz_pos.md index 67651ac1..f7f0f8b3 100644 --- a/mixs6/window_horiz_pos.md +++ b/mixs6/window_horiz_pos.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_loc.md b/mixs6/window_loc.md index 1136f85a..fec4f34e 100644 --- a/mixs6/window_loc.md +++ b/mixs6/window_loc.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_mat.md b/mixs6/window_mat.md index 4fb2fe65..814cd492 100644 --- a/mixs6/window_mat.md +++ b/mixs6/window_mat.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_open_freq.md b/mixs6/window_open_freq.md index 37a6b932..83be87ac 100644 --- a/mixs6/window_open_freq.md +++ b/mixs6/window_open_freq.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_size.md b/mixs6/window_size.md index 62f82b71..13703099 100644 --- a/mixs6/window_size.md +++ b/mixs6/window_size.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_status.md b/mixs6/window_status.md index e6d835d5..0beb873a 100644 --- a/mixs6/window_status.md +++ b/mixs6/window_status.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_type.md b/mixs6/window_type.md index 97b4928b..be177955 100644 --- a/mixs6/window_type.md +++ b/mixs6/window_type.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_vert_pos.md b/mixs6/window_vert_pos.md index b6b3a807..ee3c8bc2 100644 --- a/mixs6/window_vert_pos.md +++ b/mixs6/window_vert_pos.md @@ -21,17 +21,17 @@ None -> OPT ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/window_water_mold.md b/mixs6/window_water_mold.md index 0a137088..c3790cbf 100644 --- a/mixs6/window_water_mold.md +++ b/mixs6/window_water_mold.md @@ -21,17 +21,17 @@ None -> OPT [String](types/String.md) ## Used by * [BuiltEnvironment](BuiltEnvironment.md) - * [BuiltEnvironmentMe](BuiltEnvironmentMe.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [BuiltEnvironmentMigsOrg](BuiltEnvironmentMigsOrg.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [BuiltEnvironmentMimag](BuiltEnvironmentMimag.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [BuiltEnvironmentMisag](BuiltEnvironmentMisag.md) - * [BuiltEnvironmentMiuvig](BuiltEnvironmentMiuvig.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [BuiltEnvironmentMIMAG](BuiltEnvironmentMIMAG.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [BuiltEnvironmentMISAG](BuiltEnvironmentMISAG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) ## Other properties diff --git a/mixs6/x_16s_recover.md b/mixs6/x_16s_recover.md index efcceb87..2f57696b 100644 --- a/mixs6/x_16s_recover.md +++ b/mixs6/x_16s_recover.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞x_16s_recover](mimag_x_16s_recover.md) - * [misag➞x_16s_recover](misag_x_16s_recover.md) + * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) + * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) ## Used by diff --git a/mixs6/x_16s_recover_software.md b/mixs6/x_16s_recover_software.md index 2e8aa95f..38de87ba 100644 --- a/mixs6/x_16s_recover_software.md +++ b/mixs6/x_16s_recover_software.md @@ -17,8 +17,8 @@ None -> OPT [String](types/String.md) ## Children - * [mimag➞x_16s_recover_software](mimag_x_16s_recover_software.md) - * [misag➞x_16s_recover_software](misag_x_16s_recover_software.md) + * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) + * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) ## Used by diff --git a/mixs6/xylene.md b/mixs6/xylene.md index 30c6a247..a228244a 100644 --- a/mixs6/xylene.md +++ b/mixs6/xylene.md @@ -21,29 +21,29 @@ None -> OPT [QuantityValue](QuantityValue.md) ## Used by * [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - * [HydrocarbonResources-coresMe](HydrocarbonResources-coresMe.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-coresMigsOrg](HydrocarbonResources-coresMigsOrg.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-coresMimag](HydrocarbonResources-coresMimag.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-coresMisag](HydrocarbonResources-coresMisag.md) - * [HydrocarbonResources-coresMiuvig](HydrocarbonResources-coresMiuvig.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-coresMIMAG](HydrocarbonResources-coresMIMAG.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-coresMISAG](HydrocarbonResources-coresMISAG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) * [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - * [HydrocarbonResources-fluidsSwabsMe](HydrocarbonResources-fluidsSwabsMe.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsOrg](HydrocarbonResources-fluidsSwabsMigsOrg.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMimag](HydrocarbonResources-fluidsSwabsMimag.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMisag](HydrocarbonResources-fluidsSwabsMisag.md) - * [HydrocarbonResources-fluidsSwabsMiuvig](HydrocarbonResources-fluidsSwabsMiuvig.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIMAG](HydrocarbonResources-fluidsSwabsMIMAG.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMISAG](HydrocarbonResources-fluidsSwabsMISAG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) ## Other properties diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index 28f20e38..ece04895 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -1,9 +1,9 @@ id: http://w3id.org/mixs6 description: MIxS 6 linkml rendering imports: -- biolinkml:types +- linkml:types prefixes: - biolinkml: https://w3id.org/biolink/biolinkml/ + linkml: https://w3id.org/linkml/ mixs.vocab: https://w3id.org/mixs/vocab/ MIXS: https://w3id.org/mixs/terms/ default_prefix: mixs.vocab @@ -10025,11 +10025,11 @@ classes: range: double has raw value: string_serialization: '{has numeric value} {has unit}' - migs_eu: + MIGS eukaryote: mixin: true - description: migs_eu Checklist - todos: - - add details here + description: 'Minimal Information about a Genome Sequence: eukaryote' + aliases: + - MIGS.eu slots: - submitted_to_insdc - investigation_type @@ -10204,11 +10204,11 @@ classes: sop: comments: - conditional mandatory - migs_ba: + MIGS bacteria: mixin: true - description: migs_ba Checklist - todos: - - add details here + description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' + aliases: + - MIGS.ba slots: - submitted_to_insdc - investigation_type @@ -10387,11 +10387,11 @@ classes: sop: comments: - conditional mandatory - migs_pl: + MIGS plant: mixin: true - description: migs_pl Checklist - todos: - - add details here + description: 'Minimal Information about a Genome Sequence: plant' + aliases: + - MIGS.pl slots: - submitted_to_insdc - investigation_type @@ -10547,11 +10547,11 @@ classes: sop: comments: - conditional mandatory - migs_vi: + MIGS virus: mixin: true - description: migs_vi Checklist - todos: - - add details here + description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' + aliases: + - MIGS.ba slots: - submitted_to_insdc - investigation_type @@ -10727,11 +10727,11 @@ classes: sop: comments: - conditional mandatory - migs_org: + MIGS org: mixin: true - description: migs_org Checklist - todos: - - add details here + description: 'Minimal Information about a Genome Sequence: org' + aliases: + - MIGS.org slots: - submitted_to_insdc - investigation_type @@ -10877,11 +10877,11 @@ classes: sop: comments: - conditional mandatory - me: + ME: mixin: true - description: me Checklist - todos: - - add details here + description: Metagenome or Environmental + aliases: + - ME slots: - submitted_to_insdc - investigation_type @@ -11025,11 +11025,11 @@ classes: sop: comments: - conditional mandatory - mimarks_s: + MIMARKS specimen: mixin: true - description: mimarks_s Checklist - todos: - - add details here + description: 'Minimal Information about a Marker Specimen: specimen' + aliases: + - MIMARKS.specimen slots: - submitted_to_insdc - investigation_type @@ -11165,11 +11165,11 @@ classes: sop: comments: - conditional mandatory - mimarks_c: + MIMARKS survey: mixin: true - description: mimarks_c Checklist - todos: - - add details here + description: 'Minimal Information about a Marker Specimen: survey' + aliases: + - MIMARKS.survey slots: - submitted_to_insdc - investigation_type @@ -11286,11 +11286,11 @@ classes: sop: comments: - conditional mandatory - misag: + MISAG: mixin: true - description: misag Checklist - todos: - - add details here + description: Minimum Information About a Single Amplified Genome + aliases: + - MISAG slots: - submitted_to_insdc - investigation_type @@ -11481,11 +11481,11 @@ classes: sop: comments: - conditional mandatory - mimag: + MIMAG: mixin: true - description: mimag Checklist - todos: - - add details here + description: Minimum Information About a Metagenome-Assembled Genome + aliases: + - MIMAG slots: - submitted_to_insdc - investigation_type @@ -11673,11 +11673,11 @@ classes: sop: comments: - conditional mandatory - miuvig: + MIUVIG: mixin: true - description: miuvig Checklist - todos: - - add details here + description: Minimum Information About an Uncultivated Virus Genome + aliases: + - MIUVIG slots: - submitted_to_insdc - investigation_type @@ -13256,963 +13256,1131 @@ classes: - turbidity - water_current slot_usage: {} - air migs_eu: + air MIGS eukaryote: is_a: air mixins: - - migs_eu - description: Combinatorial checklist for air with migs_eu - air migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package air' + air MIGS bacteria: is_a: air mixins: - - migs_ba - description: Combinatorial checklist for air with migs_ba - air migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package air' + air MIGS plant: is_a: air mixins: - - migs_pl - description: Combinatorial checklist for air with migs_pl - air migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package air' + air MIGS virus: is_a: air mixins: - - migs_vi - description: Combinatorial checklist for air with migs_vi - air migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package air' + air MIGS org: is_a: air mixins: - - migs_org - description: Combinatorial checklist for air with migs_org - air me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package air' + air ME: is_a: air mixins: - - me - description: Combinatorial checklist for air with me - air mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package air + air MIMARKS specimen: is_a: air mixins: - - mimarks_s - description: Combinatorial checklist for air with mimarks_s - air mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package air' + air MIMARKS survey: is_a: air mixins: - - mimarks_c - description: Combinatorial checklist for air with mimarks_c - air misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package air' + air MISAG: is_a: air mixins: - - misag - description: Combinatorial checklist for air with misag - air mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package air + air MIMAG: is_a: air mixins: - - mimag - description: Combinatorial checklist for air with mimag - air miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package air + air MIUVIG: is_a: air mixins: - - miuvig - description: Combinatorial checklist for air with miuvig - built environment migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package air + built environment MIGS eukaryote: is_a: built environment mixins: - - migs_eu - description: Combinatorial checklist for built environment with migs_eu - built environment migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package built environment' + built environment MIGS bacteria: is_a: built environment mixins: - - migs_ba - description: Combinatorial checklist for built environment with migs_ba - built environment migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package built environment' + built environment MIGS plant: is_a: built environment mixins: - - migs_pl - description: Combinatorial checklist for built environment with migs_pl - built environment migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package built environment' + built environment MIGS virus: is_a: built environment mixins: - - migs_vi - description: Combinatorial checklist for built environment with migs_vi - built environment migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package built environment' + built environment MIGS org: is_a: built environment mixins: - - migs_org - description: Combinatorial checklist for built environment with migs_org - built environment me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package built environment' + built environment ME: is_a: built environment mixins: - - me - description: Combinatorial checklist for built environment with me - built environment mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package built environment + built environment MIMARKS specimen: is_a: built environment mixins: - - mimarks_s - description: Combinatorial checklist for built environment with mimarks_s - built environment mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package built environment' + built environment MIMARKS survey: is_a: built environment mixins: - - mimarks_c - description: Combinatorial checklist for built environment with mimarks_c - built environment misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package built environment' + built environment MISAG: is_a: built environment mixins: - - misag - description: Combinatorial checklist for built environment with misag - built environment mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package built environment + built environment MIMAG: is_a: built environment mixins: - - mimag - description: Combinatorial checklist for built environment with mimag - built environment miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package built environment + built environment MIUVIG: is_a: built environment mixins: - - miuvig - description: Combinatorial checklist for built environment with miuvig - host-associated migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package built environment + host-associated MIGS eukaryote: is_a: host-associated mixins: - - migs_eu - description: Combinatorial checklist for host-associated with migs_eu - host-associated migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package host-associated' + host-associated MIGS bacteria: is_a: host-associated mixins: - - migs_ba - description: Combinatorial checklist for host-associated with migs_ba - host-associated migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package host-associated' + host-associated MIGS plant: is_a: host-associated mixins: - - migs_pl - description: Combinatorial checklist for host-associated with migs_pl - host-associated migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package host-associated' + host-associated MIGS virus: is_a: host-associated mixins: - - migs_vi - description: Combinatorial checklist for host-associated with migs_vi - host-associated migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package host-associated' + host-associated MIGS org: is_a: host-associated mixins: - - migs_org - description: Combinatorial checklist for host-associated with migs_org - host-associated me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package host-associated' + host-associated ME: is_a: host-associated mixins: - - me - description: Combinatorial checklist for host-associated with me - host-associated mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package host-associated + host-associated MIMARKS specimen: is_a: host-associated mixins: - - mimarks_s - description: Combinatorial checklist for host-associated with mimarks_s - host-associated mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package host-associated' + host-associated MIMARKS survey: is_a: host-associated mixins: - - mimarks_c - description: Combinatorial checklist for host-associated with mimarks_c - host-associated misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package host-associated' + host-associated MISAG: is_a: host-associated mixins: - - misag - description: Combinatorial checklist for host-associated with misag - host-associated mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package host-associated + host-associated MIMAG: is_a: host-associated mixins: - - mimag - description: Combinatorial checklist for host-associated with mimag - host-associated miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package host-associated + host-associated MIUVIG: is_a: host-associated mixins: - - miuvig - description: Combinatorial checklist for host-associated with miuvig - human-associated migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package host-associated + human-associated MIGS eukaryote: is_a: human-associated mixins: - - migs_eu - description: Combinatorial checklist for human-associated with migs_eu - human-associated migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package human-associated' + human-associated MIGS bacteria: is_a: human-associated mixins: - - migs_ba - description: Combinatorial checklist for human-associated with migs_ba - human-associated migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-associated' + human-associated MIGS plant: is_a: human-associated mixins: - - migs_pl - description: Combinatorial checklist for human-associated with migs_pl - human-associated migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package human-associated' + human-associated MIGS virus: is_a: human-associated mixins: - - migs_vi - description: Combinatorial checklist for human-associated with migs_vi - human-associated migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-associated' + human-associated MIGS org: is_a: human-associated mixins: - - migs_org - description: Combinatorial checklist for human-associated with migs_org - human-associated me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package human-associated' + human-associated ME: is_a: human-associated mixins: - - me - description: Combinatorial checklist for human-associated with me - human-associated mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package human-associated + human-associated MIMARKS specimen: is_a: human-associated mixins: - - mimarks_s - description: Combinatorial checklist for human-associated with mimarks_s - human-associated mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package human-associated' + human-associated MIMARKS survey: is_a: human-associated mixins: - - mimarks_c - description: Combinatorial checklist for human-associated with mimarks_c - human-associated misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package human-associated' + human-associated MISAG: is_a: human-associated mixins: - - misag - description: Combinatorial checklist for human-associated with misag - human-associated mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package human-associated + human-associated MIMAG: is_a: human-associated mixins: - - mimag - description: Combinatorial checklist for human-associated with mimag - human-associated miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package human-associated + human-associated MIUVIG: is_a: human-associated mixins: - - miuvig - description: Combinatorial checklist for human-associated with miuvig - human-gut migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package human-associated + human-gut MIGS eukaryote: is_a: human-gut mixins: - - migs_eu - description: Combinatorial checklist for human-gut with migs_eu - human-gut migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package human-gut' + human-gut MIGS bacteria: is_a: human-gut mixins: - - migs_ba - description: Combinatorial checklist for human-gut with migs_ba - human-gut migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-gut' + human-gut MIGS plant: is_a: human-gut mixins: - - migs_pl - description: Combinatorial checklist for human-gut with migs_pl - human-gut migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package human-gut' + human-gut MIGS virus: is_a: human-gut mixins: - - migs_vi - description: Combinatorial checklist for human-gut with migs_vi - human-gut migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-gut' + human-gut MIGS org: is_a: human-gut mixins: - - migs_org - description: Combinatorial checklist for human-gut with migs_org - human-gut me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package human-gut' + human-gut ME: is_a: human-gut mixins: - - me - description: Combinatorial checklist for human-gut with me - human-gut mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package human-gut + human-gut MIMARKS specimen: is_a: human-gut mixins: - - mimarks_s - description: Combinatorial checklist for human-gut with mimarks_s - human-gut mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package human-gut' + human-gut MIMARKS survey: is_a: human-gut mixins: - - mimarks_c - description: Combinatorial checklist for human-gut with mimarks_c - human-gut misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package human-gut' + human-gut MISAG: is_a: human-gut mixins: - - misag - description: Combinatorial checklist for human-gut with misag - human-gut mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package human-gut + human-gut MIMAG: is_a: human-gut mixins: - - mimag - description: Combinatorial checklist for human-gut with mimag - human-gut miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package human-gut + human-gut MIUVIG: is_a: human-gut mixins: - - miuvig - description: Combinatorial checklist for human-gut with miuvig - human-oral migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package human-gut + human-oral MIGS eukaryote: is_a: human-oral mixins: - - migs_eu - description: Combinatorial checklist for human-oral with migs_eu - human-oral migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package human-oral' + human-oral MIGS bacteria: is_a: human-oral mixins: - - migs_ba - description: Combinatorial checklist for human-oral with migs_ba - human-oral migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-oral' + human-oral MIGS plant: is_a: human-oral mixins: - - migs_pl - description: Combinatorial checklist for human-oral with migs_pl - human-oral migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package human-oral' + human-oral MIGS virus: is_a: human-oral mixins: - - migs_vi - description: Combinatorial checklist for human-oral with migs_vi - human-oral migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-oral' + human-oral MIGS org: is_a: human-oral mixins: - - migs_org - description: Combinatorial checklist for human-oral with migs_org - human-oral me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package human-oral' + human-oral ME: is_a: human-oral mixins: - - me - description: Combinatorial checklist for human-oral with me - human-oral mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package human-oral + human-oral MIMARKS specimen: is_a: human-oral mixins: - - mimarks_s - description: Combinatorial checklist for human-oral with mimarks_s - human-oral mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package human-oral' + human-oral MIMARKS survey: is_a: human-oral mixins: - - mimarks_c - description: Combinatorial checklist for human-oral with mimarks_c - human-oral misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package human-oral' + human-oral MISAG: is_a: human-oral mixins: - - misag - description: Combinatorial checklist for human-oral with misag - human-oral mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package human-oral + human-oral MIMAG: is_a: human-oral mixins: - - mimag - description: Combinatorial checklist for human-oral with mimag - human-oral miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package human-oral + human-oral MIUVIG: is_a: human-oral mixins: - - miuvig - description: Combinatorial checklist for human-oral with miuvig - human-skin migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package human-oral + human-skin MIGS eukaryote: is_a: human-skin mixins: - - migs_eu - description: Combinatorial checklist for human-skin with migs_eu - human-skin migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package human-skin' + human-skin MIGS bacteria: is_a: human-skin mixins: - - migs_ba - description: Combinatorial checklist for human-skin with migs_ba - human-skin migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-skin' + human-skin MIGS plant: is_a: human-skin mixins: - - migs_pl - description: Combinatorial checklist for human-skin with migs_pl - human-skin migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package human-skin' + human-skin MIGS virus: is_a: human-skin mixins: - - migs_vi - description: Combinatorial checklist for human-skin with migs_vi - human-skin migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-skin' + human-skin MIGS org: is_a: human-skin mixins: - - migs_org - description: Combinatorial checklist for human-skin with migs_org - human-skin me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package human-skin' + human-skin ME: is_a: human-skin mixins: - - me - description: Combinatorial checklist for human-skin with me - human-skin mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package human-skin + human-skin MIMARKS specimen: is_a: human-skin mixins: - - mimarks_s - description: Combinatorial checklist for human-skin with mimarks_s - human-skin mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package human-skin' + human-skin MIMARKS survey: is_a: human-skin mixins: - - mimarks_c - description: Combinatorial checklist for human-skin with mimarks_c - human-skin misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package human-skin' + human-skin MISAG: is_a: human-skin mixins: - - misag - description: Combinatorial checklist for human-skin with misag - human-skin mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package human-skin + human-skin MIMAG: is_a: human-skin mixins: - - mimag - description: Combinatorial checklist for human-skin with mimag - human-skin miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package human-skin + human-skin MIUVIG: is_a: human-skin mixins: - - miuvig - description: Combinatorial checklist for human-skin with miuvig - human-vaginal migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package human-skin + human-vaginal MIGS eukaryote: is_a: human-vaginal mixins: - - migs_eu - description: Combinatorial checklist for human-vaginal with migs_eu - human-vaginal migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package human-vaginal' + human-vaginal MIGS bacteria: is_a: human-vaginal mixins: - - migs_ba - description: Combinatorial checklist for human-vaginal with migs_ba - human-vaginal migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-vaginal' + human-vaginal MIGS plant: is_a: human-vaginal mixins: - - migs_pl - description: Combinatorial checklist for human-vaginal with migs_pl - human-vaginal migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package human-vaginal' + human-vaginal MIGS virus: is_a: human-vaginal mixins: - - migs_vi - description: Combinatorial checklist for human-vaginal with migs_vi - human-vaginal migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package human-vaginal' + human-vaginal MIGS org: is_a: human-vaginal mixins: - - migs_org - description: Combinatorial checklist for human-vaginal with migs_org - human-vaginal me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package human-vaginal' + human-vaginal ME: is_a: human-vaginal mixins: - - me - description: Combinatorial checklist for human-vaginal with me - human-vaginal mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package human-vaginal + human-vaginal MIMARKS specimen: is_a: human-vaginal mixins: - - mimarks_s - description: Combinatorial checklist for human-vaginal with mimarks_s - human-vaginal mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package human-vaginal' + human-vaginal MIMARKS survey: is_a: human-vaginal mixins: - - mimarks_c - description: Combinatorial checklist for human-vaginal with mimarks_c - human-vaginal misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package human-vaginal' + human-vaginal MISAG: is_a: human-vaginal mixins: - - misag - description: Combinatorial checklist for human-vaginal with misag - human-vaginal mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package human-vaginal + human-vaginal MIMAG: is_a: human-vaginal mixins: - - mimag - description: Combinatorial checklist for human-vaginal with mimag - human-vaginal miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package human-vaginal + human-vaginal MIUVIG: is_a: human-vaginal mixins: - - miuvig - description: Combinatorial checklist for human-vaginal with miuvig - hydrocarbon resources-cores migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package human-vaginal + hydrocarbon resources-cores MIGS eukaryote: is_a: hydrocarbon resources-cores mixins: - - migs_eu - description: Combinatorial checklist for hydrocarbon resources-cores with migs_eu - hydrocarbon resources-cores migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MIGS bacteria: is_a: hydrocarbon resources-cores mixins: - - migs_ba - description: Combinatorial checklist for hydrocarbon resources-cores with migs_ba - hydrocarbon resources-cores migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MIGS plant: is_a: hydrocarbon resources-cores mixins: - - migs_pl - description: Combinatorial checklist for hydrocarbon resources-cores with migs_pl - hydrocarbon resources-cores migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MIGS virus: is_a: hydrocarbon resources-cores mixins: - - migs_vi - description: Combinatorial checklist for hydrocarbon resources-cores with migs_vi - hydrocarbon resources-cores migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MIGS org: is_a: hydrocarbon resources-cores mixins: - - migs_org - description: Combinatorial checklist for hydrocarbon resources-cores with migs_org - hydrocarbon resources-cores me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores ME: is_a: hydrocarbon resources-cores mixins: - - me - description: Combinatorial checklist for hydrocarbon resources-cores with me - hydrocarbon resources-cores mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package hydrocarbon resources-cores + hydrocarbon resources-cores MIMARKS specimen: is_a: hydrocarbon resources-cores mixins: - - mimarks_s - description: Combinatorial checklist for hydrocarbon resources-cores with mimarks_s - hydrocarbon resources-cores mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MIMARKS survey: is_a: hydrocarbon resources-cores mixins: - - mimarks_c - description: Combinatorial checklist for hydrocarbon resources-cores with mimarks_c - hydrocarbon resources-cores misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package hydrocarbon resources-cores' + hydrocarbon resources-cores MISAG: is_a: hydrocarbon resources-cores mixins: - - misag - description: Combinatorial checklist for hydrocarbon resources-cores with misag - hydrocarbon resources-cores mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package hydrocarbon resources-cores + hydrocarbon resources-cores MIMAG: is_a: hydrocarbon resources-cores mixins: - - mimag - description: Combinatorial checklist for hydrocarbon resources-cores with mimag - hydrocarbon resources-cores miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package hydrocarbon resources-cores + hydrocarbon resources-cores MIUVIG: is_a: hydrocarbon resources-cores mixins: - - miuvig - description: Combinatorial checklist for hydrocarbon resources-cores with miuvig - hydrocarbon resources-fluids_swabs migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package hydrocarbon resources-cores + hydrocarbon resources-fluids_swabs MIGS eukaryote: is_a: hydrocarbon resources-fluids_swabs mixins: - - migs_eu - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - migs_eu - hydrocarbon resources-fluids_swabs migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MIGS bacteria: is_a: hydrocarbon resources-fluids_swabs mixins: - - migs_ba - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - migs_ba - hydrocarbon resources-fluids_swabs migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MIGS plant: is_a: hydrocarbon resources-fluids_swabs mixins: - - migs_pl - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - migs_pl - hydrocarbon resources-fluids_swabs migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MIGS virus: is_a: hydrocarbon resources-fluids_swabs mixins: - - migs_vi - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - migs_vi - hydrocarbon resources-fluids_swabs migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MIGS org: is_a: hydrocarbon resources-fluids_swabs mixins: - - migs_org - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - migs_org - hydrocarbon resources-fluids_swabs me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs ME: is_a: hydrocarbon resources-fluids_swabs mixins: - - me - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - me - hydrocarbon resources-fluids_swabs mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package hydrocarbon resources-fluids_swabs + hydrocarbon resources-fluids_swabs MIMARKS specimen: is_a: hydrocarbon resources-fluids_swabs mixins: - - mimarks_s - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - mimarks_s - hydrocarbon resources-fluids_swabs mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MIMARKS survey: is_a: hydrocarbon resources-fluids_swabs mixins: - - mimarks_c - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - mimarks_c - hydrocarbon resources-fluids_swabs misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package hydrocarbon resources-fluids_swabs' + hydrocarbon resources-fluids_swabs MISAG: is_a: hydrocarbon resources-fluids_swabs mixins: - - misag - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - misag - hydrocarbon resources-fluids_swabs mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package hydrocarbon resources-fluids_swabs + hydrocarbon resources-fluids_swabs MIMAG: is_a: hydrocarbon resources-fluids_swabs mixins: - - mimag - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - mimag - hydrocarbon resources-fluids_swabs miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package hydrocarbon resources-fluids_swabs + hydrocarbon resources-fluids_swabs MIUVIG: is_a: hydrocarbon resources-fluids_swabs mixins: - - miuvig - description: Combinatorial checklist for hydrocarbon resources-fluids_swabs with - miuvig - microbial mat_biofilm migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package hydrocarbon resources-fluids_swabs + microbial mat_biofilm MIGS eukaryote: is_a: microbial mat_biofilm mixins: - - migs_eu - description: Combinatorial checklist for microbial mat_biofilm with migs_eu - microbial mat_biofilm migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package microbial mat_biofilm' + microbial mat_biofilm MIGS bacteria: is_a: microbial mat_biofilm mixins: - - migs_ba - description: Combinatorial checklist for microbial mat_biofilm with migs_ba - microbial mat_biofilm migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package microbial mat_biofilm' + microbial mat_biofilm MIGS plant: is_a: microbial mat_biofilm mixins: - - migs_pl - description: Combinatorial checklist for microbial mat_biofilm with migs_pl - microbial mat_biofilm migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package microbial mat_biofilm' + microbial mat_biofilm MIGS virus: is_a: microbial mat_biofilm mixins: - - migs_vi - description: Combinatorial checklist for microbial mat_biofilm with migs_vi - microbial mat_biofilm migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package microbial mat_biofilm' + microbial mat_biofilm MIGS org: is_a: microbial mat_biofilm mixins: - - migs_org - description: Combinatorial checklist for microbial mat_biofilm with migs_org - microbial mat_biofilm me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package microbial mat_biofilm' + microbial mat_biofilm ME: is_a: microbial mat_biofilm mixins: - - me - description: Combinatorial checklist for microbial mat_biofilm with me - microbial mat_biofilm mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package microbial mat_biofilm + microbial mat_biofilm MIMARKS specimen: is_a: microbial mat_biofilm mixins: - - mimarks_s - description: Combinatorial checklist for microbial mat_biofilm with mimarks_s - microbial mat_biofilm mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package microbial mat_biofilm' + microbial mat_biofilm MIMARKS survey: is_a: microbial mat_biofilm mixins: - - mimarks_c - description: Combinatorial checklist for microbial mat_biofilm with mimarks_c - microbial mat_biofilm misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package microbial mat_biofilm' + microbial mat_biofilm MISAG: is_a: microbial mat_biofilm mixins: - - misag - description: Combinatorial checklist for microbial mat_biofilm with misag - microbial mat_biofilm mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package microbial mat_biofilm + microbial mat_biofilm MIMAG: is_a: microbial mat_biofilm mixins: - - mimag - description: Combinatorial checklist for microbial mat_biofilm with mimag - microbial mat_biofilm miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package microbial mat_biofilm + microbial mat_biofilm MIUVIG: is_a: microbial mat_biofilm mixins: - - miuvig - description: Combinatorial checklist for microbial mat_biofilm with miuvig - miscellaneous natural or artificial environment migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package microbial mat_biofilm + miscellaneous natural or artificial environment MIGS eukaryote: is_a: miscellaneous natural or artificial environment mixins: - - migs_eu - description: Combinatorial checklist for miscellaneous natural or artificial environment - with migs_eu - miscellaneous natural or artificial environment migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package miscellaneous natural or artificial environment' + miscellaneous natural or artificial environment MIGS bacteria: is_a: miscellaneous natural or artificial environment mixins: - - migs_ba - description: Combinatorial checklist for miscellaneous natural or artificial environment - with migs_ba - miscellaneous natural or artificial environment migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package miscellaneous natural or + artificial environment' + miscellaneous natural or artificial environment MIGS plant: is_a: miscellaneous natural or artificial environment mixins: - - migs_pl - description: Combinatorial checklist for miscellaneous natural or artificial environment - with migs_pl - miscellaneous natural or artificial environment migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package miscellaneous natural or artificial environment' + miscellaneous natural or artificial environment MIGS virus: is_a: miscellaneous natural or artificial environment mixins: - - migs_vi - description: Combinatorial checklist for miscellaneous natural or artificial environment - with migs_vi - miscellaneous natural or artificial environment migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package miscellaneous natural or + artificial environment' + miscellaneous natural or artificial environment MIGS org: is_a: miscellaneous natural or artificial environment mixins: - - migs_org - description: Combinatorial checklist for miscellaneous natural or artificial environment - with migs_org - miscellaneous natural or artificial environment me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package miscellaneous natural or artificial environment' + miscellaneous natural or artificial environment ME: is_a: miscellaneous natural or artificial environment mixins: - - me - description: Combinatorial checklist for miscellaneous natural or artificial environment - with me - miscellaneous natural or artificial environment mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package miscellaneous natural or artificial environment + miscellaneous natural or artificial environment MIMARKS specimen: is_a: miscellaneous natural or artificial environment mixins: - - mimarks_s - description: Combinatorial checklist for miscellaneous natural or artificial environment - with mimarks_s - miscellaneous natural or artificial environment mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package miscellaneous natural or artificial environment' + miscellaneous natural or artificial environment MIMARKS survey: is_a: miscellaneous natural or artificial environment mixins: - - mimarks_c - description: Combinatorial checklist for miscellaneous natural or artificial environment - with mimarks_c - miscellaneous natural or artificial environment misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package miscellaneous natural or artificial environment' + miscellaneous natural or artificial environment MISAG: is_a: miscellaneous natural or artificial environment mixins: - - misag - description: Combinatorial checklist for miscellaneous natural or artificial environment - with misag - miscellaneous natural or artificial environment mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package miscellaneous natural or artificial environment + miscellaneous natural or artificial environment MIMAG: is_a: miscellaneous natural or artificial environment mixins: - - mimag - description: Combinatorial checklist for miscellaneous natural or artificial environment - with mimag - miscellaneous natural or artificial environment miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package miscellaneous natural or artificial environment + miscellaneous natural or artificial environment MIUVIG: is_a: miscellaneous natural or artificial environment mixins: - - miuvig - description: Combinatorial checklist for miscellaneous natural or artificial environment - with miuvig - plant-associated migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package miscellaneous natural or artificial + environment + plant-associated MIGS eukaryote: is_a: plant-associated mixins: - - migs_eu - description: Combinatorial checklist for plant-associated with migs_eu - plant-associated migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package plant-associated' + plant-associated MIGS bacteria: is_a: plant-associated mixins: - - migs_ba - description: Combinatorial checklist for plant-associated with migs_ba - plant-associated migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package plant-associated' + plant-associated MIGS plant: is_a: plant-associated mixins: - - migs_pl - description: Combinatorial checklist for plant-associated with migs_pl - plant-associated migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package plant-associated' + plant-associated MIGS virus: is_a: plant-associated mixins: - - migs_vi - description: Combinatorial checklist for plant-associated with migs_vi - plant-associated migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package plant-associated' + plant-associated MIGS org: is_a: plant-associated mixins: - - migs_org - description: Combinatorial checklist for plant-associated with migs_org - plant-associated me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package plant-associated' + plant-associated ME: is_a: plant-associated mixins: - - me - description: Combinatorial checklist for plant-associated with me - plant-associated mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package plant-associated + plant-associated MIMARKS specimen: is_a: plant-associated mixins: - - mimarks_s - description: Combinatorial checklist for plant-associated with mimarks_s - plant-associated mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package plant-associated' + plant-associated MIMARKS survey: is_a: plant-associated mixins: - - mimarks_c - description: Combinatorial checklist for plant-associated with mimarks_c - plant-associated misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package plant-associated' + plant-associated MISAG: is_a: plant-associated mixins: - - misag - description: Combinatorial checklist for plant-associated with misag - plant-associated mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package plant-associated + plant-associated MIMAG: is_a: plant-associated mixins: - - mimag - description: Combinatorial checklist for plant-associated with mimag - plant-associated miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package plant-associated + plant-associated MIUVIG: is_a: plant-associated mixins: - - miuvig - description: Combinatorial checklist for plant-associated with miuvig - sediment migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package plant-associated + sediment MIGS eukaryote: is_a: sediment mixins: - - migs_eu - description: Combinatorial checklist for sediment with migs_eu - sediment migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package sediment' + sediment MIGS bacteria: is_a: sediment mixins: - - migs_ba - description: Combinatorial checklist for sediment with migs_ba - sediment migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package sediment' + sediment MIGS plant: is_a: sediment mixins: - - migs_pl - description: Combinatorial checklist for sediment with migs_pl - sediment migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package sediment' + sediment MIGS virus: is_a: sediment mixins: - - migs_vi - description: Combinatorial checklist for sediment with migs_vi - sediment migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package sediment' + sediment MIGS org: is_a: sediment mixins: - - migs_org - description: Combinatorial checklist for sediment with migs_org - sediment me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package sediment' + sediment ME: is_a: sediment mixins: - - me - description: Combinatorial checklist for sediment with me - sediment mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package sediment + sediment MIMARKS specimen: is_a: sediment mixins: - - mimarks_s - description: Combinatorial checklist for sediment with mimarks_s - sediment mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package sediment' + sediment MIMARKS survey: is_a: sediment mixins: - - mimarks_c - description: Combinatorial checklist for sediment with mimarks_c - sediment misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package sediment' + sediment MISAG: is_a: sediment mixins: - - misag - description: Combinatorial checklist for sediment with misag - sediment mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package sediment + sediment MIMAG: is_a: sediment mixins: - - mimag - description: Combinatorial checklist for sediment with mimag - sediment miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package sediment + sediment MIUVIG: is_a: sediment mixins: - - miuvig - description: Combinatorial checklist for sediment with miuvig - soil migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package sediment + soil MIGS eukaryote: is_a: soil mixins: - - migs_eu - description: Combinatorial checklist for soil with migs_eu - soil migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package soil' + soil MIGS bacteria: is_a: soil mixins: - - migs_ba - description: Combinatorial checklist for soil with migs_ba - soil migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package soil' + soil MIGS plant: is_a: soil mixins: - - migs_pl - description: Combinatorial checklist for soil with migs_pl - soil migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package soil' + soil MIGS virus: is_a: soil mixins: - - migs_vi - description: Combinatorial checklist for soil with migs_vi - soil migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package soil' + soil MIGS org: is_a: soil mixins: - - migs_org - description: Combinatorial checklist for soil with migs_org - soil me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package soil' + soil ME: is_a: soil mixins: - - me - description: Combinatorial checklist for soil with me - soil mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package soil + soil MIMARKS specimen: is_a: soil mixins: - - mimarks_s - description: Combinatorial checklist for soil with mimarks_s - soil mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package soil' + soil MIMARKS survey: is_a: soil mixins: - - mimarks_c - description: Combinatorial checklist for soil with mimarks_c - soil misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package soil' + soil MISAG: is_a: soil mixins: - - misag - description: Combinatorial checklist for soil with misag - soil mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package soil + soil MIMAG: is_a: soil mixins: - - mimag - description: Combinatorial checklist for soil with mimag - soil miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package soil + soil MIUVIG: is_a: soil mixins: - - miuvig - description: Combinatorial checklist for soil with miuvig - wastewater_sludge migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package soil + wastewater_sludge MIGS eukaryote: is_a: wastewater_sludge mixins: - - migs_eu - description: Combinatorial checklist for wastewater_sludge with migs_eu - wastewater_sludge migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package wastewater_sludge' + wastewater_sludge MIGS bacteria: is_a: wastewater_sludge mixins: - - migs_ba - description: Combinatorial checklist for wastewater_sludge with migs_ba - wastewater_sludge migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package wastewater_sludge' + wastewater_sludge MIGS plant: is_a: wastewater_sludge mixins: - - migs_pl - description: Combinatorial checklist for wastewater_sludge with migs_pl - wastewater_sludge migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package wastewater_sludge' + wastewater_sludge MIGS virus: is_a: wastewater_sludge mixins: - - migs_vi - description: Combinatorial checklist for wastewater_sludge with migs_vi - wastewater_sludge migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package wastewater_sludge' + wastewater_sludge MIGS org: is_a: wastewater_sludge mixins: - - migs_org - description: Combinatorial checklist for wastewater_sludge with migs_org - wastewater_sludge me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package wastewater_sludge' + wastewater_sludge ME: is_a: wastewater_sludge mixins: - - me - description: Combinatorial checklist for wastewater_sludge with me - wastewater_sludge mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package wastewater_sludge + wastewater_sludge MIMARKS specimen: is_a: wastewater_sludge mixins: - - mimarks_s - description: Combinatorial checklist for wastewater_sludge with mimarks_s - wastewater_sludge mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package wastewater_sludge' + wastewater_sludge MIMARKS survey: is_a: wastewater_sludge mixins: - - mimarks_c - description: Combinatorial checklist for wastewater_sludge with mimarks_c - wastewater_sludge misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package wastewater_sludge' + wastewater_sludge MISAG: is_a: wastewater_sludge mixins: - - misag - description: Combinatorial checklist for wastewater_sludge with misag - wastewater_sludge mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package wastewater_sludge + wastewater_sludge MIMAG: is_a: wastewater_sludge mixins: - - mimag - description: Combinatorial checklist for wastewater_sludge with mimag - wastewater_sludge miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package wastewater_sludge + wastewater_sludge MIUVIG: is_a: wastewater_sludge mixins: - - miuvig - description: Combinatorial checklist for wastewater_sludge with miuvig - water migs_eu: + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package wastewater_sludge + water MIGS eukaryote: is_a: water mixins: - - migs_eu - description: Combinatorial checklist for water with migs_eu - water migs_ba: + - MIGS eukaryote + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + eukaryote with environmental package water' + water MIGS bacteria: is_a: water mixins: - - migs_ba - description: Combinatorial checklist for water with migs_ba - water migs_pl: + - MIGS bacteria + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package water' + water MIGS plant: is_a: water mixins: - - migs_pl - description: Combinatorial checklist for water with migs_pl - water migs_vi: + - MIGS plant + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + plant with environmental package water' + water MIGS virus: is_a: water mixins: - - migs_vi - description: Combinatorial checklist for water with migs_vi - water migs_org: + - MIGS virus + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + cultured bacteria/archaea with environmental package water' + water MIGS org: is_a: water mixins: - - migs_org - description: Combinatorial checklist for water with migs_org - water me: + - MIGS org + description: 'Combinatorial checklist Minimal Information about a Genome Sequence: + org with environmental package water' + water ME: is_a: water mixins: - - me - description: Combinatorial checklist for water with me - water mimarks_s: + - ME + description: Combinatorial checklist Metagenome or Environmental with environmental + package water + water MIMARKS specimen: is_a: water mixins: - - mimarks_s - description: Combinatorial checklist for water with mimarks_s - water mimarks_c: + - MIMARKS specimen + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + specimen with environmental package water' + water MIMARKS survey: is_a: water mixins: - - mimarks_c - description: Combinatorial checklist for water with mimarks_c - water misag: + - MIMARKS survey + description: 'Combinatorial checklist Minimal Information about a Marker Specimen: + survey with environmental package water' + water MISAG: is_a: water mixins: - - misag - description: Combinatorial checklist for water with misag - water mimag: + - MISAG + description: Combinatorial checklist Minimum Information About a Single Amplified + Genome with environmental package water + water MIMAG: is_a: water mixins: - - mimag - description: Combinatorial checklist for water with mimag - water miuvig: + - MIMAG + description: Combinatorial checklist Minimum Information About a Metagenome-Assembled + Genome with environmental package water + water MIUVIG: is_a: water mixins: - - miuvig - description: Combinatorial checklist for water with miuvig + - MIUVIG + description: Combinatorial checklist Minimum Information About an Uncultivated + Virus Genome with environmental package water subsets: {} enums: investigation_type_enum: From b31d4f9fcbd2141d42261cc9ecc8f2e2796b8517 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 23 Apr 2021 13:37:42 -0700 Subject: [PATCH 7/7] regen --- mixs6/AddRecovMethodEnum.md | 19 + mixs6/Air.md | 8 +- mixs6/AirMIGSBacteria.md | 23 +- mixs6/AirMIGSEukaryote.md | 23 +- mixs6/AirMIGSPlant.md | 23 +- mixs6/AirMIGSVirus.md | 23 +- mixs6/AirMIMARKSSpecimen.md | 23 +- mixs6/AirMIMARKSSurvey.md | 23 +- mixs6/AirMe.md | 23 +- mixs6/AirMigsBa.md | 395 - mixs6/AirMigsEu.md | 395 - mixs6/AirMigsOrg.md | 23 +- mixs6/AirMigsPl.md | 365 - mixs6/AirMigsVi.md | 390 - mixs6/AirMimag.md | 28 +- mixs6/AirMimarksC.md | 295 - mixs6/AirMimarksS.md | 315 - mixs6/AirMisag.md | 28 +- mixs6/AirMiuvig.md | 23 +- mixs6/ArchStrucEnum.md | 19 + mixs6/AssemblyQualEnum.md | 19 + mixs6/BinParamEnum.md | 19 + mixs6/BinSoftwareEnum.md | 19 + mixs6/BiolStatEnum.md | 19 + mixs6/BioticRelationshipEnum.md | 19 + mixs6/BuildDocsEnum.md | 19 + mixs6/BuildOccupTypeEnum.md | 19 + mixs6/BuildingSettingEnum.md | 19 + mixs6/BuiltEnvironment.md | 12 +- mixs6/BuiltEnvironmentMIGSBacteria.md | 27 +- mixs6/BuiltEnvironmentMIGSEukaryote.md | 27 +- mixs6/BuiltEnvironmentMIGSPlant.md | 27 +- mixs6/BuiltEnvironmentMIGSVirus.md | 27 +- mixs6/BuiltEnvironmentMIMARKSSpecimen.md | 27 +- mixs6/BuiltEnvironmentMIMARKSSurvey.md | 27 +- mixs6/BuiltEnvironmentMe.md | 27 +- mixs6/BuiltEnvironmentMigsBa.md | 935 - mixs6/BuiltEnvironmentMigsEu.md | 935 - mixs6/BuiltEnvironmentMigsOrg.md | 27 +- mixs6/BuiltEnvironmentMigsPl.md | 905 - mixs6/BuiltEnvironmentMigsVi.md | 930 - mixs6/BuiltEnvironmentMimag.md | 32 +- mixs6/BuiltEnvironmentMimarksC.md | 835 - mixs6/BuiltEnvironmentMimarksS.md | 855 - mixs6/BuiltEnvironmentMisag.md | 32 +- mixs6/BuiltEnvironmentMiuvig.md | 27 +- mixs6/CeilCondEnum.md | 19 + mixs6/CeilFinishMatEnum.md | 19 + mixs6/CeilTextureEnum.md | 19 + mixs6/CeilTypeEnum.md | 19 + mixs6/ComplApprEnum.md | 19 + mixs6/ComplScoreEnum.md | 19 + mixs6/ContamScreenParamEnum.md | 19 + mixs6/Core.md | 28 +- mixs6/CoreMe.md | 403 - mixs6/CoreMigsBa.md | 403 - mixs6/CoreMigsEu.md | 403 - mixs6/CoreMigsOrg.md | 403 - mixs6/CoreMigsPl.md | 403 - mixs6/CoreMigsVi.md | 403 - mixs6/CoreMimag.md | 403 - mixs6/CoreMimarksC.md | 403 - mixs6/CoreMimarksS.md | 403 - mixs6/CoreMisag.md | 403 - mixs6/CoreMiuvig.md | 403 - mixs6/CurLandUseEnum.md | 19 + mixs6/DecontamSoftwareEnum.md | 19 + mixs6/DeposEnvEnum.md | 19 + mixs6/DominantHandEnum.md | 19 + mixs6/DoorCompTypeEnum.md | 19 + mixs6/DoorCondEnum.md | 19 + mixs6/DoorDirectEnum.md | 19 + mixs6/DoorLocEnum.md | 19 + mixs6/DoorMatEnum.md | 19 + mixs6/DoorMoveEnum.md | 19 + mixs6/DoorTypeEnum.md | 19 + mixs6/DoorTypeMetalEnum.md | 19 + mixs6/DoorTypeWoodEnum.md | 19 + mixs6/DrainageClassEnum.md | 19 + mixs6/DrawingsEnum.md | 19 + mixs6/DrugUsageEnum.md | 19 + mixs6/EnvPackageEnum.md | 19 + mixs6/ExtWallOrientEnum.md | 19 + mixs6/ExtWindowOrientEnum.md | 19 + mixs6/FaoClassEnum.md | 19 + mixs6/FilterTypeEnum.md | 19 + mixs6/FloorCondEnum.md | 19 + mixs6/FloorFinishMatEnum.md | 19 + mixs6/FloorStrucEnum.md | 19 + mixs6/FloorWaterMoldEnum.md | 19 + mixs6/FurnitureEnum.md | 19 + mixs6/GrowthHabitEnum.md | 19 + mixs6/HandidnessEnum.md | 19 + mixs6/HcProducedEnum.md | 19 + mixs6/HcrEnum.md | 19 + mixs6/HcrGeolAgeEnum.md | 19 + mixs6/HealthDiseaseStatEnum.md | 19 + mixs6/HeatCoolTypeEnum.md | 19 + mixs6/HeatDelivLocEnum.md | 19 + mixs6/HorizonEnum.md | 19 + mixs6/Host-associated.md | 16 +- mixs6/Host-associatedMIGSBacteria.md | 31 +- mixs6/Host-associatedMIGSEukaryote.md | 31 +- mixs6/Host-associatedMIGSPlant.md | 31 +- mixs6/Host-associatedMIGSVirus.md | 31 +- mixs6/Host-associatedMIMARKSSpecimen.md | 31 +- mixs6/Host-associatedMIMARKSSurvey.md | 31 +- mixs6/Host-associatedMe.md | 31 +- mixs6/Host-associatedMigsBa.md | 475 - mixs6/Host-associatedMigsEu.md | 475 - mixs6/Host-associatedMigsOrg.md | 31 +- mixs6/Host-associatedMigsPl.md | 445 - mixs6/Host-associatedMigsVi.md | 470 - mixs6/Host-associatedMimag.md | 36 +- mixs6/Host-associatedMimarksC.md | 375 - mixs6/Host-associatedMimarksS.md | 395 - mixs6/Host-associatedMisag.md | 36 +- mixs6/Host-associatedMiuvig.md | 31 +- mixs6/HostPredApprEnum.md | 19 + mixs6/HostSexEnum.md | 19 + mixs6/Human-associated.md | 16 +- mixs6/Human-associatedMIGSBacteria.md | 31 +- mixs6/Human-associatedMIGSEukaryote.md | 31 +- mixs6/Human-associatedMIGSPlant.md | 31 +- mixs6/Human-associatedMIGSVirus.md | 31 +- mixs6/Human-associatedMIMARKSSpecimen.md | 31 +- mixs6/Human-associatedMIMARKSSurvey.md | 31 +- mixs6/Human-associatedMe.md | 31 +- mixs6/Human-associatedMigsBa.md | 491 - mixs6/Human-associatedMigsEu.md | 491 - mixs6/Human-associatedMigsOrg.md | 31 +- mixs6/Human-associatedMigsPl.md | 461 - mixs6/Human-associatedMigsVi.md | 486 - mixs6/Human-associatedMimag.md | 36 +- mixs6/Human-associatedMimarksC.md | 391 - mixs6/Human-associatedMimarksS.md | 411 - mixs6/Human-associatedMisag.md | 36 +- mixs6/Human-associatedMiuvig.md | 31 +- mixs6/Human-gut.md | 12 +- mixs6/Human-gutMIGSBacteria.md | 27 +- mixs6/Human-gutMIGSEukaryote.md | 27 +- mixs6/Human-gutMIGSPlant.md | 27 +- mixs6/Human-gutMIGSVirus.md | 27 +- mixs6/Human-gutMIMARKSSpecimen.md | 27 +- mixs6/Human-gutMIMARKSSurvey.md | 27 +- mixs6/Human-gutMe.md | 27 +- mixs6/Human-gutMigsBa.md | 431 - mixs6/Human-gutMigsEu.md | 431 - mixs6/Human-gutMigsOrg.md | 27 +- mixs6/Human-gutMigsPl.md | 401 - mixs6/Human-gutMigsVi.md | 426 - mixs6/Human-gutMimag.md | 32 +- mixs6/Human-gutMimarksC.md | 331 - mixs6/Human-gutMimarksS.md | 351 - mixs6/Human-gutMisag.md | 32 +- mixs6/Human-gutMiuvig.md | 27 +- mixs6/Human-oral.md | 12 +- mixs6/Human-oralMIGSBacteria.md | 27 +- mixs6/Human-oralMIGSEukaryote.md | 27 +- mixs6/Human-oralMIGSPlant.md | 27 +- mixs6/Human-oralMIGSVirus.md | 27 +- mixs6/Human-oralMIMARKSSpecimen.md | 27 +- mixs6/Human-oralMIMARKSSurvey.md | 27 +- mixs6/Human-oralMe.md | 27 +- mixs6/Human-oralMigsBa.md | 427 - mixs6/Human-oralMigsEu.md | 427 - mixs6/Human-oralMigsOrg.md | 27 +- mixs6/Human-oralMigsPl.md | 397 - mixs6/Human-oralMigsVi.md | 422 - mixs6/Human-oralMimag.md | 32 +- mixs6/Human-oralMimarksC.md | 327 - mixs6/Human-oralMimarksS.md | 347 - mixs6/Human-oralMisag.md | 32 +- mixs6/Human-oralMiuvig.md | 27 +- mixs6/Human-skin.md | 12 +- mixs6/Human-skinMIGSBacteria.md | 27 +- mixs6/Human-skinMIGSEukaryote.md | 27 +- mixs6/Human-skinMIGSPlant.md | 27 +- mixs6/Human-skinMIGSVirus.md | 27 +- mixs6/Human-skinMIMARKSSpecimen.md | 27 +- mixs6/Human-skinMIMARKSSurvey.md | 27 +- mixs6/Human-skinMe.md | 27 +- mixs6/Human-skinMigsBa.md | 431 - mixs6/Human-skinMigsEu.md | 431 - mixs6/Human-skinMigsOrg.md | 27 +- mixs6/Human-skinMigsPl.md | 401 - mixs6/Human-skinMigsVi.md | 426 - mixs6/Human-skinMimag.md | 32 +- mixs6/Human-skinMimarksC.md | 331 - mixs6/Human-skinMimarksS.md | 351 - mixs6/Human-skinMisag.md | 32 +- mixs6/Human-skinMiuvig.md | 27 +- mixs6/Human-vaginal.md | 22 +- mixs6/Human-vaginalMIGSBacteria.md | 37 +- mixs6/Human-vaginalMIGSEukaryote.md | 37 +- mixs6/Human-vaginalMIGSPlant.md | 37 +- mixs6/Human-vaginalMIGSVirus.md | 37 +- mixs6/Human-vaginalMIMARKSSpecimen.md | 37 +- mixs6/Human-vaginalMIMARKSSurvey.md | 37 +- mixs6/Human-vaginalMe.md | 37 +- mixs6/Human-vaginalMigsBa.md | 459 - mixs6/Human-vaginalMigsEu.md | 459 - mixs6/Human-vaginalMigsOrg.md | 37 +- mixs6/Human-vaginalMigsPl.md | 429 - mixs6/Human-vaginalMigsVi.md | 454 - mixs6/Human-vaginalMimag.md | 42 +- mixs6/Human-vaginalMimarksC.md | 359 - mixs6/Human-vaginalMimarksS.md | 379 - mixs6/Human-vaginalMisag.md | 42 +- mixs6/Human-vaginalMiuvig.md | 37 +- mixs6/HydrocarbonResources-cores.md | 12 +- .../HydrocarbonResources-coresMIGSBacteria.md | 27 +- ...HydrocarbonResources-coresMIGSEukaryote.md | 27 +- mixs6/HydrocarbonResources-coresMIGSPlant.md | 27 +- mixs6/HydrocarbonResources-coresMIGSVirus.md | 27 +- ...drocarbonResources-coresMIMARKSSpecimen.md | 27 +- ...HydrocarbonResources-coresMIMARKSSurvey.md | 27 +- mixs6/HydrocarbonResources-coresMe.md | 27 +- mixs6/HydrocarbonResources-coresMigsBa.md | 611 - mixs6/HydrocarbonResources-coresMigsEu.md | 611 - mixs6/HydrocarbonResources-coresMigsOrg.md | 27 +- mixs6/HydrocarbonResources-coresMigsPl.md | 581 - mixs6/HydrocarbonResources-coresMigsVi.md | 606 - mixs6/HydrocarbonResources-coresMimag.md | 32 +- mixs6/HydrocarbonResources-coresMimarksC.md | 511 - mixs6/HydrocarbonResources-coresMimarksS.md | 531 - mixs6/HydrocarbonResources-coresMisag.md | 32 +- mixs6/HydrocarbonResources-coresMiuvig.md | 27 +- mixs6/HydrocarbonResources-fluidsSwabs.md | 16 +- ...carbonResources-fluidsSwabsMIGSBacteria.md | 31 +- ...arbonResources-fluidsSwabsMIGSEukaryote.md | 31 +- ...drocarbonResources-fluidsSwabsMIGSPlant.md | 31 +- ...drocarbonResources-fluidsSwabsMIGSVirus.md | 31 +- ...bonResources-fluidsSwabsMIMARKSSpecimen.md | 31 +- ...arbonResources-fluidsSwabsMIMARKSSurvey.md | 31 +- mixs6/HydrocarbonResources-fluidsSwabsMe.md | 31 +- .../HydrocarbonResources-fluidsSwabsMigsBa.md | 631 - .../HydrocarbonResources-fluidsSwabsMigsEu.md | 631 - ...HydrocarbonResources-fluidsSwabsMigsOrg.md | 31 +- .../HydrocarbonResources-fluidsSwabsMigsPl.md | 601 - .../HydrocarbonResources-fluidsSwabsMigsVi.md | 626 - .../HydrocarbonResources-fluidsSwabsMimag.md | 36 +- ...ydrocarbonResources-fluidsSwabsMimarksC.md | 531 - ...ydrocarbonResources-fluidsSwabsMimarksS.md | 551 - .../HydrocarbonResources-fluidsSwabsMisag.md | 36 +- .../HydrocarbonResources-fluidsSwabsMiuvig.md | 31 +- mixs6/IndoorSpaceEnum.md | 19 + mixs6/IndoorSurfEnum.md | 19 + mixs6/IntWallCondEnum.md | 19 + mixs6/InvestigationTypeEnum.md | 19 + mixs6/LibLayoutEnum.md | 19 + mixs6/LightTypeEnum.md | 19 + mixs6/LithologyEnum.md | 19 + ..._device.md => ME_sample_collect_device.md} | 6 +- mixs6/ME_sample_collect_method.md | 47 + mixs6/MIGSBacteria.md | 12 +- mixs6/MIGSEukaryote.md | 12 +- mixs6/MIGSPlant.md | 12 +- mixs6/MIGSVirus.md | 12 +- mixs6/MIGS_bacteria_collection_date.md | 2 +- ...=> MIGS_bacteria_sample_collect_device.md} | 6 +- mixs6/MIGS_bacteria_sample_collect_method.md | 40 + mixs6/MIGS_bacteria_sample_name.md | 2 +- mixs6/MIGS_eukaryote_collection_date.md | 2 +- ...> MIGS_eukaryote_sample_collect_device.md} | 6 +- mixs6/MIGS_eukaryote_sample_collect_method.md | 40 + mixs6/MIGS_eukaryote_sample_name.md | 2 +- ...e.md => MIGS_org_sample_collect_device.md} | 6 +- mixs6/MIGS_org_sample_collect_method.md | 40 + mixs6/MIGS_plant_collection_date.md | 2 +- ...md => MIGS_plant_sample_collect_device.md} | 6 +- mixs6/MIGS_plant_sample_collect_method.md | 40 + mixs6/MIGS_plant_sample_name.md | 2 +- mixs6/MIGS_virus_collection_date.md | 2 +- ...md => MIGS_virus_sample_collect_device.md} | 6 +- mixs6/MIGS_virus_sample_collect_method.md | 40 + mixs6/MIGS_virus_sample_name.md | 2 +- ...vice.md => MIMAG_sample_collect_device.md} | 6 +- ...ware.md => MIMAG_sample_collect_method.md} | 13 +- mixs6/MIMARKSSpecimen.md | 12 +- mixs6/MIMARKSSurvey.md | 12 +- mixs6/MIMARKS_specimen_collection_date.md | 2 +- ...MIMARKS_specimen_sample_collect_device.md} | 6 +- .../MIMARKS_specimen_sample_collect_method.md | 47 + mixs6/MIMARKS_specimen_sample_name.md | 2 +- mixs6/MIMARKS_survey_collection_date.md | 2 +- ...> MIMARKS_survey_sample_collect_device.md} | 6 +- mixs6/MIMARKS_survey_sample_collect_method.md | 40 + mixs6/MIMARKS_survey_sample_name.md | 2 +- ...vice.md => MISAG_sample_collect_device.md} | 6 +- ...ware.md => MISAG_sample_collect_method.md} | 13 +- ...ice.md => MIUVIG_sample_collect_device.md} | 6 +- mixs6/MIUVIG_sample_collect_method.md | 47 + mixs6/MagCovSoftwareEnum.md | 19 + mixs6/Me.md | 12 +- mixs6/MechStrucEnum.md | 19 + mixs6/MicrobialMatBiofilm.md | 8 +- mixs6/MicrobialMatBiofilmMIGSBacteria.md | 23 +- mixs6/MicrobialMatBiofilmMIGSEukaryote.md | 23 +- mixs6/MicrobialMatBiofilmMIGSPlant.md | 23 +- mixs6/MicrobialMatBiofilmMIGSVirus.md | 23 +- mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md | 23 +- mixs6/MicrobialMatBiofilmMIMARKSSurvey.md | 23 +- mixs6/MicrobialMatBiofilmMe.md | 23 +- mixs6/MicrobialMatBiofilmMigsBa.md | 535 - mixs6/MicrobialMatBiofilmMigsEu.md | 535 - mixs6/MicrobialMatBiofilmMigsOrg.md | 23 +- mixs6/MicrobialMatBiofilmMigsPl.md | 505 - mixs6/MicrobialMatBiofilmMigsVi.md | 530 - mixs6/MicrobialMatBiofilmMimag.md | 28 +- mixs6/MicrobialMatBiofilmMimarksC.md | 435 - mixs6/MicrobialMatBiofilmMimarksS.md | 455 - mixs6/MicrobialMatBiofilmMisag.md | 28 +- mixs6/MicrobialMatBiofilmMiuvig.md | 23 +- mixs6/MigsBa.md | 145 - mixs6/MigsEu.md | 145 - mixs6/MigsOrg.md | 12 +- mixs6/MigsPl.md | 133 - mixs6/MigsVi.md | 143 - mixs6/Mimag.md | 14 +- mixs6/MimarksC.md | 105 - mixs6/MimarksS.md | 113 - mixs6/Misag.md | 14 +- ...ellaneousNaturalOrArtificialEnvironment.md | 8 +- ...uralOrArtificialEnvironmentMIGSBacteria.md | 23 +- ...ralOrArtificialEnvironmentMIGSEukaryote.md | 23 +- ...NaturalOrArtificialEnvironmentMIGSPlant.md | 23 +- ...NaturalOrArtificialEnvironmentMIGSVirus.md | 23 +- ...lOrArtificialEnvironmentMIMARKSSpecimen.md | 23 +- ...ralOrArtificialEnvironmentMIMARKSSurvey.md | 23 +- ...laneousNaturalOrArtificialEnvironmentMe.md | 23 +- ...ousNaturalOrArtificialEnvironmentMigsBa.md | 459 - ...ousNaturalOrArtificialEnvironmentMigsEu.md | 459 - ...usNaturalOrArtificialEnvironmentMigsOrg.md | 23 +- ...ousNaturalOrArtificialEnvironmentMigsPl.md | 429 - ...ousNaturalOrArtificialEnvironmentMigsVi.md | 454 - ...eousNaturalOrArtificialEnvironmentMimag.md | 28 +- ...sNaturalOrArtificialEnvironmentMimarksC.md | 359 - ...sNaturalOrArtificialEnvironmentMimarksS.md | 379 - ...eousNaturalOrArtificialEnvironmentMisag.md | 28 +- ...ousNaturalOrArtificialEnvironmentMiuvig.md | 23 +- mixs6/Miuvig.md | 12 +- mixs6/OccupDocumentEnum.md | 19 + mixs6/OrganismCountEnum.md | 19 + mixs6/OxyStatSampEnum.md | 19 + mixs6/Plant-associated.md | 20 +- mixs6/Plant-associatedMIGSBacteria.md | 31 +- mixs6/Plant-associatedMIGSEukaryote.md | 31 +- mixs6/Plant-associatedMIGSPlant.md | 31 +- mixs6/Plant-associatedMIGSVirus.md | 31 +- mixs6/Plant-associatedMIMARKSSpecimen.md | 31 +- mixs6/Plant-associatedMIMARKSSurvey.md | 31 +- mixs6/Plant-associatedMe.md | 31 +- mixs6/Plant-associatedMigsBa.md | 579 - mixs6/Plant-associatedMigsEu.md | 579 - mixs6/Plant-associatedMigsOrg.md | 31 +- mixs6/Plant-associatedMigsPl.md | 549 - mixs6/Plant-associatedMigsVi.md | 574 - mixs6/Plant-associatedMimag.md | 36 +- mixs6/Plant-associatedMimarksC.md | 479 - mixs6/Plant-associatedMimarksS.md | 499 - mixs6/Plant-associatedMisag.md | 36 +- mixs6/Plant-associatedMiuvig.md | 31 +- mixs6/PlantGrowthMedEnum.md | 19 + mixs6/PlantSexEnum.md | 19 + mixs6/PredGenomeStrucEnum.md | 19 + mixs6/PredGenomeTypeEnum.md | 19 + mixs6/PresAnimalEnum.md | 19 + mixs6/ProfilePositionEnum.md | 19 + mixs6/QuadPosEnum.md | 19 + mixs6/RelSampLocEnum.md | 19 + mixs6/RelToOxygenEnum.md | 19 + mixs6/RoomCondtEnum.md | 19 + mixs6/RoomConnectedEnum.md | 19 + mixs6/RoomLocEnum.md | 19 + mixs6/RoomSampPosEnum.md | 19 + mixs6/RoomTypeEnum.md | 19 + mixs6/SampCaptStatusEnum.md | 19 + mixs6/SampCollectionPointEnum.md | 19 + mixs6/SampDisStageEnum.md | 19 + mixs6/SampFloorEnum.md | 19 + mixs6/SampMdEnum.md | 19 + mixs6/SampSubtypeEnum.md | 19 + mixs6/SampTypeEnum.md | 19 + mixs6/SampWeatherEnum.md | 19 + mixs6/SeasonUseEnum.md | 19 + mixs6/Sediment.md | 8 +- mixs6/SedimentMIGSBacteria.md | 23 +- mixs6/SedimentMIGSEukaryote.md | 23 +- mixs6/SedimentMIGSPlant.md | 23 +- mixs6/SedimentMIGSVirus.md | 23 +- mixs6/SedimentMIMARKSSpecimen.md | 23 +- mixs6/SedimentMIMARKSSurvey.md | 23 +- mixs6/SedimentMe.md | 23 +- mixs6/SedimentMigsBa.md | 559 - mixs6/SedimentMigsEu.md | 559 - mixs6/SedimentMigsOrg.md | 23 +- mixs6/SedimentMigsPl.md | 529 - mixs6/SedimentMigsVi.md | 554 - mixs6/SedimentMimag.md | 28 +- mixs6/SedimentMimarksC.md | 459 - mixs6/SedimentMimarksS.md | 479 - mixs6/SedimentMisag.md | 28 +- mixs6/SedimentMiuvig.md | 23 +- mixs6/SedimentTypeEnum.md | 19 + mixs6/SeqMethEnum.md | 19 + mixs6/ShadingDeviceCondEnum.md | 19 + mixs6/ShadingDeviceTypeEnum.md | 19 + mixs6/SingleCellLysisApprEnum.md | 19 + mixs6/Soil.md | 14 +- mixs6/SoilMIGSBacteria.md | 29 +- mixs6/SoilMIGSEukaryote.md | 29 +- mixs6/SoilMIGSPlant.md | 29 +- mixs6/SoilMIGSVirus.md | 29 +- mixs6/SoilMIMARKSSpecimen.md | 29 +- mixs6/SoilMIMARKSSurvey.md | 29 +- mixs6/SoilMe.md | 29 +- mixs6/SoilMigsBa.md | 503 - mixs6/SoilMigsEu.md | 503 - mixs6/SoilMigsOrg.md | 29 +- mixs6/SoilMigsPl.md | 473 - mixs6/SoilMigsVi.md | 498 - mixs6/SoilMimag.md | 34 +- mixs6/SoilMimarksC.md | 403 - mixs6/SoilMimarksS.md | 423 - mixs6/SoilMisag.md | 34 +- mixs6/SoilMiuvig.md | 29 +- mixs6/SortTechEnum.md | 19 + mixs6/SourceUvigEnum.md | 19 + mixs6/SpecialDietEnum.md | 19 + mixs6/SpecificEnum.md | 19 + mixs6/SrDepEnvEnum.md | 19 + mixs6/SrGeolAgeEnum.md | 19 + mixs6/SrKerogTypeEnum.md | 19 + mixs6/SrLithologyEnum.md | 19 + mixs6/StudyCompltStatEnum.md | 19 + mixs6/SubstructureTypeEnum.md | 19 + mixs6/SurfAirContEnum.md | 19 + mixs6/SurfMaterialEnum.md | 19 + mixs6/TaxIdentEnum.md | 19 + mixs6/TidalStageEnum.md | 19 + mixs6/TillageEnum.md | 19 + mixs6/TrainLineEnum.md | 19 + mixs6/TrainStatLocEnum.md | 19 + mixs6/TrainStopLocEnum.md | 19 + mixs6/TrophicLevelEnum.md | 19 + mixs6/VirusEnrichApprEnum.md | 19 + mixs6/VisMediaEnum.md | 19 + mixs6/WallConstTypeEnum.md | 19 + mixs6/WallFinishMatEnum.md | 19 + mixs6/WallLocEnum.md | 19 + mixs6/WallSurfTreatmentEnum.md | 19 + mixs6/WallTextureEnum.md | 19 + mixs6/WastewaterSludge.md | 8 +- mixs6/WastewaterSludgeMIGSBacteria.md | 23 +- mixs6/WastewaterSludgeMIGSEukaryote.md | 23 +- mixs6/WastewaterSludgeMIGSPlant.md | 23 +- mixs6/WastewaterSludgeMIGSVirus.md | 23 +- mixs6/WastewaterSludgeMIMARKSSpecimen.md | 23 +- mixs6/WastewaterSludgeMIMARKSSurvey.md | 23 +- mixs6/WastewaterSludgeMe.md | 23 +- mixs6/WastewaterSludgeMigsBa.md | 443 - mixs6/WastewaterSludgeMigsEu.md | 443 - mixs6/WastewaterSludgeMigsOrg.md | 23 +- mixs6/WastewaterSludgeMigsPl.md | 413 - mixs6/WastewaterSludgeMigsVi.md | 438 - mixs6/WastewaterSludgeMimag.md | 28 +- mixs6/WastewaterSludgeMimarksC.md | 343 - mixs6/WastewaterSludgeMimarksS.md | 363 - mixs6/WastewaterSludgeMisag.md | 28 +- mixs6/WastewaterSludgeMiuvig.md | 23 +- mixs6/Water.md | 8 +- mixs6/WaterFeatTypeEnum.md | 19 + mixs6/WaterMIGSBacteria.md | 23 +- mixs6/WaterMIGSEukaryote.md | 23 +- mixs6/WaterMIGSPlant.md | 23 +- mixs6/WaterMIGSVirus.md | 23 +- mixs6/WaterMIMARKSSpecimen.md | 23 +- mixs6/WaterMIMARKSSurvey.md | 23 +- mixs6/WaterMe.md | 23 +- mixs6/WaterMigsBa.md | 619 - mixs6/WaterMigsEu.md | 619 - mixs6/WaterMigsOrg.md | 23 +- mixs6/WaterMigsPl.md | 589 - mixs6/WaterMigsVi.md | 614 - mixs6/WaterMimag.md | 28 +- mixs6/WaterMimarksC.md | 519 - mixs6/WaterMimarksS.md | 539 - mixs6/WaterMisag.md | 28 +- mixs6/WaterMiuvig.md | 23 +- mixs6/WeekdayEnum.md | 19 + mixs6/WindowCondEnum.md | 19 + mixs6/WindowCoverEnum.md | 19 + mixs6/WindowHorizPosEnum.md | 19 + mixs6/WindowLocEnum.md | 19 + mixs6/WindowMatEnum.md | 19 + mixs6/WindowTypeEnum.md | 19 + mixs6/WindowVertPosEnum.md | 19 + mixs6/abs_air_humidity.md | 2 +- mixs6/adapters.md | 1 - mixs6/add_recov_method.md | 3 +- mixs6/additional_info.md | 3 +- mixs6/address.md | 3 +- mixs6/adj_room.md | 3 +- mixs6/aero_struc.md | 3 +- mixs6/agrochem_addition.md | 2 +- mixs6/air_temp.md | 2 +- mixs6/air_temp_regm.md | 2 +- mixs6/al_sat.md | 2 +- mixs6/al_sat_meth.md | 3 +- mixs6/alkalinity.md | 2 +- mixs6/alkalinity_method.md | 3 +- mixs6/alkyl_diethers.md | 2 +- mixs6/alt.md | 4 +- mixs6/aminopept_act.md | 2 +- mixs6/ammonium.md | 2 +- mixs6/amniotic_fluid_color.md | 3 +- mixs6/amount_light.md | 2 +- mixs6/ances_data.md | 3 +- mixs6/annot.md | 1 - mixs6/annual_precpt.md | 2 +- mixs6/annual_temp.md | 2 +- mixs6/antibiotic_regm.md | 2 +- mixs6/api.md | 2 +- mixs6/arch_struc.md | 3 +- mixs6/aromatics_pc.md | 2 +- mixs6/asphaltenes_pc.md | 2 +- mixs6/assembly_name.md | 1 - mixs6/assembly_qual.md | 1 - mixs6/assembly_software.md | 1 - mixs6/atmospheric_data.md | 3 +- mixs6/avg_dew_point.md | 2 +- mixs6/avg_occup.md | 3 +- mixs6/avg_temp.md | 2 +- mixs6/bac_prod.md | 2 +- mixs6/bac_resp.md | 2 +- mixs6/bacteria_carb_prod.md | 2 +- mixs6/barometric_press.md | 2 +- mixs6/basin.md | 3 +- mixs6/bathroom_count.md | 3 +- mixs6/bedroom_count.md | 3 +- mixs6/benzene.md | 2 +- mixs6/bin_param.md | 1 - mixs6/bin_software.md | 1 - mixs6/biochem_oxygen_dem.md | 2 +- mixs6/biocide.md | 3 +- mixs6/biocide_admin_method.md | 2 +- mixs6/biol_stat.md | 5 +- mixs6/biomass.md | 2 +- mixs6/biotic_regm.md | 3 +- mixs6/biotic_relationship.md | 1 - mixs6/birth_control.md | 3 +- mixs6/bishomohopanol.md | 2 +- mixs6/blood_blood_disord.md | 3 +- mixs6/bromide.md | 2 +- mixs6/build_docs.md | 3 +- mixs6/build_occup_type.md | 3 +- mixs6/building_setting.md | 3 +- mixs6/built_struc_age.md | 2 +- mixs6/built_struc_set.md | 3 +- mixs6/built_struc_type.md | 3 +- mixs6/calcium.md | 2 +- mixs6/carb_dioxide.md | 2 +- mixs6/carb_monoxide.md | 2 +- mixs6/carb_nitro_ratio.md | 3 +- mixs6/ceil_area.md | 2 +- mixs6/ceil_cond.md | 3 +- mixs6/ceil_finish_mat.md | 3 +- mixs6/ceil_struc.md | 3 +- mixs6/ceil_texture.md | 3 +- mixs6/ceil_thermal_mass.md | 2 +- mixs6/ceil_type.md | 3 +- mixs6/ceil_water_mold.md | 3 +- mixs6/chem_administration.md | 3 +- mixs6/chem_mutagen.md | 2 +- mixs6/chem_oxygen_dem.md | 2 +- mixs6/chem_treatment.md | 3 +- mixs6/chem_treatment_method.md | 2 +- mixs6/chimera_check.md | 1 - mixs6/chloride.md | 2 +- mixs6/chlorophyll.md | 2 +- mixs6/climate_environment.md | 3 +- mixs6/collection_date.md | 3 +- mixs6/compl_appr.md | 1 - mixs6/compl_score.md | 1 - mixs6/compl_software.md | 1 - mixs6/conduc.md | 2 +- mixs6/contam_score.md | 1 - mixs6/contam_screen_input.md | 1 - mixs6/contam_screen_param.md | 1 - mixs6/cool_syst_id.md | 3 +- mixs6/core_field.md | 1 - mixs6/crop_rotation.md | 3 +- mixs6/cult_root_med.md | 3 +- mixs6/cur_land_use.md | 3 +- mixs6/cur_vegetation.md | 3 +- mixs6/cur_vegetation_meth.md | 3 +- mixs6/date_last_rain.md | 5 +- mixs6/decontam_software.md | 1 - mixs6/density.md | 2 +- mixs6/depos_env.md | 3 +- mixs6/depth.md | 3 +- mixs6/dermatology_disord.md | 3 +- mixs6/detec_type.md | 1 - mixs6/dew_point.md | 2 +- mixs6/diet_last_six_month.md | 3 +- mixs6/diether_lipids.md | 2 +- mixs6/diss_carb_dioxide.md | 2 +- mixs6/diss_hydrogen.md | 2 +- mixs6/diss_inorg_carb.md | 2 +- mixs6/diss_inorg_nitro.md | 2 +- mixs6/diss_inorg_phosp.md | 2 +- mixs6/diss_iron.md | 2 +- mixs6/diss_org_carb.md | 2 +- mixs6/diss_org_nitro.md | 2 +- mixs6/diss_oxygen.md | 2 +- mixs6/diss_oxygen_fluid.md | 2 +- mixs6/dominant_hand.md | 3 +- mixs6/door_comp_type.md | 3 +- mixs6/door_cond.md | 3 +- mixs6/door_direct.md | 3 +- mixs6/door_loc.md | 3 +- mixs6/door_mat.md | 3 +- mixs6/door_move.md | 3 +- mixs6/door_size.md | 2 +- mixs6/door_type.md | 3 +- mixs6/door_type_metal.md | 3 +- mixs6/door_type_wood.md | 3 +- mixs6/door_water_mold.md | 3 +- mixs6/douche.md | 5 +- mixs6/down_par.md | 2 +- mixs6/drainage_class.md | 3 +- mixs6/drawings.md | 3 +- mixs6/drug_usage.md | 3 +- mixs6/efficiency_percent.md | 2 +- mixs6/elev.md | 1 - mixs6/elevator.md | 3 +- mixs6/emulsions.md | 2 +- mixs6/encoded_traits.md | 1 - mixs6/env_broad_scale.md | 1 - mixs6/env_local_scale.md | 1 - mixs6/env_medium.md | 1 - mixs6/env_package.md | 1 - mixs6/environment_field.md | 2 + mixs6/escalator.md | 3 +- mixs6/estimated_size.md | 1 - mixs6/ethylbenzene.md | 2 +- mixs6/exp_duct.md | 2 +- mixs6/exp_pipe.md | 3 +- mixs6/experimental_factor.md | 1 - mixs6/ext_door.md | 3 +- mixs6/ext_wall_orient.md | 3 +- mixs6/ext_window_orient.md | 3 +- mixs6/extrachrom_elements.md | 1 - mixs6/extreme_event.md | 5 +- mixs6/extreme_salinity.md | 2 +- mixs6/fao_class.md | 3 +- mixs6/feat_pred.md | 1 - mixs6/fertilizer_regm.md | 2 +- mixs6/field.md | 3 +- mixs6/filter_type.md | 3 +- mixs6/fire.md | 5 +- mixs6/fireplace_type.md | 3 +- mixs6/flooding.md | 5 +- mixs6/floor_age.md | 2 +- mixs6/floor_area.md | 2 +- mixs6/floor_cond.md | 3 +- mixs6/floor_count.md | 3 +- mixs6/floor_finish_mat.md | 3 +- mixs6/floor_struc.md | 3 +- mixs6/floor_thermal_mass.md | 2 +- mixs6/floor_water_mold.md | 3 +- mixs6/fluor.md | 2 +- mixs6/foetal_health_stat.md | 3 +- mixs6/freq_clean.md | 3 +- mixs6/freq_cook.md | 3 +- mixs6/fungicide_regm.md | 2 +- mixs6/furniture.md | 3 +- mixs6/gaseous_environment.md | 2 +- mixs6/gaseous_substances.md | 2 +- mixs6/gastrointest_disord.md | 3 +- mixs6/gender_restroom.md | 3 +- mixs6/genetic_mod.md | 3 +- mixs6/geo_loc_name.md | 1 - mixs6/gestation_state.md | 3 +- mixs6/glucosidase_act.md | 2 +- mixs6/gravidity.md | 3 +- mixs6/gravity.md | 2 +- mixs6/growth_facil.md | 3 +- mixs6/growth_habit.md | 3 +- mixs6/growth_hormone_regm.md | 2 +- mixs6/gynecologic_disord.md | 3 +- mixs6/hall_count.md | 3 +- mixs6/handidness.md | 3 +- mixs6/hc_produced.md | 3 +- mixs6/hcr.md | 3 +- mixs6/hcr_fw_salinity.md | 2 +- mixs6/hcr_geol_age.md | 3 +- mixs6/hcr_pressure.md | 2 +- mixs6/hcr_temp.md | 2 +- mixs6/health_disease_stat.md | 1 - mixs6/heat_cool_type.md | 3 +- mixs6/heat_deliv_loc.md | 3 +- mixs6/heat_system_deliv_meth.md | 3 +- mixs6/heat_system_id.md | 3 +- mixs6/heavy_metals.md | 2 +- mixs6/heavy_metals_meth.md | 3 +- mixs6/height_carper_fiber.md | 2 +- mixs6/herbicide_regm.md | 2 +- mixs6/horizon.md | 3 +- mixs6/horizon_meth.md | 3 +- mixs6/host_age.md | 2 +- mixs6/host_blood_press_diast.md | 2 +- mixs6/host_blood_press_syst.md | 2 +- mixs6/host_body_habitat.md | 3 +- mixs6/host_body_mass_index.md | 2 +- mixs6/host_body_product.md | 3 +- mixs6/host_body_site.md | 3 +- mixs6/host_body_temp.md | 2 +- mixs6/host_color.md | 3 +- mixs6/host_common_name.md | 3 +- mixs6/host_diet.md | 3 +- mixs6/host_disease_stat.md | 3 +- mixs6/host_dry_mass.md | 2 +- mixs6/host_family_relationship.md | 3 +- mixs6/host_genotype.md | 3 +- mixs6/host_growth_cond.md | 3 +- mixs6/host_height.md | 2 +- mixs6/host_hiv_stat.md | 3 +- mixs6/host_infra_specific_name.md | 3 +- mixs6/host_infra_specific_rank.md | 3 +- mixs6/host_last_meal.md | 3 +- mixs6/host_length.md | 2 +- mixs6/host_life_stage.md | 3 +- mixs6/host_occupation.md | 3 +- mixs6/host_phenotype.md | 3 +- mixs6/host_pred_appr.md | 1 - mixs6/host_pred_est_acc.md | 1 - mixs6/host_pulse.md | 2 +- mixs6/host_sex.md | 3 +- mixs6/host_shape.md | 3 +- mixs6/host_spec_range.md | 1 - mixs6/host_subject_id.md | 3 +- mixs6/host_substrate.md | 3 +- mixs6/host_symbiont.md | 117 + mixs6/host_taxid.md | 3 +- mixs6/host_tot_mass.md | 2 +- mixs6/host_wet_mass.md | 2 +- mixs6/hrt.md | 5 +- mixs6/humidity.md | 2 +- mixs6/humidity_regm.md | 2 +- mixs6/hysterectomy.md | 3 +- mixs6/ihmc_ethnicity.md | 3 +- mixs6/ihmc_medication_code.md | 3 +- mixs6/index.md | 213 +- mixs6/indoor_space.md | 3 +- mixs6/indoor_surf.md | 3 +- mixs6/indust_eff_percent.md | 2 +- mixs6/inorg_particles.md | 2 +- mixs6/inside_lux.md | 2 +- mixs6/int_wall_cond.md | 3 +- mixs6/investigation_field.md | 1 + mixs6/investigation_type.md | 1 - mixs6/isol_growth_condt.md | 1 - mixs6/iw_bt_date_well.md | 5 +- mixs6/iwf.md | 2 +- mixs6/kidney_disord.md | 47 + mixs6/last_clean.md | 5 +- mixs6/lat_lon.md | 1 - mixs6/lib_layout.md | 1 - mixs6/lib_reads_seqd.md | 1 - mixs6/lib_screen.md | 1 - mixs6/lib_size.md | 1 - mixs6/lib_vector.md | 1 - mixs6/light_intensity.md | 2 +- mixs6/light_regm.md | 2 +- mixs6/light_type.md | 3 +- mixs6/link_addit_analys.md | 3 +- mixs6/link_class_info.md | 3 +- mixs6/link_climate_info.md | 3 +- mixs6/lithology.md | 3 +- mixs6/liver_disord.md | 3 +- mixs6/local_class.md | 3 +- mixs6/local_class_meth.md | 3 +- mixs6/mag_cov_software.md | 1 - mixs6/magnesium.md | 2 +- mixs6/maternal_health_stat.md | 3 +- mixs6/max_occup.md | 3 +- mixs6/me_collection_date.md | 2 +- mixs6/me_sample_name.md | 2 +- mixs6/mean_frict_vel.md | 2 +- mixs6/mean_peak_frict_vel.md | 2 +- mixs6/mech_struc.md | 3 +- mixs6/mechanical_damage.md | 3 +- mixs6/medic_hist_perform.md | 3 +- mixs6/menarche.md | 5 +- mixs6/menopause.md | 5 +- mixs6/methane.md | 2 +- mixs6/microbial_biomass.md | 2 +- mixs6/microbial_biomass_meth.md | 3 +- mixs6/mid.md | 1 - mixs6/migs_ba_adapters.md | 47 - mixs6/migs_ba_annot.md | 47 - mixs6/migs_ba_assembly_name.md | 47 - mixs6/migs_ba_assembly_qual.md | 40 - mixs6/migs_ba_assembly_software.md | 40 - mixs6/migs_ba_biotic_relationship.md | 47 - mixs6/migs_ba_collection_date.md | 23 - mixs6/migs_ba_compl_score.md | 40 - mixs6/migs_ba_compl_software.md | 40 - mixs6/migs_ba_encoded_traits.md | 40 - mixs6/migs_ba_env_broad_scale.md | 23 - mixs6/migs_ba_env_local_scale.md | 23 - mixs6/migs_ba_env_medium.md | 23 - mixs6/migs_ba_env_package.md | 47 - mixs6/migs_ba_estimated_size.md | 40 - mixs6/migs_ba_experimental_factor.md | 40 - mixs6/migs_ba_extrachrom_elements.md | 47 - mixs6/migs_ba_feat_pred.md | 40 - mixs6/migs_ba_geo_loc_name.md | 23 - mixs6/migs_ba_health_disease_stat.md | 47 - mixs6/migs_ba_host_spec_range.md | 40 - mixs6/migs_ba_investigation_type.md | 40 - mixs6/migs_ba_isol_growth_condt.md | 40 - mixs6/migs_ba_lat_lon.md | 23 - mixs6/migs_ba_lib_layout.md | 40 - mixs6/migs_ba_lib_reads_seqd.md | 40 - mixs6/migs_ba_lib_screen.md | 40 - mixs6/migs_ba_lib_size.md | 40 - mixs6/migs_ba_lib_vector.md | 40 - mixs6/migs_ba_nucl_acid_amp.md | 47 - mixs6/migs_ba_nucl_acid_ext.md | 47 - mixs6/migs_ba_num_replicons.md | 40 - mixs6/migs_ba_number_contig.md | 40 - mixs6/migs_ba_pathogenicity.md | 47 - mixs6/migs_ba_project_name.md | 40 - mixs6/migs_ba_ref_biomaterial.md | 40 - mixs6/migs_ba_ref_db.md | 40 - mixs6/migs_ba_rel_to_oxygen.md | 47 - mixs6/migs_ba_samp_collect_device.md | 40 - mixs6/migs_ba_samp_mat_process.md | 40 - mixs6/migs_ba_samp_size.md | 40 - mixs6/migs_ba_sample_name.md | 40 - mixs6/migs_ba_seq_meth.md | 40 - mixs6/migs_ba_sim_search_meth.md | 40 - mixs6/migs_ba_sop.md | 47 - mixs6/migs_ba_source_mat_id.md | 47 - mixs6/migs_ba_specific_host.md | 47 - mixs6/migs_ba_submitted_to_insdc.md | 40 - mixs6/migs_ba_subspecf_gen_lin.md | 47 - mixs6/migs_ba_tax_class.md | 40 - mixs6/migs_ba_tax_ident.md | 47 - mixs6/migs_ba_trophic_level.md | 47 - mixs6/migs_ba_url.md | 47 - mixs6/migs_eu_adapters.md | 47 - mixs6/migs_eu_annot.md | 47 - mixs6/migs_eu_assembly_name.md | 47 - mixs6/migs_eu_assembly_qual.md | 40 - mixs6/migs_eu_assembly_software.md | 40 - mixs6/migs_eu_biotic_relationship.md | 40 - mixs6/migs_eu_collection_date.md | 23 - mixs6/migs_eu_compl_score.md | 40 - mixs6/migs_eu_compl_software.md | 40 - mixs6/migs_eu_env_broad_scale.md | 23 - mixs6/migs_eu_env_local_scale.md | 23 - mixs6/migs_eu_env_medium.md | 23 - mixs6/migs_eu_env_package.md | 47 - mixs6/migs_eu_estimated_size.md | 40 - mixs6/migs_eu_experimental_factor.md | 40 - mixs6/migs_eu_extrachrom_elements.md | 40 - mixs6/migs_eu_feat_pred.md | 40 - mixs6/migs_eu_geo_loc_name.md | 23 - mixs6/migs_eu_health_disease_stat.md | 40 - mixs6/migs_eu_host_spec_range.md | 40 - mixs6/migs_eu_investigation_type.md | 40 - mixs6/migs_eu_isol_growth_condt.md | 40 - mixs6/migs_eu_lat_lon.md | 23 - mixs6/migs_eu_lib_layout.md | 40 - mixs6/migs_eu_lib_reads_seqd.md | 40 - mixs6/migs_eu_lib_screen.md | 40 - mixs6/migs_eu_lib_size.md | 40 - mixs6/migs_eu_lib_vector.md | 40 - mixs6/migs_eu_nucl_acid_amp.md | 47 - mixs6/migs_eu_nucl_acid_ext.md | 47 - mixs6/migs_eu_num_replicons.md | 40 - mixs6/migs_eu_number_contig.md | 40 - mixs6/migs_eu_pathogenicity.md | 47 - mixs6/migs_eu_ploidy.md | 40 - mixs6/migs_eu_project_name.md | 40 - mixs6/migs_eu_propagation.md | 47 - mixs6/migs_eu_ref_biomaterial.md | 40 - mixs6/migs_eu_ref_db.md | 40 - mixs6/migs_eu_samp_collect_device.md | 40 - mixs6/migs_eu_samp_mat_process.md | 40 - mixs6/migs_eu_samp_size.md | 40 - mixs6/migs_eu_sample_name.md | 40 - mixs6/migs_eu_seq_meth.md | 40 - mixs6/migs_eu_sim_search_meth.md | 40 - mixs6/migs_eu_sop.md | 47 - mixs6/migs_eu_source_mat_id.md | 47 - mixs6/migs_eu_specific_host.md | 40 - mixs6/migs_eu_submitted_to_insdc.md | 40 - mixs6/migs_eu_subspecf_gen_lin.md | 47 - mixs6/migs_eu_tax_class.md | 40 - mixs6/migs_eu_tax_ident.md | 47 - mixs6/migs_eu_trophic_level.md | 47 - mixs6/migs_eu_url.md | 47 - mixs6/migs_org_collection_date.md | 2 +- mixs6/migs_org_sample_name.md | 2 +- mixs6/migs_pl_adapters.md | 47 - mixs6/migs_pl_annot.md | 47 - mixs6/migs_pl_assembly_name.md | 47 - mixs6/migs_pl_assembly_qual.md | 40 - mixs6/migs_pl_assembly_software.md | 40 - mixs6/migs_pl_collection_date.md | 23 - mixs6/migs_pl_compl_score.md | 40 - mixs6/migs_pl_compl_software.md | 40 - mixs6/migs_pl_encoded_traits.md | 47 - mixs6/migs_pl_env_broad_scale.md | 23 - mixs6/migs_pl_env_local_scale.md | 23 - mixs6/migs_pl_env_medium.md | 23 - mixs6/migs_pl_env_package.md | 47 - mixs6/migs_pl_estimated_size.md | 40 - mixs6/migs_pl_experimental_factor.md | 40 - mixs6/migs_pl_feat_pred.md | 40 - mixs6/migs_pl_geo_loc_name.md | 23 - mixs6/migs_pl_host_spec_range.md | 40 - mixs6/migs_pl_investigation_type.md | 40 - mixs6/migs_pl_isol_growth_condt.md | 40 - mixs6/migs_pl_lat_lon.md | 23 - mixs6/migs_pl_lib_layout.md | 40 - mixs6/migs_pl_lib_reads_seqd.md | 40 - mixs6/migs_pl_lib_screen.md | 40 - mixs6/migs_pl_lib_size.md | 40 - mixs6/migs_pl_lib_vector.md | 40 - mixs6/migs_pl_nucl_acid_amp.md | 47 - mixs6/migs_pl_nucl_acid_ext.md | 47 - mixs6/migs_pl_number_contig.md | 40 - mixs6/migs_pl_project_name.md | 40 - mixs6/migs_pl_propagation.md | 40 - mixs6/migs_pl_ref_biomaterial.md | 40 - mixs6/migs_pl_ref_db.md | 40 - mixs6/migs_pl_samp_collect_device.md | 40 - mixs6/migs_pl_samp_mat_process.md | 40 - mixs6/migs_pl_samp_size.md | 40 - mixs6/migs_pl_sample_name.md | 40 - mixs6/migs_pl_seq_meth.md | 40 - mixs6/migs_pl_sim_search_meth.md | 40 - mixs6/migs_pl_sop.md | 47 - mixs6/migs_pl_source_mat_id.md | 47 - mixs6/migs_pl_specific_host.md | 47 - mixs6/migs_pl_submitted_to_insdc.md | 40 - mixs6/migs_pl_subspecf_gen_lin.md | 47 - mixs6/migs_pl_tax_class.md | 40 - mixs6/migs_pl_tax_ident.md | 47 - mixs6/migs_pl_url.md | 47 - mixs6/migs_vi_adapters.md | 47 - mixs6/migs_vi_annot.md | 47 - mixs6/migs_vi_assembly_name.md | 47 - mixs6/migs_vi_assembly_qual.md | 40 - mixs6/migs_vi_assembly_software.md | 40 - mixs6/migs_vi_biotic_relationship.md | 40 - mixs6/migs_vi_collection_date.md | 23 - mixs6/migs_vi_compl_score.md | 40 - mixs6/migs_vi_compl_software.md | 40 - mixs6/migs_vi_encoded_traits.md | 47 - mixs6/migs_vi_env_broad_scale.md | 23 - mixs6/migs_vi_env_local_scale.md | 23 - mixs6/migs_vi_env_medium.md | 23 - mixs6/migs_vi_env_package.md | 47 - mixs6/migs_vi_estimated_size.md | 40 - mixs6/migs_vi_experimental_factor.md | 40 - mixs6/migs_vi_feat_pred.md | 40 - mixs6/migs_vi_geo_loc_name.md | 23 - mixs6/migs_vi_health_disease_stat.md | 47 - mixs6/migs_vi_host_spec_range.md | 47 - mixs6/migs_vi_investigation_type.md | 40 - mixs6/migs_vi_isol_growth_condt.md | 40 - mixs6/migs_vi_lat_lon.md | 23 - mixs6/migs_vi_lib_layout.md | 40 - mixs6/migs_vi_lib_reads_seqd.md | 40 - mixs6/migs_vi_lib_screen.md | 40 - mixs6/migs_vi_lib_size.md | 40 - mixs6/migs_vi_lib_vector.md | 40 - mixs6/migs_vi_nucl_acid_amp.md | 47 - mixs6/migs_vi_nucl_acid_ext.md | 47 - mixs6/migs_vi_num_replicons.md | 47 - mixs6/migs_vi_number_contig.md | 40 - mixs6/migs_vi_pathogenicity.md | 47 - mixs6/migs_vi_project_name.md | 40 - mixs6/migs_vi_propagation.md | 40 - mixs6/migs_vi_ref_biomaterial.md | 40 - mixs6/migs_vi_ref_db.md | 40 - mixs6/migs_vi_samp_collect_device.md | 40 - mixs6/migs_vi_samp_mat_process.md | 40 - mixs6/migs_vi_samp_size.md | 40 - mixs6/migs_vi_sample_name.md | 40 - mixs6/migs_vi_seq_meth.md | 40 - mixs6/migs_vi_sim_search_meth.md | 40 - mixs6/migs_vi_sop.md | 47 - mixs6/migs_vi_source_mat_id.md | 47 - mixs6/migs_vi_specific_host.md | 47 - mixs6/migs_vi_submitted_to_insdc.md | 40 - mixs6/migs_vi_subspecf_gen_lin.md | 47 - mixs6/migs_vi_tax_class.md | 40 - mixs6/migs_vi_tax_ident.md | 47 - mixs6/migs_vi_url.md | 47 - mixs6/migs_vi_virus_enrich_appr.md | 47 - mixs6/mimag_collection_date.md | 2 +- mixs6/mimag_sample_name.md | 2 +- mixs6/mimarks_c_biotic_relationship.md | 47 - mixs6/mimarks_c_chimera_check.md | 47 - mixs6/mimarks_c_collection_date.md | 23 - mixs6/mimarks_c_env_broad_scale.md | 23 - mixs6/mimarks_c_env_local_scale.md | 23 - mixs6/mimarks_c_env_medium.md | 23 - mixs6/mimarks_c_env_package.md | 47 - mixs6/mimarks_c_experimental_factor.md | 40 - mixs6/mimarks_c_extrachrom_elements.md | 40 - mixs6/mimarks_c_geo_loc_name.md | 23 - mixs6/mimarks_c_investigation_type.md | 40 - mixs6/mimarks_c_isol_growth_condt.md | 40 - mixs6/mimarks_c_lat_lon.md | 23 - mixs6/mimarks_c_nucl_acid_amp.md | 47 - mixs6/mimarks_c_nucl_acid_ext.md | 47 - mixs6/mimarks_c_pcr_cond.md | 47 - mixs6/mimarks_c_pcr_primers.md | 47 - mixs6/mimarks_c_project_name.md | 40 - mixs6/mimarks_c_rel_to_oxygen.md | 47 - mixs6/mimarks_c_samp_collect_device.md | 40 - mixs6/mimarks_c_samp_mat_process.md | 47 - mixs6/mimarks_c_samp_size.md | 40 - mixs6/mimarks_c_sample_name.md | 40 - mixs6/mimarks_c_seq_meth.md | 40 - mixs6/mimarks_c_seq_quality_check.md | 47 - mixs6/mimarks_c_sop.md | 47 - mixs6/mimarks_c_source_mat_id.md | 47 - mixs6/mimarks_c_submitted_to_insdc.md | 40 - mixs6/mimarks_c_subspecf_gen_lin.md | 47 - mixs6/mimarks_c_target_gene.md | 40 - mixs6/mimarks_c_target_subfragment.md | 47 - mixs6/mimarks_c_trophic_level.md | 47 - mixs6/mimarks_c_url.md | 47 - mixs6/mimarks_s_adapters.md | 47 - mixs6/mimarks_s_assembly_software.md | 47 - mixs6/mimarks_s_chimera_check.md | 47 - mixs6/mimarks_s_collection_date.md | 23 - mixs6/mimarks_s_env_broad_scale.md | 23 - mixs6/mimarks_s_env_local_scale.md | 23 - mixs6/mimarks_s_env_medium.md | 23 - mixs6/mimarks_s_env_package.md | 47 - mixs6/mimarks_s_experimental_factor.md | 47 - mixs6/mimarks_s_geo_loc_name.md | 23 - mixs6/mimarks_s_investigation_type.md | 40 - mixs6/mimarks_s_lat_lon.md | 23 - mixs6/mimarks_s_lib_layout.md | 47 - mixs6/mimarks_s_lib_reads_seqd.md | 47 - mixs6/mimarks_s_lib_screen.md | 47 - mixs6/mimarks_s_lib_size.md | 47 - mixs6/mimarks_s_lib_vector.md | 47 - mixs6/mimarks_s_mid.md | 47 - mixs6/mimarks_s_nucl_acid_amp.md | 47 - mixs6/mimarks_s_nucl_acid_ext.md | 47 - mixs6/mimarks_s_pcr_cond.md | 47 - mixs6/mimarks_s_pcr_primers.md | 47 - mixs6/mimarks_s_project_name.md | 40 - mixs6/mimarks_s_rel_to_oxygen.md | 40 - mixs6/mimarks_s_samp_collect_device.md | 47 - mixs6/mimarks_s_samp_mat_process.md | 47 - mixs6/mimarks_s_samp_size.md | 47 - mixs6/mimarks_s_sample_name.md | 40 - mixs6/mimarks_s_seq_meth.md | 40 - mixs6/mimarks_s_seq_quality_check.md | 47 - mixs6/mimarks_s_size_frac.md | 40 - mixs6/mimarks_s_sop.md | 47 - mixs6/mimarks_s_source_mat_id.md | 47 - mixs6/mimarks_s_submitted_to_insdc.md | 40 - mixs6/mimarks_s_target_gene.md | 40 - mixs6/mimarks_s_target_subfragment.md | 47 - mixs6/mimarks_s_url.md | 47 - mixs6/mineral_nutr_regm.md | 2 +- mixs6/misag_collection_date.md | 2 +- mixs6/misag_sample_name.md | 2 +- mixs6/misc_param.md | 3 +- mixs6/miuvig_collection_date.md | 2 +- mixs6/miuvig_sample_name.md | 2 +- mixs6/n_alkanes.md | 2 +- mixs6/nitrate.md | 2 +- mixs6/nitrite.md | 2 +- mixs6/nitro.md | 2 +- mixs6/non_mineral_nutr_regm.md | 2 +- mixs6/nose_mouth_teeth_throat_disord.md | 3 +- mixs6/nose_throat_disord.md | 3 +- mixs6/nucl_acid_amp.md | 1 - mixs6/nucl_acid_ext.md | 1 - mixs6/nucleic_acid_sequence_source_field.md | 3 +- mixs6/num_replicons.md | 1 - mixs6/number_contig.md | 1 - mixs6/number_pets.md | 3 +- mixs6/number_plants.md | 3 +- mixs6/number_resident.md | 3 +- mixs6/occup_density_samp.md | 3 +- mixs6/occup_document.md | 3 +- mixs6/occup_samp.md | 3 +- mixs6/org_carb.md | 2 +- mixs6/org_matter.md | 2 +- mixs6/org_nitro.md | 2 +- mixs6/org_particles.md | 2 +- mixs6/organism_count.md | 2 +- mixs6/organism_count_qpcr_info.md | 2 +- mixs6/owc_tvdss.md | 2 +- mixs6/oxy_stat_samp.md | 3 +- mixs6/oxygen.md | 2 +- mixs6/part_org_carb.md | 2 +- mixs6/part_org_nitro.md | 2 +- mixs6/particle_class.md | 2 +- mixs6/pathogenicity.md | 1 - mixs6/pcr_cond.md | 1 - mixs6/pcr_primers.md | 1 - mixs6/permeability.md | 2 +- mixs6/perturbation.md | 3 +- mixs6/pesticide_regm.md | 2 +- mixs6/pet_farm_animal.md | 3 +- mixs6/petroleum_hydrocarb.md | 2 +- mixs6/ph.md | 3 +- mixs6/ph_meth.md | 3 +- mixs6/ph_regm.md | 3 +- mixs6/phaeopigments.md | 2 +- mixs6/phosphate.md | 2 +- mixs6/phosplipid_fatt_acid.md | 2 +- mixs6/photon_flux.md | 2 +- mixs6/plant_growth_med.md | 3 +- mixs6/plant_product.md | 3 +- mixs6/plant_sex.md | 3 +- mixs6/plant_struc.md | 3 +- mixs6/ploidy.md | 1 - mixs6/pollutants.md | 2 +- mixs6/pool_dna_extracts.md | 3 +- mixs6/porosity.md | 2 +- mixs6/potassium.md | 2 +- mixs6/pour_point.md | 2 +- mixs6/pre_treatment.md | 3 +- mixs6/pred_genome_struc.md | 1 - mixs6/pred_genome_type.md | 1 - mixs6/pregnancy.md | 5 +- mixs6/pres_animal.md | 3 +- mixs6/pressure.md | 2 +- mixs6/previous_land_use.md | 3 +- mixs6/previous_land_use_meth.md | 3 +- mixs6/primary_prod.md | 2 +- mixs6/primary_treatment.md | 3 +- mixs6/prod_rate.md | 2 +- mixs6/prod_start_date.md | 5 +- mixs6/profile_position.md | 3 +- mixs6/project_name.md | 5 +- mixs6/propagation.md | 1 - mixs6/pulmonary_disord.md | 3 +- mixs6/quad_pos.md | 3 +- mixs6/radiation_regm.md | 2 +- mixs6/rainfall_regm.md | 2 +- mixs6/reactor_type.md | 3 +- mixs6/reassembly_bin.md | 1 - mixs6/redox_potential.md | 2 +- mixs6/ref_biomaterial.md | 1 - mixs6/ref_db.md | 1 - mixs6/rel_air_humidity.md | 2 +- mixs6/rel_humidity_out.md | 2 +- mixs6/rel_samp_loc.md | 3 +- mixs6/rel_to_oxygen.md | 1 - mixs6/reservoir.md | 3 +- mixs6/resins_pc.md | 2 +- mixs6/resp_part_matter.md | 2 +- mixs6/room_air_exch_rate.md | 2 +- mixs6/room_architec_element.md | 3 +- mixs6/room_condt.md | 3 +- mixs6/room_connected.md | 3 +- mixs6/room_count.md | 3 +- mixs6/room_dim.md | 2 +- mixs6/room_door_dist.md | 2 +- mixs6/room_door_share.md | 3 +- mixs6/room_hallway.md | 3 +- mixs6/room_loc.md | 3 +- mixs6/room_moist_damage_hist.md | 3 +- mixs6/room_net_area.md | 2 +- mixs6/room_occup.md | 3 +- mixs6/room_samp_pos.md | 3 +- mixs6/room_type.md | 3 +- mixs6/room_vol.md | 2 +- mixs6/room_wall_share.md | 3 +- mixs6/room_window_count.md | 3 +- mixs6/root_cond.md | 3 +- mixs6/root_med_carbon.md | 2 +- mixs6/root_med_macronutr.md | 2 +- mixs6/root_med_micronutr.md | 2 +- mixs6/root_med_ph.md | 3 +- mixs6/root_med_regl.md | 2 +- mixs6/root_med_solid.md | 3 +- mixs6/root_med_suppl.md | 2 +- mixs6/salinity.md | 2 +- mixs6/salinity_meth.md | 3 +- mixs6/salt_regm.md | 2 +- mixs6/samp_capt_status.md | 3 +- mixs6/samp_collect_device.md | 45 - mixs6/samp_collection_point.md | 3 +- mixs6/samp_dis_stage.md | 7 +- mixs6/samp_floor.md | 3 +- mixs6/samp_loc_corr_rate.md | 2 +- mixs6/samp_mat_process.md | 5 +- mixs6/samp_md.md | 2 +- mixs6/samp_preserv.md | 2 +- mixs6/samp_room_id.md | 3 +- mixs6/samp_salinity.md | 2 +- mixs6/samp_sort_meth.md | 3 +- mixs6/samp_store_dur.md | 3 +- mixs6/samp_store_loc.md | 3 +- mixs6/samp_store_temp.md | 2 +- mixs6/samp_subtype.md | 3 +- mixs6/samp_time_out.md | 2 +- mixs6/samp_transport_cond.md | 2 +- mixs6/samp_tvdss.md | 2 +- mixs6/samp_type.md | 3 +- mixs6/samp_vol_we_dna_ext.md | 2 +- mixs6/samp_weather.md | 3 +- mixs6/samp_well_name.md | 3 +- mixs6/sample_collect_device.md | 44 + mixs6/sample_collect_method.md | 43 + mixs6/sample_name.md | 9 +- mixs6/saturates_pc.md | 2 +- mixs6/season.md | 3 +- mixs6/season_environment.md | 3 +- mixs6/season_precpt.md | 2 +- mixs6/season_temp.md | 2 +- mixs6/season_use.md | 3 +- mixs6/secondary_treatment.md | 3 +- mixs6/sediment_type.md | 3 +- mixs6/seq_meth.md | 1 - mixs6/seq_quality_check.md | 1 - mixs6/sequencing_field.md | 1 - mixs6/sewage_type.md | 3 +- mixs6/sexual_act.md | 3 +- mixs6/shading_device_cond.md | 3 +- mixs6/shading_device_loc.md | 3 +- mixs6/shading_device_mat.md | 3 +- mixs6/shading_device_type.md | 3 +- mixs6/shading_device_water_mold.md | 3 +- mixs6/sieving.md | 3 +- mixs6/silicate.md | 2 +- mixs6/sim_search_meth.md | 1 - mixs6/single_cell_lysis_appr.md | 1 - mixs6/single_cell_lysis_prot.md | 1 - mixs6/size_frac.md | 1 - mixs6/size_frac_low.md | 2 +- mixs6/size_frac_up.md | 2 +- mixs6/slope_aspect.md | 2 +- mixs6/slope_gradient.md | 2 +- mixs6/sludge_retent_time.md | 2 +- mixs6/smoker.md | 3 +- mixs6/sodium.md | 2 +- mixs6/soil_type.md | 3 +- mixs6/soil_type_meth.md | 3 +- mixs6/solar_irradiance.md | 2 +- mixs6/soluble_inorg_mat.md | 2 +- mixs6/soluble_org_mat.md | 2 +- mixs6/soluble_react_phosp.md | 2 +- mixs6/sop.md | 1 - mixs6/sort_tech.md | 1 - mixs6/source_mat_id.md | 1 - mixs6/source_uvig.md | 1 - mixs6/space_typ_state.md | 3 +- mixs6/special_diet.md | 3 +- mixs6/specific.md | 3 +- mixs6/specific_host.md | 1 - mixs6/specific_humidity.md | 2 +- mixs6/sr_dep_env.md | 3 +- mixs6/sr_geol_age.md | 3 +- mixs6/sr_kerog_type.md | 3 +- mixs6/sr_lithology.md | 3 +- mixs6/standing_water_regm.md | 3 +- mixs6/store_cond.md | 3 +- mixs6/study_complt_stat.md | 3 +- mixs6/submitted_to_insdc.md | 1 - mixs6/subspecf_gen_lin.md | 1 - mixs6/substructure_type.md | 3 +- mixs6/sulfate.md | 2 +- mixs6/sulfate_fw.md | 2 +- mixs6/sulfide.md | 2 +- mixs6/surf_air_cont.md | 3 +- mixs6/surf_humidity.md | 2 +- mixs6/surf_material.md | 3 +- mixs6/surf_moisture.md | 2 +- mixs6/surf_moisture_ph.md | 3 +- mixs6/surf_temp.md | 2 +- mixs6/suspend_part_matter.md | 2 +- mixs6/suspend_solids.md | 2 +- mixs6/tan.md | 2 +- mixs6/target_gene.md | 1 - mixs6/target_subfragment.md | 1 - mixs6/tax_class.md | 1 - mixs6/tax_ident.md | 1 - mixs6/temp.md | 2 +- mixs6/temp_out.md | 2 +- mixs6/tertiary_treatment.md | 3 +- mixs6/texture.md | 3 +- mixs6/texture_meth.md | 3 +- mixs6/tidal_stage.md | 3 +- mixs6/tillage.md | 3 +- mixs6/time_last_toothbrush.md | 3 +- mixs6/time_since_last_wash.md | 3 +- mixs6/tiss_cult_growth_med.md | 3 +- mixs6/toluene.md | 2 +- mixs6/tot_carb.md | 2 +- mixs6/tot_depth_water_col.md | 2 +- mixs6/tot_diss_nitro.md | 2 +- mixs6/tot_inorg_nitro.md | 2 +- mixs6/tot_iron.md | 2 +- mixs6/tot_nitro.md | 2 +- mixs6/tot_nitro_content.md | 2 +- mixs6/tot_nitro_content_meth.md | 3 +- mixs6/tot_org_c_meth.md | 3 +- mixs6/tot_org_carb.md | 2 +- mixs6/tot_part_carb.md | 2 +- mixs6/tot_phosp.md | 2 +- mixs6/tot_phosphate.md | 2 +- mixs6/tot_sulfur.md | 2 +- mixs6/train_line.md | 3 +- mixs6/train_stat_loc.md | 3 +- mixs6/train_stop_loc.md | 3 +- mixs6/travel_out_six_month.md | 3 +- mixs6/trna_ext_software.md | 1 - mixs6/trnas.md | 1 - mixs6/trophic_level.md | 1 - mixs6/turbidity.md | 2 +- mixs6/tvdss_of_hcr_pressure.md | 4 +- mixs6/tvdss_of_hcr_temp.md | 4 +- mixs6/twin_sibling.md | 3 +- mixs6/typ_occup_density.md | 3 +- mixs6/urine_collect_meth.md | 3 +- mixs6/url.md | 1 - mixs6/urogenit_disord.md | 3 +- mixs6/urogenit_tract_disor.md | 3 +- mixs6/ventilation_rate.md 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mixs6/wga_amp_appr.md | 1 - mixs6/wga_amp_kit.md | 1 - mixs6/win.md | 3 +- mixs6/wind_direction.md | 3 +- mixs6/wind_speed.md | 2 +- mixs6/window_cond.md | 3 +- mixs6/window_cover.md | 3 +- mixs6/window_horiz_pos.md | 3 +- mixs6/window_loc.md | 3 +- mixs6/window_mat.md | 3 +- mixs6/window_open_freq.md | 3 +- mixs6/window_size.md | 2 +- mixs6/window_status.md | 3 +- mixs6/window_type.md | 3 +- mixs6/window_vert_pos.md | 3 +- mixs6/window_water_mold.md | 3 +- mixs6/x_16s_recover.md | 1 - mixs6/x_16s_recover_software.md | 36 - mixs6/xylene.md | 2 +- src/schema/mixs.yaml | 15673 +--------------- 1393 files changed, 7303 insertions(+), 85535 deletions(-) create mode 100644 mixs6/AddRecovMethodEnum.md delete mode 100644 mixs6/AirMigsBa.md delete mode 100644 mixs6/AirMigsEu.md delete mode 100644 mixs6/AirMigsPl.md delete mode 100644 mixs6/AirMigsVi.md delete mode 100644 mixs6/AirMimarksC.md delete mode 100644 mixs6/AirMimarksS.md create mode 100644 mixs6/ArchStrucEnum.md create mode 100644 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delete mode 100644 mixs6/mimarks_s_url.md delete mode 100644 mixs6/samp_collect_device.md create mode 100644 mixs6/sample_collect_device.md create mode 100644 mixs6/sample_collect_method.md delete mode 100644 mixs6/x_16s_recover_software.md diff --git a/mixs6/AddRecovMethodEnum.md b/mixs6/AddRecovMethodEnum.md new file mode 100644 index 00000000..f61f39d8 --- /dev/null +++ b/mixs6/AddRecovMethodEnum.md @@ -0,0 +1,19 @@ + +# Enum: add_recov_method_enum + + + + +URI: [mixs.vocab:add_recov_method_enum](https://w3id.org/mixs/vocab/add_recov_method_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Air.md b/mixs6/Air.md index 6e6c9e3d..60d4738f 100644 --- a/mixs6/Air.md +++ b/mixs6/Air.md @@ -7,7 +7,7 @@ air URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG],[AirMISAG],[AirMIMARKSSurvey],[AirMIMARKSSpecimen],[AirMIMAG],[AirMIGSVirus],[AirMIGSPlant],[AirMIGSOrg],[AirMIGSEukaryote],[AirMIGSBacteria],[AirME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -53,10 +53,10 @@ URI: [mixs.vocab:Air](https://w3id.org/mixs/vocab/Air) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT diff --git a/mixs6/AirMIGSBacteria.md b/mixs6/AirMIGSBacteria.md index 67ca36bd..1376f6ab 100644 --- a/mixs6/AirMIGSBacteria.md +++ b/mixs6/AirMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:AirMIGSBacteria](https://w3id.org/mixs/vocab/AirMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSBacteria],[Air]^-[AirMIGSBacteria],[Air],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Air]^-[AirMIGSBacteria],[Air],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIGSBacteria](https://w3id.org/mixs/vocab/AirMIGSBacteria) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIGSBacteria](https://w3id.org/mixs/vocab/AirMIGSBacteria) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -321,22 +321,27 @@ URI: [mixs.vocab:AirMIGSBacteria](https://w3id.org/mixs/vocab/AirMIGSBacteria) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/AirMIGSEukaryote.md b/mixs6/AirMIGSEukaryote.md index 1b49ba89..9c2969ee 100644 --- a/mixs6/AirMIGSEukaryote.md +++ b/mixs6/AirMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Air]^-[AirMIGSEukaryote],[Air],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Air]^-[AirMIGSEukaryote],[Air],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -321,22 +321,27 @@ URI: [mixs.vocab:AirMIGSEukaryote](https://w3id.org/mixs/vocab/AirMIGSEukaryote) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/AirMIGSPlant.md b/mixs6/AirMIGSPlant.md index 94723967..20fdac0d 100644 --- a/mixs6/AirMIGSPlant.md +++ b/mixs6/AirMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSPlant],[Air]^-[AirMIGSPlant],[Air],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Air]^-[AirMIGSPlant],[Air],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -296,22 +296,27 @@ URI: [mixs.vocab:AirMIGSPlant](https://w3id.org/mixs/vocab/AirMIGSPlant) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/AirMIGSVirus.md b/mixs6/AirMIGSVirus.md index 50281d25..0a1015d6 100644 --- a/mixs6/AirMIGSVirus.md +++ b/mixs6/AirMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSVirus],[Air]^-[AirMIGSVirus],[Air],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Air]^-[AirMIGSVirus],[Air],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -316,22 +316,27 @@ URI: [mixs.vocab:AirMIGSVirus](https://w3id.org/mixs/vocab/AirMIGSVirus) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/AirMIMARKSSpecimen.md b/mixs6/AirMIMARKSSpecimen.md index a475d061..de955396 100644 --- a/mixs6/AirMIMARKSSpecimen.md +++ b/mixs6/AirMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Air]^-[AirMIMARKSSpecimen],[Air],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Air]^-[AirMIMARKSSpecimen],[Air],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpeci ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpeci * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -251,22 +251,27 @@ URI: [mixs.vocab:AirMIMARKSSpecimen](https://w3id.org/mixs/vocab/AirMIMARKSSpeci ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/AirMIMARKSSurvey.md b/mixs6/AirMIMARKSSurvey.md index 7a804a29..a8a16564 100644 --- a/mixs6/AirMIMARKSSurvey.md +++ b/mixs6/AirMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Air]^-[AirMIMARKSSurvey],[Air],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Air]^-[AirMIMARKSSurvey],[Air],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -226,22 +226,27 @@ URI: [mixs.vocab:AirMIMARKSSurvey](https://w3id.org/mixs/vocab/AirMIMARKSSurvey) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md index 4146ef90..5e56040d 100644 --- a/mixs6/AirMe.md +++ b/mixs6/AirMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package a URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[ME],[Air]^-[AirME],[Air],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Air]^-[AirME],[Air],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -271,22 +271,27 @@ URI: [mixs.vocab:AirME](https://w3id.org/mixs/vocab/AirME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/AirMigsBa.md b/mixs6/AirMigsBa.md deleted file mode 100644 index 98553550..00000000 --- a/mixs6/AirMigsBa.md +++ /dev/null @@ -1,395 +0,0 @@ - -# Class: AirMigsBa - - -Combinatorial checklist for air with migs_ba - -URI: [mixs.vocab:AirMigsBa](https://w3id.org/mixs/vocab/AirMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[AirMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsBa],[Air]^-[AirMigsBa],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMigsEu.md b/mixs6/AirMigsEu.md deleted file mode 100644 index 3d02b098..00000000 --- a/mixs6/AirMigsEu.md +++ /dev/null @@ -1,395 +0,0 @@ - -# Class: AirMigsEu - - -Combinatorial checklist for air with migs_eu - -URI: [mixs.vocab:AirMigsEu](https://w3id.org/mixs/vocab/AirMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[AirMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsEu],[Air]^-[AirMigsEu],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md index 40a8324c..dfd17cd8 100644 --- a/mixs6/AirMigsOrg.md +++ b/mixs6/AirMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIGSOrg],[Air]^-[AirMIGSOrg],[Air],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Air]^-[AirMIGSOrg],[Air],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -286,22 +286,27 @@ URI: [mixs.vocab:AirMIGSOrg](https://w3id.org/mixs/vocab/AirMIGSOrg) ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/AirMigsPl.md b/mixs6/AirMigsPl.md deleted file mode 100644 index 61101aab..00000000 --- a/mixs6/AirMigsPl.md +++ /dev/null @@ -1,365 +0,0 @@ - -# Class: AirMigsPl - - -Combinatorial checklist for air with migs_pl - -URI: [mixs.vocab:AirMigsPl](https://w3id.org/mixs/vocab/AirMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[AirMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsPl],[Air]^-[AirMigsPl],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMigsVi.md b/mixs6/AirMigsVi.md deleted file mode 100644 index d2e69c97..00000000 --- a/mixs6/AirMigsVi.md +++ /dev/null @@ -1,390 +0,0 @@ - -# Class: AirMigsVi - - -Combinatorial checklist for air with migs_vi - -URI: [mixs.vocab:AirMigsVi](https://w3id.org/mixs/vocab/AirMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[AirMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MigsVi],[Air]^-[AirMigsVi],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md index 5377572d..fea24eca 100644 --- a/mixs6/AirMimag.md +++ b/mixs6/AirMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIMAG],[Air]^-[AirMIMAG],[Air],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Air]^-[AirMIMAG],[Air],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -326,22 +326,27 @@ URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -403,8 +408,3 @@ URI: [mixs.vocab:AirMIMAG](https://w3id.org/mixs/vocab/AirMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMimarksC.md b/mixs6/AirMimarksC.md deleted file mode 100644 index 29d27af6..00000000 --- a/mixs6/AirMimarksC.md +++ /dev/null @@ -1,295 +0,0 @@ - -# Class: AirMimarksC - - -Combinatorial checklist for air with mimarks_c - -URI: [mixs.vocab:AirMimarksC](https://w3id.org/mixs/vocab/AirMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[AirMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MimarksC],[Air]^-[AirMimarksC],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMimarksS.md b/mixs6/AirMimarksS.md deleted file mode 100644 index 99fe9ddb..00000000 --- a/mixs6/AirMimarksS.md +++ /dev/null @@ -1,315 +0,0 @@ - -# Class: AirMimarksS - - -Combinatorial checklist for air with mimarks_s - -URI: [mixs.vocab:AirMimarksS](https://w3id.org/mixs/vocab/AirMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[AirMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MimarksS],[Air]^-[AirMimarksS],[Air]) - -## Parents - - * is_a: [Air](Air.md) - air - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from air: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [barometric_press](barometric_press.md) OPT - * Description: Force per unit area exerted against a surface by the weight of air above that surface - * range: [QuantityValue](QuantityValue.md) - * Example: 5 millibar None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [carb_monoxide](carb_monoxide.md) OPT - * Description: Carbon monoxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 parts per million None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [humidity](humidity.md) OPT - * Description: Amount of water vapour in the air, at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 gram per cubic meter None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [oxygen](oxygen.md) OPT - * Description: Oxygen (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 600 parts per million None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pollutants](pollutants.md) OPT - * Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant - * range: [String](types/String.md) - * Example: lead;0.15 microgram per cubic meter None - * [resp_part_matter](resp_part_matter.md) OPT - * Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM - * range: [String](types/String.md) - * Example: PM2.5;10 microgram per cubic meter None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [solar_irradiance](solar_irradiance.md) OPT - * Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval - * range: [QuantityValue](QuantityValue.md) - * Example: 1.36 kilowatts per square meter per day None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [ventilation_rate](ventilation_rate.md) OPT - * Description: Ventilation rate of the system in the sampled premises - * range: [QuantityValue](QuantityValue.md) - * Example: 750 cubic meter per minute None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [volatile_org_comp](volatile_org_comp.md) OPT - * Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound - * range: [String](types/String.md) - * Example: formaldehyde;500 nanogram per liter None - * [wind_direction](wind_direction.md) OPT - * Description: Wind direction is the direction from which a wind originates - * range: [String](types/String.md) - * Example: Northwest None - * [wind_speed](wind_speed.md) OPT - * Description: Speed of wind measured at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 21 kilometer per hour None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md index 82dccc08..94dac860 100644 --- a/mixs6/AirMisag.md +++ b/mixs6/AirMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MISAG],[Air]^-[AirMISAG],[Air],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Air]^-[AirMISAG],[Air],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -306,22 +306,27 @@ URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -408,8 +413,3 @@ URI: [mixs.vocab:AirMISAG](https://w3id.org/mixs/vocab/AirMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md index c4a97eb5..54689c55 100644 --- a/mixs6/AirMiuvig.md +++ b/mixs6/AirMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F]uses%20-.->[MIUVIG],[Air]^-[AirMIUVIG],[Air],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[AirMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;perturbation(i):string%20%3F;pollutants(i):string%20%3F;resp_part_matter(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;ventilation_type(i):string%20%3F;volatile_org_comp(i):string%20%3F;wind_direction(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Air]^-[AirMIUVIG],[Air],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) ### Inherited from air: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [barometric_press](barometric_press.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -346,22 +346,27 @@ URI: [mixs.vocab:AirMIUVIG](https://w3id.org/mixs/vocab/AirMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/ArchStrucEnum.md b/mixs6/ArchStrucEnum.md new file mode 100644 index 00000000..06972db2 --- /dev/null +++ b/mixs6/ArchStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: arch_struc_enum + + + + +URI: [mixs.vocab:arch_struc_enum](https://w3id.org/mixs/vocab/arch_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/AssemblyQualEnum.md b/mixs6/AssemblyQualEnum.md new file mode 100644 index 00000000..20827320 --- /dev/null +++ b/mixs6/AssemblyQualEnum.md @@ -0,0 +1,19 @@ + +# Enum: assembly_qual_enum + + + + +URI: [mixs.vocab:assembly_qual_enum](https://w3id.org/mixs/vocab/assembly_qual_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BinParamEnum.md b/mixs6/BinParamEnum.md new file mode 100644 index 00000000..24138fc6 --- /dev/null +++ b/mixs6/BinParamEnum.md @@ -0,0 +1,19 @@ + +# Enum: bin_param_enum + + + + +URI: [mixs.vocab:bin_param_enum](https://w3id.org/mixs/vocab/bin_param_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BinSoftwareEnum.md b/mixs6/BinSoftwareEnum.md new file mode 100644 index 00000000..7eb39477 --- /dev/null +++ b/mixs6/BinSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: bin_software_enum + + + + +URI: [mixs.vocab:bin_software_enum](https://w3id.org/mixs/vocab/bin_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BiolStatEnum.md b/mixs6/BiolStatEnum.md new file mode 100644 index 00000000..115e7238 --- /dev/null +++ b/mixs6/BiolStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: biol_stat_enum + + + + +URI: [mixs.vocab:biol_stat_enum](https://w3id.org/mixs/vocab/biol_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BioticRelationshipEnum.md b/mixs6/BioticRelationshipEnum.md new file mode 100644 index 00000000..d1f48423 --- /dev/null +++ b/mixs6/BioticRelationshipEnum.md @@ -0,0 +1,19 @@ + +# Enum: biotic_relationship_enum + + + + +URI: [mixs.vocab:biotic_relationship_enum](https://w3id.org/mixs/vocab/biotic_relationship_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildDocsEnum.md b/mixs6/BuildDocsEnum.md new file mode 100644 index 00000000..c15bca12 --- /dev/null +++ b/mixs6/BuildDocsEnum.md @@ -0,0 +1,19 @@ + +# Enum: build_docs_enum + + + + +URI: [mixs.vocab:build_docs_enum](https://w3id.org/mixs/vocab/build_docs_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildOccupTypeEnum.md b/mixs6/BuildOccupTypeEnum.md new file mode 100644 index 00000000..e30cc7ef --- /dev/null +++ b/mixs6/BuildOccupTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: build_occup_type_enum + + + + +URI: [mixs.vocab:build_occup_type_enum](https://w3id.org/mixs/vocab/build_occup_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuildingSettingEnum.md b/mixs6/BuildingSettingEnum.md new file mode 100644 index 00000000..05422a26 --- /dev/null +++ b/mixs6/BuildingSettingEnum.md @@ -0,0 +1,19 @@ + +# Enum: building_setting_enum + + + + +URI: [mixs.vocab:building_setting_enum](https://w3id.org/mixs/vocab/building_setting_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/BuiltEnvironment.md b/mixs6/BuiltEnvironment.md index c921c955..a2251412 100644 --- a/mixs6/BuiltEnvironment.md +++ b/mixs6/BuiltEnvironment.md @@ -7,7 +7,7 @@ built environment URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG],[BuiltEnvironmentMISAG],[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironmentMIMAG],[BuiltEnvironmentMIGSVirus],[BuiltEnvironmentMIGSPlant],[BuiltEnvironmentMIGSOrg],[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironmentMIGSBacteria],[BuiltEnvironmentME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -145,7 +145,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -153,10 +153,10 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -361,7 +361,7 @@ URI: [mixs.vocab:BuiltEnvironment](https://w3id.org/mixs/vocab/BuiltEnvironment) * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system diff --git a/mixs6/BuiltEnvironmentMIGSBacteria.md b/mixs6/BuiltEnvironmentMIGSBacteria.md index 70cec7d4..357c7377 100644 --- a/mixs6/BuiltEnvironmentMIGSBacteria.md +++ b/mixs6/BuiltEnvironmentMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSBacteria],[BuiltEnvironment]^-[BuiltEnvironmentMIGSBacteria],[BuiltEnvironment],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSBacteria],[BuiltEnvironment]^-[BuiltEnvironmentMIGSBacteria],[BuiltEnvironment],[MIGSBacteria]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/Built * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/Built * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/Built * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/Built * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -861,22 +861,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/Built ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/BuiltEnvironmentMIGSEukaryote.md b/mixs6/BuiltEnvironmentMIGSEukaryote.md index 9918f0a8..956bd9e5 100644 --- a/mixs6/BuiltEnvironmentMIGSEukaryote.md +++ b/mixs6/BuiltEnvironmentMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSEukaryote],[BuiltEnvironment]^-[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironment],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSEukaryote],[BuiltEnvironment]^-[BuiltEnvironmentMIGSEukaryote],[BuiltEnvironment],[MIGSEukaryote]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/Buil * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/Buil * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/Buil * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/Buil * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -861,22 +861,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/Buil ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/BuiltEnvironmentMIGSPlant.md b/mixs6/BuiltEnvironmentMIGSPlant.md index ee3f07a0..ad15194b 100644 --- a/mixs6/BuiltEnvironmentMIGSPlant.md +++ b/mixs6/BuiltEnvironmentMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSPlant],[BuiltEnvironment]^-[BuiltEnvironmentMIGSPlant],[BuiltEnvironment],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSPlant],[BuiltEnvironment]^-[BuiltEnvironmentMIGSPlant],[BuiltEnvironment],[MIGSPlant]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnv * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnv * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnv * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnv * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -836,22 +836,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/BuiltEnv ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/BuiltEnvironmentMIGSVirus.md b/mixs6/BuiltEnvironmentMIGSVirus.md index 15207d05..c17b8b74 100644 --- a/mixs6/BuiltEnvironmentMIGSVirus.md +++ b/mixs6/BuiltEnvironmentMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSVirus],[BuiltEnvironment]^-[BuiltEnvironmentMIGSVirus],[BuiltEnvironment],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSVirus],[BuiltEnvironment]^-[BuiltEnvironmentMIGSVirus],[BuiltEnvironment],[MIGSVirus]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnv * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnv * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnv * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnv * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -856,22 +856,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/BuiltEnv ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/BuiltEnvironmentMIMARKSSpecimen.md b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md index 13f82861..a007bd0a 100644 --- a/mixs6/BuiltEnvironmentMIMARKSSpecimen.md +++ b/mixs6/BuiltEnvironmentMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironment],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSpecimen],[BuiltEnvironment],[MIMARKSSpecimen]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/Bu * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/Bu * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/Bu * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/Bu * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -791,22 +791,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/Bu ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/BuiltEnvironmentMIMARKSSurvey.md b/mixs6/BuiltEnvironmentMIMARKSSurvey.md index 353f9a7b..1fa95f7e 100644 --- a/mixs6/BuiltEnvironmentMIMARKSSurvey.md +++ b/mixs6/BuiltEnvironmentMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSurvey],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironment],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMARKSSurvey],[BuiltEnvironment]^-[BuiltEnvironmentMIMARKSSurvey],[BuiltEnvironment],[MIMARKSSurvey]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/Buil * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/Buil * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/Buil * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/Buil * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -766,22 +766,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/Buil ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/BuiltEnvironmentMe.md b/mixs6/BuiltEnvironmentMe.md index 527b7d0c..fcdc2c32 100644 --- a/mixs6/BuiltEnvironmentMe.md +++ b/mixs6/BuiltEnvironmentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package b URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[ME],[BuiltEnvironment]^-[BuiltEnvironmentME],[BuiltEnvironment],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[ME],[BuiltEnvironment]^-[BuiltEnvironmentME],[BuiltEnvironment],[ME]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmen * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmen * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -811,22 +811,27 @@ URI: [mixs.vocab:BuiltEnvironmentME](https://w3id.org/mixs/vocab/BuiltEnvironmen ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/BuiltEnvironmentMigsBa.md b/mixs6/BuiltEnvironmentMigsBa.md deleted file mode 100644 index f68d3071..00000000 --- a/mixs6/BuiltEnvironmentMigsBa.md +++ /dev/null @@ -1,935 +0,0 @@ - -# Class: BuiltEnvironmentMigsBa - - -Combinatorial checklist for built environment with migs_ba - -URI: [mixs.vocab:BuiltEnvironmentMigsBa](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[BuiltEnvironmentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsBa],[BuiltEnvironment]^-[BuiltEnvironmentMigsBa],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsEu.md b/mixs6/BuiltEnvironmentMigsEu.md deleted file mode 100644 index 9871f7a7..00000000 --- a/mixs6/BuiltEnvironmentMigsEu.md +++ /dev/null @@ -1,935 +0,0 @@ - -# Class: BuiltEnvironmentMigsEu - - -Combinatorial checklist for built environment with migs_eu - -URI: [mixs.vocab:BuiltEnvironmentMigsEu](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[BuiltEnvironmentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsEu],[BuiltEnvironment]^-[BuiltEnvironmentMigsEu],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsOrg.md b/mixs6/BuiltEnvironmentMigsOrg.md index 99550dc9..9869e4b2 100644 --- a/mixs6/BuiltEnvironmentMigsOrg.md +++ b/mixs6/BuiltEnvironmentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvironmentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSOrg],[BuiltEnvironment]^-[BuiltEnvironmentMIGSOrg],[BuiltEnvironment],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIGSOrg],[BuiltEnvironment]^-[BuiltEnvironmentMIGSOrg],[BuiltEnvironment],[MIGSOrg]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvir * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvir * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -826,22 +826,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/BuiltEnvir ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/BuiltEnvironmentMigsPl.md b/mixs6/BuiltEnvironmentMigsPl.md deleted file mode 100644 index 72596b81..00000000 --- a/mixs6/BuiltEnvironmentMigsPl.md +++ /dev/null @@ -1,905 +0,0 @@ - -# Class: BuiltEnvironmentMigsPl - - -Combinatorial checklist for built environment with migs_pl - -URI: [mixs.vocab:BuiltEnvironmentMigsPl](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[BuiltEnvironmentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsPl],[BuiltEnvironment]^-[BuiltEnvironmentMigsPl],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMigsVi.md b/mixs6/BuiltEnvironmentMigsVi.md deleted file mode 100644 index 106076ee..00000000 --- a/mixs6/BuiltEnvironmentMigsVi.md +++ /dev/null @@ -1,930 +0,0 @@ - -# Class: BuiltEnvironmentMigsVi - - -Combinatorial checklist for built environment with migs_vi - -URI: [mixs.vocab:BuiltEnvironmentMigsVi](https://w3id.org/mixs/vocab/BuiltEnvironmentMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[BuiltEnvironmentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MigsVi],[BuiltEnvironment]^-[BuiltEnvironmentMigsVi],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/BuiltEnvironmentMimag.md b/mixs6/BuiltEnvironmentMimag.md index 3794f823..9f3c29db 100644 --- a/mixs6/BuiltEnvironmentMimag.md +++ b/mixs6/BuiltEnvironmentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMAG],[BuiltEnvironment]^-[BuiltEnvironmentMIMAG],[BuiltEnvironment],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIMAG],[BuiltEnvironment]^-[BuiltEnvironmentMIMAG],[BuiltEnvironment],[MIMAG]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -866,22 +866,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -943,8 +948,3 @@ URI: [mixs.vocab:BuiltEnvironmentMIMAG](https://w3id.org/mixs/vocab/BuiltEnviron * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimarksC.md b/mixs6/BuiltEnvironmentMimarksC.md deleted file mode 100644 index cd61e641..00000000 --- a/mixs6/BuiltEnvironmentMimarksC.md +++ /dev/null @@ -1,835 +0,0 @@ - -# Class: BuiltEnvironmentMimarksC - - -Combinatorial checklist for built environment with mimarks_c - -URI: [mixs.vocab:BuiltEnvironmentMimarksC](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[BuiltEnvironmentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksC],[BuiltEnvironment]^-[BuiltEnvironmentMimarksC],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMimarksS.md b/mixs6/BuiltEnvironmentMimarksS.md deleted file mode 100644 index f4b6a99a..00000000 --- a/mixs6/BuiltEnvironmentMimarksS.md +++ /dev/null @@ -1,855 +0,0 @@ - -# Class: BuiltEnvironmentMimarksS - - -Combinatorial checklist for built environment with mimarks_s - -URI: [mixs.vocab:BuiltEnvironmentMimarksS](https://w3id.org/mixs/vocab/BuiltEnvironmentMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[BuiltEnvironmentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MimarksS],[BuiltEnvironment]^-[BuiltEnvironmentMimarksS],[BuiltEnvironment]) - -## Parents - - * is_a: [BuiltEnvironment](BuiltEnvironment.md) - built environment - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from built environment: - - * [abs_air_humidity](abs_air_humidity.md) OPT - * Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture - * range: [QuantityValue](QuantityValue.md) - * Example: 9 gram per gram None - * [address](address.md) OPT - * Description: The street name and building number where the sampling occurred. - * range: [String](types/String.md) - * Example: None - * [adj_room](adj_room.md) OPT - * Description: List of rooms (room number, room name) immediately adjacent to the sampling room - * range: [String](types/String.md) - * Example: None - * [aero_struc](aero_struc.md) OPT - * Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together - * range: [String](types/String.md) - * Example: plane None - * [air_temp](air_temp.md) OPT - * Description: Temperature of the air at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 20 degree Celsius None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amount_light](amount_light.md) OPT - * Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [arch_struc](arch_struc.md) OPT - * Description: An architectural structure is a human-made, free-standing, immobile outdoor construction - * range: - * Example: shed None - * [avg_dew_point](avg_dew_point.md) OPT - * Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 25.5 degree Celsius None - * [avg_occup](avg_occup.md) OPT - * Description: Daily average occupancy of room - * range: [Double](types/Double.md) - * Example: 2 None - * [avg_temp](avg_temp.md) OPT - * Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [bathroom_count](bathroom_count.md) OPT - * Description: The number of bathrooms in the building - * range: [String](types/String.md) - * Example: 1 None - * [bedroom_count](bedroom_count.md) OPT - * Description: The number of bedrooms in the building - * range: [String](types/String.md) - * Example: 2 None - * [build_docs](build_docs.md) OPT - * Description: The building design, construction and operation documents - * range: - * Example: maintenance plans None - * [build_occup_type](build_occup_type.md) OPT - * Description: The primary function for which a building or discrete part of a building is intended to be used - * range: - * Example: market None - * [building_setting](building_setting.md) OPT - * Description: A location (geography) where a building is set - * range: - * Example: rural None - * [built_struc_age](built_struc_age.md) OPT - * Description: The age of the built structure since construction - * range: [QuantityValue](QuantityValue.md) - * Example: 15 None - * [built_struc_set](built_struc_set.md) OPT - * Description: The characterization of the location of the built structure as high or low human density - * range: [String](types/String.md) - * Example: rural None - * [built_struc_type](built_struc_type.md) OPT - * Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads - * range: [String](types/String.md) - * Example: None - * [carb_dioxide](carb_dioxide.md) OPT - * Description: Carbon dioxide (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 410 parts per million None - * [ceil_area](ceil_area.md) OPT - * Description: The area of the ceiling space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: 25 square meter None - * [ceil_cond](ceil_cond.md) OPT - * Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [ceil_finish_mat](ceil_finish_mat.md) OPT - * Description: The type of material used to finish a ceiling - * range: - * Example: stucco None - * [ceil_struc](ceil_struc.md) OPT - * Description: The construction format of the ceiling - * range: [String](types/String.md) - * Example: concrete None - * [ceil_texture](ceil_texture.md) OPT - * Description: The feel, appearance, or consistency of a ceiling surface - * range: - * Example: popcorn None - * [ceil_thermal_mass](ceil_thermal_mass.md) OPT - * Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [ceil_type](ceil_type.md) OPT - * Description: The type of ceiling according to the ceiling's appearance or construction - * range: - * Example: coffered None - * [ceil_water_mold](ceil_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the ceiling - * range: [String](types/String.md) - * Example: presence of mold visible None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cool_syst_id](cool_syst_id.md) OPT - * Description: The cooling system identifier - * range: [String](types/String.md) - * Example: 12345 None - * [date_last_rain](date_last_rain.md) OPT - * Description: The date of the last time it rained - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dew_point](dew_point.md) OPT - * Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. - * range: [QuantityValue](QuantityValue.md) - * Example: 22 degree Celsius None - * [door_comp_type](door_comp_type.md) OPT - * Description: The composite type of the door - * range: - * Example: revolving None - * [door_cond](door_cond.md) OPT - * Description: The phsical condition of the door - * range: - * Example: new None - * [door_direct](door_direct.md) OPT - * Description: The direction the door opens - * range: - * Example: inward None - * [door_loc](door_loc.md) OPT - * Description: The relative location of the door in the room - * range: - * Example: north None - * [door_mat](door_mat.md) OPT - * Description: The material the door is composed of - * range: - * Example: wood None - * [door_move](door_move.md) OPT - * Description: The type of movement of the door - * range: - * Example: swinging None - * [door_size](door_size.md) OPT - * Description: The size of the door - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 square meter None - * [door_type](door_type.md) OPT - * Description: The type of door material - * range: - * Example: wooden None - * [door_type_metal](door_type_metal.md) OPT - * Description: The type of metal door - * range: - * Example: hollow None - * [door_type_wood](door_type_wood.md) OPT - * Description: The type of wood door - * range: - * Example: battened None - * [door_water_mold](door_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a door - * range: [String](types/String.md) - * Example: presence of mold visible None - * [drawings](drawings.md) OPT - * Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents - * range: - * Example: sketch None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [elevator](elevator.md) OPT - * Description: The number of elevators within the built structure - * range: [String](types/String.md) - * Example: 2 None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [escalator](escalator.md) OPT - * Description: The number of escalators within the built structure - * range: [String](types/String.md) - * Example: 4 None - * [exp_duct](exp_duct.md) OPT - * Description: The amount of exposed ductwork in the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [exp_pipe](exp_pipe.md) OPT - * Description: The number of exposed pipes in the room - * range: [String](types/String.md) - * Example: None - * [ext_door](ext_door.md) OPT - * Description: The number of exterior doors in the built structure - * range: [String](types/String.md) - * Example: None - * [ext_wall_orient](ext_wall_orient.md) OPT - * Description: The orientation of the exterior wall - * range: - * Example: northwest None - * [ext_window_orient](ext_window_orient.md) OPT - * Description: The compass direction the exterior window of the room is facing - * range: - * Example: southwest None - * [filter_type](filter_type.md) OPT - * Description: A device which removes solid particulates or airborne molecular contaminants - * range: - * Example: HEPA None - * [fireplace_type](fireplace_type.md) OPT - * Description: A firebox with chimney - * range: [String](types/String.md) - * Example: wood burning None - * [floor_age](floor_age.md) OPT - * Description: The time period since installment of the carpet or flooring - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_area](floor_area.md) OPT - * Description: The area of the floor space within the room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_cond](floor_cond.md) OPT - * Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: new None - * [floor_count](floor_count.md) OPT - * Description: The number of floors in the building, including basements and mechanical penthouse - * range: [String](types/String.md) - * Example: None - * [floor_finish_mat](floor_finish_mat.md) OPT - * Description: The floor covering type; the finished surface that is walked on - * range: - * Example: carpet None - * [floor_struc](floor_struc.md) OPT - * Description: Refers to the structural elements and subfloor upon which the finish flooring is installed - * range: - * Example: concrete None - * [floor_thermal_mass](floor_thermal_mass.md) OPT - * Description: The ability of the floor to provide inertia against temperature fluctuations - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [floor_water_mold](floor_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew in a room - * range: - * Example: ceiling discoloration None - * [freq_clean](freq_clean.md) OPT - * Description: The number of times the building is cleaned per week - * range: [String](types/String.md) - * Example: None - * [freq_cook](freq_cook.md) OPT - * Description: The number of times a meal is cooked per week - * range: [String](types/String.md) - * Example: None - * [furniture](furniture.md) OPT - * Description: The types of furniture present in the sampled room - * range: - * Example: chair None - * [gender_restroom](gender_restroom.md) OPT - * Description: The gender type of the restroom - * range: [String](types/String.md) - * Example: male None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hall_count](hall_count.md) OPT - * Description: The total count of hallways and cooridors in the built structure - * range: [String](types/String.md) - * Example: None - * [handidness](handidness.md) OPT - * Description: The handidness of the individual sampled - * range: - * Example: right handedness None - * [heat_cool_type](heat_cool_type.md) OPT - * Description: Methods of conditioning or heating a room or building - * range: - * Example: heat pump None - * [heat_deliv_loc](heat_deliv_loc.md) OPT - * Description: The location of heat delivery within the room - * range: - * Example: north None - * [heat_system_deliv_meth](heat_system_deliv_meth.md) OPT - * Description: The method by which the heat is delivered through the system - * range: [String](types/String.md) - * Example: radiant None - * [heat_system_id](heat_system_id.md) OPT - * Description: The heating system identifier - * range: [String](types/String.md) - * Example: None - * [height_carper_fiber](height_carper_fiber.md) OPT - * Description: The average carpet fiber height in the indoor environment - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [indoor_space](indoor_space.md) OPT - * Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used - * range: - * Example: foyer None - * [indoor_surf](indoor_surf.md) OPT - * Description: Type of indoor surface - * range: - * Example: wall None - * [inside_lux](inside_lux.md) OPT - * Description: The recorded value at sampling time (power density) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [int_wall_cond](int_wall_cond.md) OPT - * Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas - * range: - * Example: damaged None - * [last_clean](last_clean.md) OPT - * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) - * Example: 2018-05-11:T14:30Z None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_type](light_type.md) OPT - * Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light - * range: - * Example: desk lamp None - * [max_occup](max_occup.md) OPT - * Description: The maximum amount of people allowed in the indoor environment - * range: [String](types/String.md) - * Example: None - * [mech_struc](mech_struc.md) OPT - * Description: mechanical structure: a moving structure - * range: - * Example: elevator None - * [number_pets](number_pets.md) OPT - * Description: The number of pets residing in the sampled space - * range: [String](types/String.md) - * Example: None - * [number_plants](number_plants.md) OPT - * Description: The number of plant(s) in the sampling space - * range: [String](types/String.md) - * Example: None - * [number_resident](number_resident.md) OPT - * Description: The number of individuals currently occupying in the sampling location - * range: [String](types/String.md) - * Example: None - * [occup_density_samp](occup_density_samp.md) OPT - * Description: Average number of occupants at time of sampling per square footage - * range: [Double](types/Double.md) - * Example: None - * [occup_document](occup_document.md) OPT - * Description: The type of documentation of occupancy - * range: - * Example: estimate None - * [occup_samp](occup_samp.md) OPT - * Description: Number of occupants present at time of sample within the given space - * range: [String](types/String.md) - * Example: 10 None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [pres_animal](pres_animal.md) OPT - * Description: The number and type of animals present in the sampling space - * range: - * Example: cat;5 None - * [quad_pos](quad_pos.md) OPT - * Description: The quadrant position of the sampling room within the building - * range: - * Example: West side None - * [rel_air_humidity](rel_air_humidity.md) OPT - * Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air - * range: [QuantityValue](QuantityValue.md) - * Example: 80% None - * [rel_humidity_out](rel_humidity_out.md) OPT - * Description: The recorded outside relative humidity value at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 12 per kilogram of air None - * [rel_samp_loc](rel_samp_loc.md) OPT - * Description: The sampling location within the train car - * range: - * Example: center of car None - * [room_air_exch_rate](room_air_exch_rate.md) OPT - * Description: The rate at which outside air replaces indoor air in a given space - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [room_architec_element](room_architec_element.md) OPT - * Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure - * range: [String](types/String.md) - * Example: None - * [room_condt](room_condt.md) OPT - * Description: The condition of the room at the time of sampling - * range: - * Example: new None - * [room_connected](room_connected.md) OPT - * Description: List of rooms connected to the sampling room by a doorway - * range: - * Example: office None - * [room_count](room_count.md) OPT - * Description: The total count of rooms in the built structure including all room types - * range: [String](types/String.md) - * Example: None - * [room_dim](room_dim.md) OPT - * Description: The length, width and height of sampling room - * range: [String](types/String.md) - * Example: None - * [room_door_dist](room_door_dist.md) OPT - * Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms - * range: [String](types/String.md) - * Example: None - * [room_door_share](room_door_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a door with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_hallway](room_hallway.md) OPT - * Description: List of room(s) (room number, room name) located in the same hallway as sampling room - * range: [String](types/String.md) - * Example: None - * [room_loc](room_loc.md) OPT - * Description: The position of the room within the building - * range: - * Example: interior room None - * [room_moist_damage_hist](room_moist_damage_hist.md) OPT - * Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed - * range: [String](types/String.md) - * Example: None - * [room_net_area](room_net_area.md) OPT - * Description: The net floor area of sampling room. Net area excludes wall thicknesses - * range: [String](types/String.md) - * Example: None - * [room_occup](room_occup.md) OPT - * Description: Count of room occupancy at time of sampling - * range: [String](types/String.md) - * Example: None - * [room_samp_pos](room_samp_pos.md) OPT - * Description: The horizontal sampling position in the room relative to architectural elements - * range: - * Example: south corner None - * [room_type](room_type.md) OPT - * Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure - * range: - * Example: bathroom None - * [room_vol](room_vol.md) OPT - * Description: Volume of sampling room - * range: [String](types/String.md) - * Example: None - * [room_wall_share](room_wall_share.md) OPT - * Description: List of room(s) (room number, room name) sharing a wall with the sampling room - * range: [String](types/String.md) - * Example: None - * [room_window_count](room_window_count.md) OPT - * Description: Number of windows in the room - * range: [String](types/String.md) - * Example: None - * [samp_floor](samp_floor.md) OPT - * Description: The floor of the building, where the sampling room is located - * range: - * Example: 4th floor None - * [samp_room_id](samp_room_id.md) OPT - * Description: Sampling room number. This ID should be consistent with the designations on the building floor plans - * range: [String](types/String.md) - * Example: None - * [samp_sort_meth](samp_sort_meth.md) OPT - * Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. - * range: [String](types/String.md) - * Example: None - * [samp_time_out](samp_time_out.md) OPT - * Description: The recent and long term history of outside sampling - * range: [Double](types/Double.md) - * Example: None - * [samp_weather](samp_weather.md) OPT - * Description: The weather on the sampling day - * range: - * Example: foggy None - * [season](season.md) OPT - * Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - * range: [String](types/String.md) - * Example: autumn [NCIT:C94733] None - * [season_use](season_use.md) OPT - * Description: The seasons the space is occupied - * range: - * Example: Winter None - * [shading_device_cond](shading_device_cond.md) OPT - * Description: The physical condition of the shading device at the time of sampling - * range: - * Example: new None - * [shading_device_loc](shading_device_loc.md) OPT - * Description: The location of the shading device in relation to the built structure - * range: [String](types/String.md) - * Example: exterior None - * [shading_device_mat](shading_device_mat.md) OPT - * Description: The material the shading device is composed of - * range: [String](types/String.md) - * Example: None - * [shading_device_type](shading_device_type.md) OPT - * Description: The type of shading device - * range: - * Example: slatted aluminum awning None - * [shading_device_water_mold](shading_device_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the shading device - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [space_typ_state](space_typ_state.md) OPT - * Description: Customary or normal state of the space - * range: [String](types/String.md) - * Example: typically occupied None - * [specific](specific.md) OPT - * Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents - * range: - * Example: construction None - * [specific_humidity](specific_humidity.md) OPT - * Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. - * range: [QuantityValue](QuantityValue.md) - * Example: 15 per kilogram of air None - * [substructure_type](substructure_type.md) OPT - * Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level - * range: - * Example: basement None - * [surf_air_cont](surf_air_cont.md) OPT - * Description: Contaminant identified on surface - * range: - * Example: radon None - * [surf_humidity](surf_humidity.md) OPT - * Description: Surfaces: water activity as a function of air and material moisture - * range: [QuantityValue](QuantityValue.md) - * Example: 10% None - * [surf_material](surf_material.md) OPT - * Description: Surface materials at the point of sampling - * range: - * Example: wood None - * [surf_moisture](surf_moisture.md) OPT - * Description: Water held on a surface - * range: [QuantityValue](QuantityValue.md) - * Example: 0.01 gram per square meter None - * [surf_moisture_ph](surf_moisture_ph.md) OPT - * Description: ph measurement of surface - * range: [Double](types/Double.md) - * Example: 7 None - * [surf_temp](surf_temp.md) OPT - * Description: Temperature of the surface at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [temp_out](temp_out.md) OPT - * Description: The recorded temperature value at sampling time outside - * range: [QuantityValue](QuantityValue.md) - * Example: 5 degree Celsius None - * [train_line](train_line.md) OPT - * Description: The subway line name - * range: - * Example: red None - * [train_stat_loc](train_stat_loc.md) OPT - * Description: The train station collection location - * range: - * Example: forest hills None - * [train_stop_loc](train_stop_loc.md) OPT - * Description: The train stop collection location - * range: - * Example: end None - * [typ_occup_density](typ_occup_density.md) OPT - * Description: Customary or normal density of occupants - * range: [Double](types/Double.md) - * Example: 25 None - * [ventilation_type](ventilation_type.md) OPT - * Description: Ventilation system used in the sampled premises - * range: [String](types/String.md) - * Example: Operable windows None - * [vis_media](vis_media.md) OPT - * Description: The building visual media - * range: - * Example: 3D scans None - * [wall_area](wall_area.md) OPT - * Description: The total area of the sampled room's walls - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_const_type](wall_const_type.md) OPT - * Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. - * range: - * Example: fire resistive None - * [wall_finish_mat](wall_finish_mat.md) OPT - * Description: The material utilized to finish the outer most layer of the wall - * range: - * Example: wood None - * [wall_height](wall_height.md) OPT - * Description: The average height of the walls in the sampled room - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_loc](wall_loc.md) OPT - * Description: The relative location of the wall within the room - * range: - * Example: north None - * [wall_surf_treatment](wall_surf_treatment.md) OPT - * Description: The surface treatment of interior wall - * range: - * Example: paneling None - * [wall_texture](wall_texture.md) OPT - * Description: The feel, appearance, or consistency of a wall surface - * range: - * Example: popcorn None - * [wall_thermal_mass](wall_thermal_mass.md) OPT - * Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wall_water_mold](wall_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on a wall - * range: [String](types/String.md) - * Example: no presence of mold visible None - * [water_feat_size](water_feat_size.md) OPT - * Description: The size of the water feature - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_feat_type](water_feat_type.md) OPT - * Description: The type of water feature present within the building being sampled - * range: - * Example: stream None - * [weekday](weekday.md) OPT - * Description: The day of the week when sampling occurred - * range: - * Example: Sunday None - * [window_cond](window_cond.md) OPT - * Description: The physical condition of the window at the time of sampling - * range: - * Example: rupture None - * [window_cover](window_cover.md) OPT - * Description: The type of window covering - * range: - * Example: curtains None - * [window_horiz_pos](window_horiz_pos.md) OPT - * Description: The horizontal position of the window on the wall - * range: - * Example: middle None - * [window_loc](window_loc.md) OPT - * Description: The relative location of the window within the room - * range: - * Example: west None - * [window_mat](window_mat.md) OPT - * Description: The type of material used to finish a window - * range: - * Example: wood None - * [window_open_freq](window_open_freq.md) OPT - * Description: The number of times windows are opened per week - * range: [String](types/String.md) - * Example: None - * [window_size](window_size.md) OPT - * Description: The window's length and width - * range: [String](types/String.md) - * Example: None - * [window_status](window_status.md) OPT - * Description: Defines whether the windows were open or closed during environmental testing - * range: [String](types/String.md) - * Example: open None - * [window_type](window_type.md) OPT - * Description: The type of windows - * range: - * Example: fixed window None - * [window_vert_pos](window_vert_pos.md) OPT - * Description: The vertical position of the window on the wall - * range: - * Example: middle None - * [window_water_mold](window_water_mold.md) OPT - * Description: Signs of the presence of mold or mildew on the window. - * range: [String](types/String.md) - * Example: no presence of mold visible None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMisag.md b/mixs6/BuiltEnvironmentMisag.md index be839ce8..01391baf 100644 --- a/mixs6/BuiltEnvironmentMisag.md +++ b/mixs6/BuiltEnvironmentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnvironmentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MISAG],[BuiltEnvironment]^-[BuiltEnvironmentMISAG],[BuiltEnvironment],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MISAG],[BuiltEnvironment]^-[BuiltEnvironmentMISAG],[BuiltEnvironment],[MISAG]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -846,22 +846,27 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -948,8 +953,3 @@ URI: [mixs.vocab:BuiltEnvironmentMISAG](https://w3id.org/mixs/vocab/BuiltEnviron * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/BuiltEnvironmentMiuvig.md b/mixs6/BuiltEnvironmentMiuvig.md index 8a08aebc..f0f39932 100644 --- a/mixs6/BuiltEnvironmentMiuvig.md +++ b/mixs6/BuiltEnvironmentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnvironmentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):string%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):string%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIUVIG],[BuiltEnvironment]^-[BuiltEnvironmentMIUVIG],[BuiltEnvironment],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[BuiltEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;surf_material(i):surf_material_enum%20%3F;surf_air_cont(i):surf_air_cont_enum%20%3F;surf_moisture_ph(i):double%20%3F;build_occup_type(i):build_occup_type_enum%20%3F;ventilation_type(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;indoor_space(i):indoor_space_enum%20%3F;indoor_surf(i):indoor_surf_enum%20%3F;filter_type(i):filter_type_enum%20%3F;heat_cool_type(i):heat_cool_type_enum%20%3F;substructure_type(i):substructure_type_enum%20%3F;building_setting(i):building_setting_enum%20%3F;light_type(i):light_type_enum%20%3F;samp_sort_meth(i):string%20%3F;space_typ_state(i):string%20%3F;typ_occup_density(i):double%20%3F;occup_samp(i):string%20%3F;occup_density_samp(i):double%20%3F;address(i):string%20%3F;adj_room(i):string%20%3F;aero_struc(i):string%20%3F;arch_struc(i):arch_struc_enum%20%3F;avg_occup(i):double%20%3F;bathroom_count(i):string%20%3F;bedroom_count(i):string%20%3F;built_struc_set(i):string%20%3F;built_struc_type(i):string%20%3F;ceil_cond(i):ceil_cond_enum%20%3F;ceil_finish_mat(i):ceil_finish_mat_enum%20%3F;ceil_water_mold(i):string%20%3F;ceil_struc(i):string%20%3F;ceil_texture(i):ceil_texture_enum%20%3F;ceil_type(i):ceil_type_enum%20%3F;cool_syst_id(i):string%20%3F;date_last_rain(i):date%20%3F;build_docs(i):build_docs_enum%20%3F;door_cond(i):door_cond_enum%20%3F;door_direct(i):door_direct_enum%20%3F;door_loc(i):door_loc_enum%20%3F;door_mat(i):door_mat_enum%20%3F;door_move(i):door_move_enum%20%3F;door_water_mold(i):string%20%3F;door_type(i):door_type_enum%20%3F;door_comp_type(i):door_comp_type_enum%20%3F;door_type_metal(i):door_type_metal_enum%20%3F;door_type_wood(i):door_type_wood_enum%20%3F;drawings(i):drawings_enum%20%3F;elevator(i):string%20%3F;escalator(i):string%20%3F;exp_pipe(i):string%20%3F;ext_door(i):string%20%3F;fireplace_type(i):string%20%3F;floor_cond(i):floor_cond_enum%20%3F;floor_count(i):string%20%3F;floor_finish_mat(i):floor_finish_mat_enum%20%3F;floor_water_mold(i):floor_water_mold_enum%20%3F;floor_struc(i):floor_struc_enum%20%3F;freq_clean(i):string%20%3F;freq_cook(i):string%20%3F;furniture(i):furniture_enum%20%3F;gender_restroom(i):string%20%3F;hall_count(i):string%20%3F;handidness(i):handidness_enum%20%3F;heat_deliv_loc(i):heat_deliv_loc_enum%20%3F;heat_system_deliv_meth(i):string%20%3F;heat_system_id(i):string%20%3F;int_wall_cond(i):int_wall_cond_enum%20%3F;last_clean(i):date%20%3F;max_occup(i):string%20%3F;mech_struc(i):mech_struc_enum%20%3F;number_plants(i):string%20%3F;number_pets(i):string%20%3F;number_resident(i):string%20%3F;occup_document(i):occup_document_enum%20%3F;ext_wall_orient(i):ext_wall_orient_enum%20%3F;ext_window_orient(i):ext_window_orient_enum%20%3F;pres_animal(i):pres_animal_enum%20%3F;quad_pos(i):quad_pos_enum%20%3F;rel_samp_loc(i):rel_samp_loc_enum%20%3F;room_architec_element(i):string%20%3F;room_condt(i):room_condt_enum%20%3F;room_count(i):string%20%3F;room_dim(i):string%20%3F;room_door_dist(i):string%20%3F;room_loc(i):room_loc_enum%20%3F;room_moist_damage_hist(i):string%20%3F;room_net_area(i):string%20%3F;room_occup(i):string%20%3F;room_samp_pos(i):room_samp_pos_enum%20%3F;room_type(i):room_type_enum%20%3F;room_vol(i):string%20%3F;room_window_count(i):string%20%3F;room_connected(i):room_connected_enum%20%3F;room_hallway(i):string%20%3F;room_door_share(i):string%20%3F;room_wall_share(i):string%20%3F;samp_weather(i):samp_weather_enum%20%3F;samp_floor(i):samp_floor_enum%20%3F;samp_room_id(i):string%20%3F;samp_time_out(i):double%20%3F;season(i):string%20%3F;season_use(i):season_use_enum%20%3F;shading_device_cond(i):shading_device_cond_enum%20%3F;shading_device_loc(i):string%20%3F;shading_device_mat(i):string%20%3F;shading_device_water_mold(i):string%20%3F;shading_device_type(i):shading_device_type_enum%20%3F;specific(i):specific_enum%20%3F;train_line(i):train_line_enum%20%3F;train_stat_loc(i):train_stat_loc_enum%20%3F;train_stop_loc(i):train_stop_loc_enum%20%3F;vis_media(i):vis_media_enum%20%3F;wall_const_type(i):wall_const_type_enum%20%3F;wall_finish_mat(i):wall_finish_mat_enum%20%3F;wall_loc(i):wall_loc_enum%20%3F;wall_water_mold(i):string%20%3F;wall_surf_treatment(i):wall_surf_treatment_enum%20%3F;wall_texture(i):wall_texture_enum%20%3F;water_feat_type(i):water_feat_type_enum%20%3F;weekday(i):weekday_enum%20%3F;window_size(i):string%20%3F;window_cond(i):window_cond_enum%20%3F;window_cover(i):window_cover_enum%20%3F;window_horiz_pos(i):window_horiz_pos_enum%20%3F;window_loc(i):window_loc_enum%20%3F;window_mat(i):window_mat_enum%20%3F;window_open_freq(i):string%20%3F;window_water_mold(i):string%20%3F;window_status(i):string%20%3F;window_type(i):window_type_enum%20%3F;window_vert_pos(i):window_vert_pos_enum%20%3F]uses%20-.->[MIUVIG],[BuiltEnvironment]^-[BuiltEnvironmentMIUVIG],[BuiltEnvironment],[MIUVIG]) ## Parents @@ -43,7 +43,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnviro * range: [QuantityValue](QuantityValue.md) * Example: 20 degree Celsius None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amount_light](amount_light.md) OPT @@ -136,7 +136,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnviro * Example: presence of mold visible None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cool_syst_id](cool_syst_id.md) OPT * Description: The cooling system identifier @@ -144,10 +144,10 @@ URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnviro * Example: 12345 None * [date_last_rain](date_last_rain.md) OPT * Description: The date of the last time it rained - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dew_point](dew_point.md) OPT @@ -352,7 +352,7 @@ URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnviro * Example: damaged None * [last_clean](last_clean.md) OPT * Description: The last time the floor was cleaned (swept, mopped, vacuumed) - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11:T14:30Z None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system @@ -886,22 +886,27 @@ URI: [mixs.vocab:BuiltEnvironmentMIUVIG](https://w3id.org/mixs/vocab/BuiltEnviro ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/CeilCondEnum.md b/mixs6/CeilCondEnum.md new file mode 100644 index 00000000..00363aa1 --- /dev/null +++ b/mixs6/CeilCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_cond_enum + + + + +URI: [mixs.vocab:ceil_cond_enum](https://w3id.org/mixs/vocab/ceil_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilFinishMatEnum.md b/mixs6/CeilFinishMatEnum.md new file mode 100644 index 00000000..866f5463 --- /dev/null +++ b/mixs6/CeilFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_finish_mat_enum + + + + +URI: [mixs.vocab:ceil_finish_mat_enum](https://w3id.org/mixs/vocab/ceil_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilTextureEnum.md b/mixs6/CeilTextureEnum.md new file mode 100644 index 00000000..22812a2d --- /dev/null +++ b/mixs6/CeilTextureEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_texture_enum + + + + +URI: [mixs.vocab:ceil_texture_enum](https://w3id.org/mixs/vocab/ceil_texture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/CeilTypeEnum.md b/mixs6/CeilTypeEnum.md new file mode 100644 index 00000000..73773347 --- /dev/null +++ b/mixs6/CeilTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: ceil_type_enum + + + + +URI: [mixs.vocab:ceil_type_enum](https://w3id.org/mixs/vocab/ceil_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ComplApprEnum.md b/mixs6/ComplApprEnum.md new file mode 100644 index 00000000..7c5b3760 --- /dev/null +++ b/mixs6/ComplApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: compl_appr_enum + + + + +URI: [mixs.vocab:compl_appr_enum](https://w3id.org/mixs/vocab/compl_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ComplScoreEnum.md b/mixs6/ComplScoreEnum.md new file mode 100644 index 00000000..1ee12a34 --- /dev/null +++ b/mixs6/ComplScoreEnum.md @@ -0,0 +1,19 @@ + +# Enum: compl_score_enum + + + + +URI: [mixs.vocab:compl_score_enum](https://w3id.org/mixs/vocab/compl_score_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ContamScreenParamEnum.md b/mixs6/ContamScreenParamEnum.md new file mode 100644 index 00000000..2a3c2fbc --- /dev/null +++ b/mixs6/ContamScreenParamEnum.md @@ -0,0 +1,19 @@ + +# Enum: contam_screen_param_enum + + + + +URI: [mixs.vocab:contam_screen_param_enum](https://w3id.org/mixs/vocab/contam_screen_param_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Core.md b/mixs6/Core.md index 37ab3fec..78978bb0 100644 --- a/mixs6/Core.md +++ b/mixs6/Core.md @@ -7,7 +7,7 @@ Core package. Do not use this directly, this is used to build other packages URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annot](annot.md) OPT @@ -56,7 +56,7 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * Example: uchime;v4.1;default parameters None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [compl_appr](compl_appr.md) OPT * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome @@ -87,7 +87,7 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * range: * Example: anvi'o None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [detec_type](detec_type.md) OPT @@ -258,22 +258,26 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments * range: * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * Description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. * range: [String](types/String.md) * Example: filtering of seawater, storing samples in ethanol None * [samp_size](samp_size.md) OPT * Description: Amount or size of sample (volume, mass or area) that was collected * range: [QuantityValue](QuantityValue.md) * Example: 5 liter None + * [sample_collect_device](sample_collect_device.md) OPT + * Description: The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + * range: [String](types/String.md) + * Example: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] None + * [sample_collect_method](sample_collect_method.md) OPT + * Description: The method employed for collecting the sample. + * range: [String](types/String.md) + * Example: swabbing None * [sample_name](sample_name.md) OPT * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. * range: [String](types/String.md) - * Example: None + * Example: ISDsoil1 None * [seq_meth](seq_meth.md) OPT * Description: Sequencing method used; e.g. Sanger, ABI-solid * range: @@ -389,7 +393,3 @@ URI: [mixs.vocab:Core](https://w3id.org/mixs/vocab/Core) * Description: Can a 16S gene be recovered from the submitted SAG or MAG? * range: [String](types/String.md) * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMe.md b/mixs6/CoreMe.md deleted file mode 100644 index 6ade50ce..00000000 --- a/mixs6/CoreMe.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMe - - -Combinatorial checklist for core with me - -URI: [mixs.vocab:CoreMe](https://w3id.org/mixs/vocab/CoreMe) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Me],[CoreMe|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Me],[Core]^-[CoreMe],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [Me](Me.md) - me Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsBa.md b/mixs6/CoreMigsBa.md deleted file mode 100644 index c8fa9ec9..00000000 --- a/mixs6/CoreMigsBa.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMigsBa - - -Combinatorial checklist for core with migs_ba - -URI: [mixs.vocab:CoreMigsBa](https://w3id.org/mixs/vocab/CoreMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsBa],[CoreMigsBa|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsBa],[Core]^-[CoreMigsBa],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsEu.md b/mixs6/CoreMigsEu.md deleted file mode 100644 index 26ff6cd5..00000000 --- a/mixs6/CoreMigsEu.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMigsEu - - -Combinatorial checklist for core with migs_eu - -URI: [mixs.vocab:CoreMigsEu](https://w3id.org/mixs/vocab/CoreMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsEu],[CoreMigsEu|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsEu],[Core]^-[CoreMigsEu],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsOrg.md b/mixs6/CoreMigsOrg.md deleted file mode 100644 index 228cacfb..00000000 --- a/mixs6/CoreMigsOrg.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMigsOrg - - -Combinatorial checklist for core with migs_org - -URI: [mixs.vocab:CoreMigsOrg](https://w3id.org/mixs/vocab/CoreMigsOrg) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsOrg],[CoreMigsOrg|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsOrg],[Core]^-[CoreMigsOrg],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MigsOrg](MigsOrg.md) - migs_org Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsPl.md b/mixs6/CoreMigsPl.md deleted file mode 100644 index 98b195db..00000000 --- a/mixs6/CoreMigsPl.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMigsPl - - -Combinatorial checklist for core with migs_pl - -URI: [mixs.vocab:CoreMigsPl](https://w3id.org/mixs/vocab/CoreMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsPl],[CoreMigsPl|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsPl],[Core]^-[CoreMigsPl],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMigsVi.md b/mixs6/CoreMigsVi.md deleted file mode 100644 index a2e15080..00000000 --- a/mixs6/CoreMigsVi.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMigsVi - - -Combinatorial checklist for core with migs_vi - -URI: [mixs.vocab:CoreMigsVi](https://w3id.org/mixs/vocab/CoreMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MigsVi],[CoreMigsVi|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MigsVi],[Core]^-[CoreMigsVi],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimag.md b/mixs6/CoreMimag.md deleted file mode 100644 index 3f4e8185..00000000 --- a/mixs6/CoreMimag.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMimag - - -Combinatorial checklist for core with mimag - -URI: [mixs.vocab:CoreMimag](https://w3id.org/mixs/vocab/CoreMimag) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Mimag],[CoreMimag|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Mimag],[Core]^-[CoreMimag],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [Mimag](Mimag.md) - mimag Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimarksC.md b/mixs6/CoreMimarksC.md deleted file mode 100644 index 32fe375b..00000000 --- a/mixs6/CoreMimarksC.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMimarksC - - -Combinatorial checklist for core with mimarks_c - -URI: [mixs.vocab:CoreMimarksC](https://w3id.org/mixs/vocab/CoreMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksC],[CoreMimarksC|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MimarksC],[Core]^-[CoreMimarksC],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMimarksS.md b/mixs6/CoreMimarksS.md deleted file mode 100644 index 31d9c705..00000000 --- a/mixs6/CoreMimarksS.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMimarksS - - -Combinatorial checklist for core with mimarks_s - -URI: [mixs.vocab:CoreMimarksS](https://w3id.org/mixs/vocab/CoreMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[MimarksS],[CoreMimarksS|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[MimarksS],[Core]^-[CoreMimarksS],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMisag.md b/mixs6/CoreMisag.md deleted file mode 100644 index 4d4c6fae..00000000 --- a/mixs6/CoreMisag.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMisag - - -Combinatorial checklist for core with misag - -URI: [mixs.vocab:CoreMisag](https://w3id.org/mixs/vocab/CoreMisag) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Misag],[CoreMisag|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Misag],[Core]^-[CoreMisag],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [Misag](Misag.md) - misag Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CoreMiuvig.md b/mixs6/CoreMiuvig.md deleted file mode 100644 index ac8dda6c..00000000 --- a/mixs6/CoreMiuvig.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: CoreMiuvig - - -Combinatorial checklist for core with miuvig - -URI: [mixs.vocab:CoreMiuvig](https://w3id.org/mixs/vocab/CoreMiuvig) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Miuvig],[CoreMiuvig|submitted_to_insdc(i):string%20%3F;investigation_type(i):investigation_type_enum%20%3F;sample_name(i):string%20%3F;project_name(i):string%20%3F;experimental_factor(i):string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;alt(i):string%20%3F;elev(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;env_package(i):env_package_enum%20%3F;subspecf_gen_lin(i):string%20%3F;ploidy(i):string%20%3F;num_replicons(i):string%20%3F;extrachrom_elements(i):string%20%3F;estimated_size(i):string%20%3F;ref_biomaterial(i):string%20%3F;source_mat_id(i):string%20%3F;pathogenicity(i):string%20%3F;biotic_relationship(i):biotic_relationship_enum%20%3F;specific_host(i):string%20%3F;host_spec_range(i):string%20%3F;health_disease_stat(i):health_disease_stat_enum%20%3F;trophic_level(i):trophic_level_enum%20%3F;propagation(i):string%20%3F;encoded_traits(i):string%20%3F;rel_to_oxygen(i):rel_to_oxygen_enum%20%3F;isol_growth_condt(i):string%20%3F;samp_collect_device(i):string%20%3F;samp_mat_process(i):string%20%3F;size_frac(i):string%20%3F;samp_size(i):string%20%3F;source_uvig(i):source_uvig_enum%20%3F;virus_enrich_appr(i):virus_enrich_appr_enum%20%3F;nucl_acid_ext(i):string%20%3F;nucl_acid_amp(i):string%20%3F;lib_size(i):string%20%3F;lib_reads_seqd(i):string%20%3F;lib_layout(i):lib_layout_enum%20%3F;lib_vector(i):string%20%3F;lib_screen(i):string%20%3F;target_gene(i):string%20%3F;target_subfragment(i):string%20%3F;pcr_primers(i):string%20%3F;mid(i):string%20%3F;adapters(i):string%20%3F;pcr_cond(i):string%20%3F;seq_meth(i):seq_meth_enum%20%3F;seq_quality_check(i):string%20%3F;chimera_check(i):string%20%3F;tax_ident(i):tax_ident_enum%20%3F;assembly_qual(i):assembly_qual_enum%20%3F;assembly_name(i):string%20%3F;assembly_software(i):string%20%3F;annot(i):string%20%3F;number_contig(i):string%20%3F;feat_pred(i):string%20%3F;ref_db(i):string%20%3F;sim_search_meth(i):string%20%3F;tax_class(i):string%20%3F;x_16s_recover(i):string%20%3F;x_16s_recover_software(i):string%20%3F;trnas(i):string%20%3F;trna_ext_software(i):string%20%3F;compl_score(i):compl_score_enum%20%3F;compl_software(i):string%20%3F;compl_appr(i):compl_appr_enum%20%3F;contam_score(i):string%20%3F;contam_screen_input(i):string%20%3F;contam_screen_param(i):contam_screen_param_enum%20%3F;decontam_software(i):decontam_software_enum%20%3F;sort_tech(i):sort_tech_enum%20%3F;single_cell_lysis_appr(i):single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot(i):string%20%3F;wga_amp_appr(i):string%20%3F;wga_amp_kit(i):string%20%3F;bin_param(i):bin_param_enum%20%3F;bin_software(i):bin_software_enum%20%3F;reassembly_bin(i):string%20%3F;mag_cov_software(i):mag_cov_software_enum%20%3F;vir_ident_software(i):string%20%3F;pred_genome_type(i):pred_genome_type_enum%20%3F;pred_genome_struc(i):pred_genome_struc_enum%20%3F;detec_type(i):string%20%3F;votu_class_appr(i):string%20%3F;votu_seq_comp_appr(i):string%20%3F;votu_db(i):string%20%3F;host_pred_appr(i):host_pred_appr_enum%20%3F;host_pred_est_acc(i):string%20%3F;url(i):string%20%3F;sop(i):string%20%3F]uses%20-.->[Miuvig],[Core]^-[CoreMiuvig],[Core]) - -## Parents - - * is_a: [Core](Core.md) - core package - -## Uses Mixins - - * mixin: [Miuvig](Miuvig.md) - miuvig Checklist - -## Attributes - - -### Inherited from core: - - * [adapters](adapters.md) OPT - * Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - * range: [String](types/String.md) - * Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [String](types/String.md) - * Example: 100 meter None - * [annot](annot.md) OPT - * Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - * range: [String](types/String.md) - * Example: prokka None - * [assembly_name](assembly_name.md) OPT - * Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - * range: [String](types/String.md) - * Example: HuRef, JCVI_ISG_i3_1.0 None - * [assembly_qual](assembly_qual.md) OPT - * Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated - * range: - * Example: High-quality draft genome None - * [assembly_software](assembly_software.md) OPT - * Description: Tool(s) used for assembly, including version number and parameters - * range: [String](types/String.md) - * Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None - * [bin_param](bin_param.md) OPT - * Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets - * range: - * Example: coverage and kmer None - * [bin_software](bin_software.md) OPT - * Description: Tool(s) used for the extraction of genomes from metagenomic datasets - * range: - * Example: concoct and maxbin None - * [biotic_relationship](biotic_relationship.md) OPT - * Description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object - * range: - * Example: free living None - * [chimera_check](chimera_check.md) OPT - * Description: A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point - * range: [String](types/String.md) - * Example: uchime;v4.1;default parameters None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [compl_appr](compl_appr.md) OPT - * Description: The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome - * range: - * Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None - * [compl_score](compl_score.md) OPT - * Description: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores - * range: - * Example: med;60% None - * [compl_software](compl_software.md) OPT - * Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - * range: [String](types/String.md) - * Example: checkm None - * [contam_score](contam_score.md) OPT - * Description: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - * range: [String](types/String.md) - * Example: 1% None - * [contam_screen_input](contam_screen_input.md) OPT - * Description: The type of sequence data used as input - * range: [String](types/String.md) - * Example: contigs None - * [contam_screen_param](contam_screen_param.md) OPT - * Description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer - * range: - * Example: kmer None - * [decontam_software](decontam_software.md) OPT - * Description: Tool(s) used in contamination screening - * range: - * Example: anvi'o None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [detec_type](detec_type.md) OPT - * Description: Type of UViG detection - * range: [String](types/String.md) - * Example: independent sequence (UViG) None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [String](types/String.md) - * Example: 100 meter None - * [encoded_traits](encoded_traits.md) OPT - * Description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage - * range: [String](types/String.md) - * Example: beta-lactamase class A None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [env_package](env_package.md) OPT - * Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - * range: - * Example: soil None - * [estimated_size](estimated_size.md) OPT - * Description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - * range: [String](types/String.md) - * Example: 300000 bp None - * [experimental_factor](experimental_factor.md) OPT - * Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: time series design [EFO:EFO_0001779] None - * [extrachrom_elements](extrachrom_elements.md) OPT - * Description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) - * range: [String](types/String.md) - * Example: 5 None - * [feat_pred](feat_pred.md) OPT - * Description: Method used to predict UViGs features such as ORFs, integration site, etc. - * range: [String](types/String.md) - * Example: Prodigal;2.6.3;default parameters None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [health_disease_stat](health_disease_stat.md) OPT - * Description: Health or disease status of specific host at time of collection - * range: - * Example: dead None - * [host_pred_appr](host_pred_appr.md) OPT - * Description: Tool or approach used for host prediction - * range: - * Example: CRISPR spacer match None - * [host_pred_est_acc](host_pred_est_acc.md) OPT - * Description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature - * range: [String](types/String.md) - * Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None - * [host_spec_range](host_spec_range.md) OPT - * Description: The NCBI taxonomy identifier of the specific host if it is known - * range: [String](types/String.md) - * Example: 9606 None - * [investigation_type](investigation_type.md) OPT - * Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome - * range: - * Example: metagenome None - * [isol_growth_condt](isol_growth_condt.md) OPT - * Description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material - * range: [String](types/String.md) - * Example: doi: 10.1016/j.syapm.2018.01.009 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lib_layout](lib_layout.md) OPT - * Description: Specify whether to expect single, paired, or other configuration of reads - * range: - * Example: paired None - * [lib_reads_seqd](lib_reads_seqd.md) OPT - * Description: Total number of clones sequenced from the library - * range: [String](types/String.md) - * Example: 20 None - * [lib_screen](lib_screen.md) OPT - * Description: Specific enrichment or screening methods applied before and/or after creating libraries - * range: [String](types/String.md) - * Example: enriched, screened, normalized None - * [lib_size](lib_size.md) OPT - * Description: Total number of clones in the library prepared for the project - * range: [String](types/String.md) - * Example: 50 None - * [lib_vector](lib_vector.md) OPT - * Description: Cloning vector type(s) used in construction of libraries - * range: [String](types/String.md) - * Example: Bacteriophage P1 None - * [mag_cov_software](mag_cov_software.md) OPT - * Description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets - * range: - * Example: bbmap None - * [mid](mid.md) OPT - * Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: GTGAATAT None - * [nucl_acid_amp](nucl_acid_amp.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids - * range: [String](types/String.md) - * Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None - * [nucl_acid_ext](nucl_acid_ext.md) OPT - * Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample - * range: [String](types/String.md) - * Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None - * [num_replicons](num_replicons.md) OPT - * Description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote - * range: [String](types/String.md) - * Example: 2 None - * [number_contig](number_contig.md) OPT - * Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG - * range: [String](types/String.md) - * Example: 40 None - * [pathogenicity](pathogenicity.md) OPT - * Description: To what is the entity pathogenic - * range: [String](types/String.md) - * Example: human, animal, plant, fungi, bacteria None - * [pcr_cond](pcr_cond.md) OPT - * Description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' - * range: [String](types/String.md) - * Example: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 None - * [pcr_primers](pcr_primers.md) OPT - * Description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters - * range: [String](types/String.md) - * Example: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT None - * [ploidy](ploidy.md) OPT - * Description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO - * range: [String](types/String.md) - * Example: allopolyploidy [PATO:0001379] None - * [pred_genome_struc](pred_genome_struc.md) OPT - * Description: Expected structure of the viral genome - * range: - * Example: non-segmented None - * [pred_genome_type](pred_genome_type.md) OPT - * Description: Type of genome predicted for the UViG - * range: - * Example: dsDNA None - * [project_name](project_name.md) OPT - * Description: Name of the project within which the sequencing was organized - * range: [String](types/String.md) - * Example: Forest soil metagenome None - * [propagation](propagation.md) OPT - * Description: This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice - * range: [String](types/String.md) - * Example: lytic None - * [reassembly_bin](reassembly_bin.md) OPT - * Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? - * range: [String](types/String.md) - * Example: no None - * [ref_biomaterial](ref_biomaterial.md) OPT - * Description: Primary publication if isolated before genome publication; otherwise, primary genome report - * range: [String](types/String.md) - * Example: doi:10.1016/j.syapm.2018.01.009 None - * [ref_db](ref_db.md) OPT - * Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication - * range: [String](types/String.md) - * Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None - * [rel_to_oxygen](rel_to_oxygen.md) OPT - * Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments - * range: - * Example: aerobe None - * [samp_collect_device](samp_collect_device.md) OPT - * Description: The method or device employed for collecting the sample - * range: [String](types/String.md) - * Example: environmental swab sampling, biopsy, niskin bottle, push core None - * [samp_mat_process](samp_mat_process.md) OPT - * Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - * range: [String](types/String.md) - * Example: filtering of seawater, storing samples in ethanol None - * [samp_size](samp_size.md) OPT - * Description: Amount or size of sample (volume, mass or area) that was collected - * range: [String](types/String.md) - * Example: 5 liter None - * [sample_name](sample_name.md) OPT - * Description: Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * range: [String](types/String.md) - * Example: None - * [seq_meth](seq_meth.md) OPT - * Description: Sequencing method used; e.g. Sanger, ABI-solid - * range: - * Example: Illumina HiSeq 1500 None - * [seq_quality_check](seq_quality_check.md) OPT - * Description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA - * range: [String](types/String.md) - * Example: none None - * [sim_search_meth](sim_search_meth.md) OPT - * Description: Tool used to compare ORFs with database, along with version and cutoffs used - * range: [String](types/String.md) - * Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None - * [single_cell_lysis_appr](single_cell_lysis_appr.md) OPT - * Description: Method used to free DNA from interior of the cell(s) or particle(s) - * range: - * Example: enzymatic None - * [single_cell_lysis_prot](single_cell_lysis_prot.md) OPT - * Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis - * range: [String](types/String.md) - * Example: ambion single cell lysis kit None - * [size_frac](size_frac.md) OPT - * Description: Filtering pore size used in sample preparation - * range: [String](types/String.md) - * Example: 0-0.22 micrometer None - * [sop](sop.md) OPT - * Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences - * range: [String](types/String.md) - * Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None - * [sort_tech](sort_tech.md) OPT - * Description: Method used to sort/isolate cells or particles of interest - * range: - * Example: optical manipulation None - * [source_mat_id](source_mat_id.md) OPT - * Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). - * range: [String](types/String.md) - * Example: MPI012345 None - * [source_uvig](source_uvig.md) OPT - * Description: Type of dataset from which the UViG was obtained - * range: - * Example: viral fraction metagenome (virome) None - * [specific_host](specific_host.md) OPT - * Description: If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) - * range: [String](types/String.md) - * Example: 9606 None - * [submitted_to_insdc](submitted_to_insdc.md) OPT - * Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases - * range: [String](types/String.md) - * Example: yes None - * [subspecf_gen_lin](subspecf_gen_lin.md) OPT - * Description: This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - * range: [String](types/String.md) - * Example: serovar:Newport None - * [target_gene](target_gene.md) OPT - * Description: Targeted gene or locus name for marker gene studies - * range: [String](types/String.md) - * Example: 16S rRNA, 18S rRNA, nif, amoA, rpo None - * [target_subfragment](target_subfragment.md) OPT - * Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA - * range: [String](types/String.md) - * Example: V6, V9, ITS None - * [tax_class](tax_class.md) OPT - * Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes - * range: [String](types/String.md) - * Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None - * [tax_ident](tax_ident.md) OPT - * Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG - * range: - * Example: other: rpoB gene None - * [trna_ext_software](trna_ext_software.md) OPT - * Description: Tools used for tRNA identification - * range: [String](types/String.md) - * Example: infernal;v2;default parameters None - * [trnas](trnas.md) OPT - * Description: The total number of tRNAs identified from the SAG or MAG - * range: [String](types/String.md) - * Example: 18 None - * [trophic_level](trophic_level.md) OPT - * Description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) - * range: - * Example: heterotroph None - * [url](url.md) OPT - * range: [String](types/String.md) - * Example: http://www.earthmicrobiome.org/ None - * [vir_ident_software](vir_ident_software.md) OPT - * Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used - * range: [String](types/String.md) - * Example: VirSorter; 1.0.4; Virome database, category 2 None - * [virus_enrich_appr](virus_enrich_appr.md) OPT - * Description: List of approaches used to enrich the sample for viruses, if any - * range: - * Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None - * [votu_class_appr](votu_class_appr.md) OPT - * Description: Cutoffs and approach used when clustering new UViGs in “species-level” vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis - * range: [String](types/String.md) - * Example: 95% ANI;85% AF; greedy incremental clustering None - * [votu_db](votu_db.md) OPT - * Description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any - * range: [String](types/String.md) - * Example: NCBI Viral RefSeq;83 None - * [votu_seq_comp_appr](votu_seq_comp_appr.md) OPT - * Description: Tool and thresholds used to compare sequences when computing "species-level" vOTUs - * range: [String](types/String.md) - * Example: blastn;2.6.0+;e-value cutoff: 0.001 None - * [wga_amp_appr](wga_amp_appr.md) OPT - * Description: Method used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: mda based None - * [wga_amp_kit](wga_amp_kit.md) OPT - * Description: Kit used to amplify genomic DNA in preparation for sequencing - * range: [String](types/String.md) - * Example: qiagen repli-g None - * [x_16s_recover](x_16s_recover.md) OPT - * Description: Can a 16S gene be recovered from the submitted SAG or MAG? - * range: [String](types/String.md) - * Example: yes None - * [x_16s_recover_software](x_16s_recover_software.md) OPT - * Description: Tools used for 16S rRNA gene extraction - * range: [String](types/String.md) - * Example: rambl;v2;default parameters None diff --git a/mixs6/CurLandUseEnum.md b/mixs6/CurLandUseEnum.md new file mode 100644 index 00000000..9ac62b25 --- /dev/null +++ b/mixs6/CurLandUseEnum.md @@ -0,0 +1,19 @@ + +# Enum: cur_land_use_enum + + + + +URI: [mixs.vocab:cur_land_use_enum](https://w3id.org/mixs/vocab/cur_land_use_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DecontamSoftwareEnum.md b/mixs6/DecontamSoftwareEnum.md new file mode 100644 index 00000000..8830f0da --- /dev/null +++ b/mixs6/DecontamSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: decontam_software_enum + + + + +URI: [mixs.vocab:decontam_software_enum](https://w3id.org/mixs/vocab/decontam_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DeposEnvEnum.md b/mixs6/DeposEnvEnum.md new file mode 100644 index 00000000..2b432441 --- /dev/null +++ b/mixs6/DeposEnvEnum.md @@ -0,0 +1,19 @@ + +# Enum: depos_env_enum + + + + +URI: [mixs.vocab:depos_env_enum](https://w3id.org/mixs/vocab/depos_env_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DominantHandEnum.md b/mixs6/DominantHandEnum.md new file mode 100644 index 00000000..a9fa1d26 --- /dev/null +++ b/mixs6/DominantHandEnum.md @@ -0,0 +1,19 @@ + +# Enum: dominant_hand_enum + + + + +URI: [mixs.vocab:dominant_hand_enum](https://w3id.org/mixs/vocab/dominant_hand_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorCompTypeEnum.md b/mixs6/DoorCompTypeEnum.md new file mode 100644 index 00000000..8d12d7df --- /dev/null +++ b/mixs6/DoorCompTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_comp_type_enum + + + + +URI: [mixs.vocab:door_comp_type_enum](https://w3id.org/mixs/vocab/door_comp_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorCondEnum.md b/mixs6/DoorCondEnum.md new file mode 100644 index 00000000..3515588e --- /dev/null +++ b/mixs6/DoorCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_cond_enum + + + + +URI: [mixs.vocab:door_cond_enum](https://w3id.org/mixs/vocab/door_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorDirectEnum.md b/mixs6/DoorDirectEnum.md new file mode 100644 index 00000000..be251896 --- /dev/null +++ b/mixs6/DoorDirectEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_direct_enum + + + + +URI: [mixs.vocab:door_direct_enum](https://w3id.org/mixs/vocab/door_direct_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorLocEnum.md b/mixs6/DoorLocEnum.md new file mode 100644 index 00000000..26fff28d --- /dev/null +++ b/mixs6/DoorLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_loc_enum + + + + +URI: [mixs.vocab:door_loc_enum](https://w3id.org/mixs/vocab/door_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorMatEnum.md b/mixs6/DoorMatEnum.md new file mode 100644 index 00000000..a1087468 --- /dev/null +++ b/mixs6/DoorMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_mat_enum + + + + +URI: [mixs.vocab:door_mat_enum](https://w3id.org/mixs/vocab/door_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorMoveEnum.md b/mixs6/DoorMoveEnum.md new file mode 100644 index 00000000..66920cc7 --- /dev/null +++ b/mixs6/DoorMoveEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_move_enum + + + + +URI: [mixs.vocab:door_move_enum](https://w3id.org/mixs/vocab/door_move_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeEnum.md b/mixs6/DoorTypeEnum.md new file mode 100644 index 00000000..42f85a21 --- /dev/null +++ b/mixs6/DoorTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_enum + + + + +URI: [mixs.vocab:door_type_enum](https://w3id.org/mixs/vocab/door_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeMetalEnum.md b/mixs6/DoorTypeMetalEnum.md new file mode 100644 index 00000000..72f827ce --- /dev/null +++ b/mixs6/DoorTypeMetalEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_metal_enum + + + + +URI: [mixs.vocab:door_type_metal_enum](https://w3id.org/mixs/vocab/door_type_metal_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DoorTypeWoodEnum.md b/mixs6/DoorTypeWoodEnum.md new file mode 100644 index 00000000..3955d511 --- /dev/null +++ b/mixs6/DoorTypeWoodEnum.md @@ -0,0 +1,19 @@ + +# Enum: door_type_wood_enum + + + + +URI: [mixs.vocab:door_type_wood_enum](https://w3id.org/mixs/vocab/door_type_wood_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrainageClassEnum.md b/mixs6/DrainageClassEnum.md new file mode 100644 index 00000000..d014a33b --- /dev/null +++ b/mixs6/DrainageClassEnum.md @@ -0,0 +1,19 @@ + +# Enum: drainage_class_enum + + + + +URI: [mixs.vocab:drainage_class_enum](https://w3id.org/mixs/vocab/drainage_class_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrawingsEnum.md b/mixs6/DrawingsEnum.md new file mode 100644 index 00000000..cf8f0401 --- /dev/null +++ b/mixs6/DrawingsEnum.md @@ -0,0 +1,19 @@ + +# Enum: drawings_enum + + + + +URI: [mixs.vocab:drawings_enum](https://w3id.org/mixs/vocab/drawings_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/DrugUsageEnum.md b/mixs6/DrugUsageEnum.md new file mode 100644 index 00000000..43353654 --- /dev/null +++ b/mixs6/DrugUsageEnum.md @@ -0,0 +1,19 @@ + +# Enum: drug_usage_enum + + + + +URI: [mixs.vocab:drug_usage_enum](https://w3id.org/mixs/vocab/drug_usage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/EnvPackageEnum.md b/mixs6/EnvPackageEnum.md new file mode 100644 index 00000000..5bcb16e7 --- /dev/null +++ b/mixs6/EnvPackageEnum.md @@ -0,0 +1,19 @@ + +# Enum: env_package_enum + + + + +URI: [mixs.vocab:env_package_enum](https://w3id.org/mixs/vocab/env_package_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ExtWallOrientEnum.md b/mixs6/ExtWallOrientEnum.md new file mode 100644 index 00000000..019a00f3 --- /dev/null +++ b/mixs6/ExtWallOrientEnum.md @@ -0,0 +1,19 @@ + +# Enum: ext_wall_orient_enum + + + + +URI: [mixs.vocab:ext_wall_orient_enum](https://w3id.org/mixs/vocab/ext_wall_orient_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ExtWindowOrientEnum.md b/mixs6/ExtWindowOrientEnum.md new file mode 100644 index 00000000..6cf9893d --- /dev/null +++ b/mixs6/ExtWindowOrientEnum.md @@ -0,0 +1,19 @@ + +# Enum: ext_window_orient_enum + + + + +URI: [mixs.vocab:ext_window_orient_enum](https://w3id.org/mixs/vocab/ext_window_orient_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FaoClassEnum.md b/mixs6/FaoClassEnum.md new file mode 100644 index 00000000..4c41fd09 --- /dev/null +++ b/mixs6/FaoClassEnum.md @@ -0,0 +1,19 @@ + +# Enum: fao_class_enum + + + + +URI: [mixs.vocab:fao_class_enum](https://w3id.org/mixs/vocab/fao_class_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FilterTypeEnum.md b/mixs6/FilterTypeEnum.md new file mode 100644 index 00000000..14a1bc88 --- /dev/null +++ b/mixs6/FilterTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: filter_type_enum + + + + +URI: [mixs.vocab:filter_type_enum](https://w3id.org/mixs/vocab/filter_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorCondEnum.md b/mixs6/FloorCondEnum.md new file mode 100644 index 00000000..fdb715ab --- /dev/null +++ b/mixs6/FloorCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_cond_enum + + + + +URI: [mixs.vocab:floor_cond_enum](https://w3id.org/mixs/vocab/floor_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorFinishMatEnum.md b/mixs6/FloorFinishMatEnum.md new file mode 100644 index 00000000..d162ea24 --- /dev/null +++ b/mixs6/FloorFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_finish_mat_enum + + + + +URI: [mixs.vocab:floor_finish_mat_enum](https://w3id.org/mixs/vocab/floor_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorStrucEnum.md b/mixs6/FloorStrucEnum.md new file mode 100644 index 00000000..ffa28c50 --- /dev/null +++ b/mixs6/FloorStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_struc_enum + + + + +URI: [mixs.vocab:floor_struc_enum](https://w3id.org/mixs/vocab/floor_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FloorWaterMoldEnum.md b/mixs6/FloorWaterMoldEnum.md new file mode 100644 index 00000000..a748764d --- /dev/null +++ b/mixs6/FloorWaterMoldEnum.md @@ -0,0 +1,19 @@ + +# Enum: floor_water_mold_enum + + + + +URI: [mixs.vocab:floor_water_mold_enum](https://w3id.org/mixs/vocab/floor_water_mold_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/FurnitureEnum.md b/mixs6/FurnitureEnum.md new file mode 100644 index 00000000..1dc61975 --- /dev/null +++ b/mixs6/FurnitureEnum.md @@ -0,0 +1,19 @@ + +# Enum: furniture_enum + + + + +URI: [mixs.vocab:furniture_enum](https://w3id.org/mixs/vocab/furniture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/GrowthHabitEnum.md b/mixs6/GrowthHabitEnum.md new file mode 100644 index 00000000..3885f19d --- /dev/null +++ b/mixs6/GrowthHabitEnum.md @@ -0,0 +1,19 @@ + +# Enum: growth_habit_enum + + + + +URI: [mixs.vocab:growth_habit_enum](https://w3id.org/mixs/vocab/growth_habit_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HandidnessEnum.md b/mixs6/HandidnessEnum.md new file mode 100644 index 00000000..e668a948 --- /dev/null +++ b/mixs6/HandidnessEnum.md @@ -0,0 +1,19 @@ + +# Enum: handidness_enum + + + + +URI: [mixs.vocab:handidness_enum](https://w3id.org/mixs/vocab/handidness_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcProducedEnum.md b/mixs6/HcProducedEnum.md new file mode 100644 index 00000000..aee509e6 --- /dev/null +++ b/mixs6/HcProducedEnum.md @@ -0,0 +1,19 @@ + +# Enum: hc_produced_enum + + + + +URI: [mixs.vocab:hc_produced_enum](https://w3id.org/mixs/vocab/hc_produced_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcrEnum.md b/mixs6/HcrEnum.md new file mode 100644 index 00000000..67994695 --- /dev/null +++ b/mixs6/HcrEnum.md @@ -0,0 +1,19 @@ + +# Enum: hcr_enum + + + + +URI: [mixs.vocab:hcr_enum](https://w3id.org/mixs/vocab/hcr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HcrGeolAgeEnum.md b/mixs6/HcrGeolAgeEnum.md new file mode 100644 index 00000000..c5ce3298 --- /dev/null +++ b/mixs6/HcrGeolAgeEnum.md @@ -0,0 +1,19 @@ + +# Enum: hcr_geol_age_enum + + + + +URI: [mixs.vocab:hcr_geol_age_enum](https://w3id.org/mixs/vocab/hcr_geol_age_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HealthDiseaseStatEnum.md b/mixs6/HealthDiseaseStatEnum.md new file mode 100644 index 00000000..b6c9eb67 --- /dev/null +++ b/mixs6/HealthDiseaseStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: health_disease_stat_enum + + + + +URI: [mixs.vocab:health_disease_stat_enum](https://w3id.org/mixs/vocab/health_disease_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HeatCoolTypeEnum.md b/mixs6/HeatCoolTypeEnum.md new file mode 100644 index 00000000..d00438f4 --- /dev/null +++ b/mixs6/HeatCoolTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: heat_cool_type_enum + + + + +URI: [mixs.vocab:heat_cool_type_enum](https://w3id.org/mixs/vocab/heat_cool_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HeatDelivLocEnum.md b/mixs6/HeatDelivLocEnum.md new file mode 100644 index 00000000..70ceedab --- /dev/null +++ b/mixs6/HeatDelivLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: heat_deliv_loc_enum + + + + +URI: [mixs.vocab:heat_deliv_loc_enum](https://w3id.org/mixs/vocab/heat_deliv_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HorizonEnum.md b/mixs6/HorizonEnum.md new file mode 100644 index 00000000..84a3fa5f --- /dev/null +++ b/mixs6/HorizonEnum.md @@ -0,0 +1,19 @@ + +# Enum: horizon_enum + + + + +URI: [mixs.vocab:horizon_enum](https://w3id.org/mixs/vocab/horizon_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Host-associated.md b/mixs6/Host-associated.md index fac780fd..fc327ca1 100644 --- a/mixs6/Host-associated.md +++ b/mixs6/Host-associated.md @@ -7,7 +7,7 @@ host-associated URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG],[Host-associatedMISAG],[Host-associatedMIMARKSSurvey],[Host-associatedMIMARKSSpecimen],[Host-associatedMIMAG],[Host-associatedMIGSVirus],[Host-associatedMIGSPlant],[Host-associatedMIGSOrg],[Host-associatedMIGSEukaryote],[Host-associatedMIGSBacteria],[Host-associatedME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -40,7 +40,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -49,10 +49,10 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -187,6 +187,10 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -221,7 +225,7 @@ URI: [mixs.vocab:Host-associated](https://w3id.org/mixs/vocab/Host-associated) * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater diff --git a/mixs6/Host-associatedMIGSBacteria.md b/mixs6/Host-associatedMIGSBacteria.md index 6cc8641c..f2ce2577 100644 --- a/mixs6/Host-associatedMIGSBacteria.md +++ b/mixs6/Host-associatedMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-associatedMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Host-associated]^-[Host-associatedMIGSBacteria],[Host-associated],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Host-associated]^-[Host-associatedMIGSBacteria],[Host-associated],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -401,22 +405,27 @@ URI: [mixs.vocab:Host-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Host-a ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Host-associatedMIGSEukaryote.md b/mixs6/Host-associatedMIGSEukaryote.md index 63032bb0..5d1f64d1 100644 --- a/mixs6/Host-associatedMIGSEukaryote.md +++ b/mixs6/Host-associatedMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host-associatedMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Host-associated]^-[Host-associatedMIGSEukaryote],[Host-associated],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Host-associated]^-[Host-associatedMIGSEukaryote],[Host-associated],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -401,22 +405,27 @@ URI: [mixs.vocab:Host-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Host- ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Host-associatedMIGSPlant.md b/mixs6/Host-associatedMIGSPlant.md index f2f3498d..876b342b 100644 --- a/mixs6/Host-associatedMIGSPlant.md +++ b/mixs6/Host-associatedMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-associatedMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Host-associated]^-[Host-associatedMIGSPlant],[Host-associated],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Host-associated]^-[Host-associatedMIGSPlant],[Host-associated],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -376,22 +380,27 @@ URI: [mixs.vocab:Host-associatedMIGSPlant](https://w3id.org/mixs/vocab/Host-asso ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Host-associatedMIGSVirus.md b/mixs6/Host-associatedMIGSVirus.md index 3da0b62d..e7acd728 100644 --- a/mixs6/Host-associatedMIGSVirus.md +++ b/mixs6/Host-associatedMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-associatedMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Host-associated]^-[Host-associatedMIGSVirus],[Host-associated],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Host-associated]^-[Host-associatedMIGSVirus],[Host-associated],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -396,22 +400,27 @@ URI: [mixs.vocab:Host-associatedMIGSVirus](https://w3id.org/mixs/vocab/Host-asso ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Host-associatedMIMARKSSpecimen.md b/mixs6/Host-associatedMIMARKSSpecimen.md index 08ab1057..315e419a 100644 --- a/mixs6/Host-associatedMIMARKSSpecimen.md +++ b/mixs6/Host-associatedMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Host-associated]^-[Host-associatedMIMARKSSpecimen],[Host-associated],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Host-associated]^-[Host-associatedMIMARKSSpecimen],[Host-associated],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -331,22 +335,27 @@ URI: [mixs.vocab:Host-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hos ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Host-associatedMIMARKSSurvey.md b/mixs6/Host-associatedMIMARKSSurvey.md index 593b685b..4e66d89d 100644 --- a/mixs6/Host-associatedMIMARKSSurvey.md +++ b/mixs6/Host-associatedMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host-associatedMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Host-associated]^-[Host-associatedMIMARKSSurvey],[Host-associated],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Host-associated]^-[Host-associatedMIMARKSSurvey],[Host-associated],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -306,22 +310,27 @@ URI: [mixs.vocab:Host-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Host- ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Host-associatedMe.md b/mixs6/Host-associatedMe.md index f07b4bb6..3b8844c2 100644 --- a/mixs6/Host-associatedMe.md +++ b/mixs6/Host-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Host-associated]^-[Host-associatedME],[Host-associated],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Host-associated]^-[Host-associatedME],[Host-associated],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -351,22 +355,27 @@ URI: [mixs.vocab:Host-associatedME](https://w3id.org/mixs/vocab/Host-associatedM ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Host-associatedMigsBa.md b/mixs6/Host-associatedMigsBa.md deleted file mode 100644 index d604faf4..00000000 --- a/mixs6/Host-associatedMigsBa.md +++ /dev/null @@ -1,475 +0,0 @@ - -# Class: Host-associatedMigsBa - - -Combinatorial checklist for host-associated with migs_ba - -URI: [mixs.vocab:Host-associatedMigsBa](https://w3id.org/mixs/vocab/Host-associatedMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Host-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Host-associated]^-[Host-associatedMigsBa],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsEu.md b/mixs6/Host-associatedMigsEu.md deleted file mode 100644 index eff49de4..00000000 --- a/mixs6/Host-associatedMigsEu.md +++ /dev/null @@ -1,475 +0,0 @@ - -# Class: Host-associatedMigsEu - - -Combinatorial checklist for host-associated with migs_eu - -URI: [mixs.vocab:Host-associatedMigsEu](https://w3id.org/mixs/vocab/Host-associatedMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Host-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Host-associated]^-[Host-associatedMigsEu],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsOrg.md b/mixs6/Host-associatedMigsOrg.md index 2d62128d..302800e1 100644 --- a/mixs6/Host-associatedMigsOrg.md +++ b/mixs6/Host-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Host-associated]^-[Host-associatedMIGSOrg],[Host-associated],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Host-associated]^-[Host-associatedMIGSOrg],[Host-associated],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -366,22 +370,27 @@ URI: [mixs.vocab:Host-associatedMIGSOrg](https://w3id.org/mixs/vocab/Host-associ ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Host-associatedMigsPl.md b/mixs6/Host-associatedMigsPl.md deleted file mode 100644 index 4ddbbefc..00000000 --- a/mixs6/Host-associatedMigsPl.md +++ /dev/null @@ -1,445 +0,0 @@ - -# Class: Host-associatedMigsPl - - -Combinatorial checklist for host-associated with migs_pl - -URI: [mixs.vocab:Host-associatedMigsPl](https://w3id.org/mixs/vocab/Host-associatedMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Host-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Host-associated]^-[Host-associatedMigsPl],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMigsVi.md b/mixs6/Host-associatedMigsVi.md deleted file mode 100644 index 0017d829..00000000 --- a/mixs6/Host-associatedMigsVi.md +++ /dev/null @@ -1,470 +0,0 @@ - -# Class: Host-associatedMigsVi - - -Combinatorial checklist for host-associated with migs_vi - -URI: [mixs.vocab:Host-associatedMigsVi](https://w3id.org/mixs/vocab/Host-associatedMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Host-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Host-associated]^-[Host-associatedMigsVi],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Host-associatedMimag.md b/mixs6/Host-associatedMimag.md index c6287d88..0ec00560 100644 --- a/mixs6/Host-associatedMimag.md +++ b/mixs6/Host-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Host-associated]^-[Host-associatedMIMAG],[Host-associated],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Host-associated]^-[Host-associatedMIMAG],[Host-associated],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -406,22 +410,27 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -483,8 +492,3 @@ URI: [mixs.vocab:Host-associatedMIMAG](https://w3id.org/mixs/vocab/Host-associat * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimarksC.md b/mixs6/Host-associatedMimarksC.md deleted file mode 100644 index 5e96e37d..00000000 --- a/mixs6/Host-associatedMimarksC.md +++ /dev/null @@ -1,375 +0,0 @@ - -# Class: Host-associatedMimarksC - - -Combinatorial checklist for host-associated with mimarks_c - -URI: [mixs.vocab:Host-associatedMimarksC](https://w3id.org/mixs/vocab/Host-associatedMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Host-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Host-associated]^-[Host-associatedMimarksC],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMimarksS.md b/mixs6/Host-associatedMimarksS.md deleted file mode 100644 index 415226b3..00000000 --- a/mixs6/Host-associatedMimarksS.md +++ /dev/null @@ -1,395 +0,0 @@ - -# Class: Host-associatedMimarksS - - -Combinatorial checklist for host-associated with mimarks_s - -URI: [mixs.vocab:Host-associatedMimarksS](https://w3id.org/mixs/vocab/Host-associatedMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Host-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Host-associated]^-[Host-associatedMimarksS],[Host-associated]) - -## Parents - - * is_a: [Host-associated](Host-associated.md) - host-associated - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from host-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravidity](gravidity.md) OPT - * Description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used - * range: [String](types/String.md) - * Example: yes;due date:2018-05-11 None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_blood_press_diast](host_blood_press_diast.md) OPT - * Description: Resting diastolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_blood_press_syst](host_blood_press_syst.md) OPT - * Description: Resting systolic blood pressure, measured as mm mercury - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [host_body_habitat](host_body_habitat.md) OPT - * Description: Original body habitat where the sample was obtained from - * range: [String](types/String.md) - * Example: nasopharynx None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_color](host_color.md) OPT - * Description: The color of host - * range: [String](types/String.md) - * Example: None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_growth_cond](host_growth_cond.md) OPT - * Description: Literature reference giving growth conditions of the host - * range: [String](types/String.md) - * Example: https://academic.oup.com/icesjms/article/68/2/349/617247 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_shape](host_shape.md) OPT - * Description: Morphological shape of host - * range: [String](types/String.md) - * Example: round None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_substrate](host_substrate.md) OPT - * Description: The growth substrate of the host - * range: [String](types/String.md) - * Example: rock None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMisag.md b/mixs6/Host-associatedMisag.md index 7ed6c9cd..26f60b0a 100644 --- a/mixs6/Host-associatedMisag.md +++ b/mixs6/Host-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Host-associated]^-[Host-associatedMISAG],[Host-associated],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Host-associated]^-[Host-associatedMISAG],[Host-associated],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -386,22 +390,27 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -488,8 +497,3 @@ URI: [mixs.vocab:Host-associatedMISAG](https://w3id.org/mixs/vocab/Host-associat * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Host-associatedMiuvig.md b/mixs6/Host-associatedMiuvig.md index 4fe1924c..8186d515 100644 --- a/mixs6/Host-associatedMiuvig.md +++ b/mixs6/Host-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Host-associated]^-[Host-associatedMIUVIG],[Host-associated],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Host-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;ances_data(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;genetic_mod(i):string%20%3F;host_common_name(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;host_taxid(i):string%20%3F;host_subject_id(i):string%20%3F;host_life_stage(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;chem_administration(i):string%20%3F;host_body_habitat(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_growth_cond(i):string%20%3F;host_substrate(i):string%20%3F;host_family_relationship(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;host_color(i):string%20%3F;host_shape(i):string%20%3F;gravidity(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Host-associated]^-[Host-associatedMIUVIG],[Host-associated],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa ### Inherited from host-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -31,7 +31,7 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa * range: [String](types/String.md) * Example: A/3*B None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [chem_administration](chem_administration.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -178,6 +178,10 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa * Description: The growth substrate of the host * range: [String](types/String.md) * Example: rock None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -212,7 +216,7 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -426,22 +430,27 @@ URI: [mixs.vocab:Host-associatedMIUVIG](https://w3id.org/mixs/vocab/Host-associa ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/HostPredApprEnum.md b/mixs6/HostPredApprEnum.md new file mode 100644 index 00000000..6c853164 --- /dev/null +++ b/mixs6/HostPredApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: host_pred_appr_enum + + + + +URI: [mixs.vocab:host_pred_appr_enum](https://w3id.org/mixs/vocab/host_pred_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/HostSexEnum.md b/mixs6/HostSexEnum.md new file mode 100644 index 00000000..890f4a59 --- /dev/null +++ b/mixs6/HostSexEnum.md @@ -0,0 +1,19 @@ + +# Enum: host_sex_enum + + + + +URI: [mixs.vocab:host_sex_enum](https://w3id.org/mixs/vocab/host_sex_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Human-associated.md b/mixs6/Human-associated.md index de763b3e..eb50f697 100644 --- a/mixs6/Human-associated.md +++ b/mixs6/Human-associated.md @@ -7,7 +7,7 @@ human-associated URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG],[Human-associatedMISAG],[Human-associatedMIMARKSSurvey],[Human-associatedMIMARKSSpecimen],[Human-associatedMIMAG],[Human-associatedMIGSVirus],[Human-associatedMIGSPlant],[Human-associatedMIGSOrg],[Human-associatedMIGSEukaryote],[Human-associatedMIGSBacteria],[Human-associatedME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -49,10 +49,10 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -159,6 +159,10 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -171,6 +175,10 @@ URI: [mixs.vocab:Human-associated](https://w3id.org/mixs/vocab/Human-associated) * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMIGSBacteria.md b/mixs6/Human-associatedMIGSBacteria.md index 28105cf7..8f4f475d 100644 --- a/mixs6/Human-associatedMIGSBacteria.md +++ b/mixs6/Human-associatedMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human-associatedMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-associated]^-[Human-associatedMIGSBacteria],[Human-associated],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-associated]^-[Human-associatedMIGSBacteria],[Human-associated],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -417,22 +425,27 @@ URI: [mixs.vocab:Human-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Human ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Human-associatedMIGSEukaryote.md b/mixs6/Human-associatedMIGSEukaryote.md index 53b53776..4e5a9b22 100644 --- a/mixs6/Human-associatedMIGSEukaryote.md +++ b/mixs6/Human-associatedMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Human-associatedMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-associated]^-[Human-associatedMIGSEukaryote],[Human-associated],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-associated]^-[Human-associatedMIGSEukaryote],[Human-associated],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Huma ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Huma * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Huma * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Huma * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -417,22 +425,27 @@ URI: [mixs.vocab:Human-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Huma ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Human-associatedMIGSPlant.md b/mixs6/Human-associatedMIGSPlant.md index c6c2b181..00e67271 100644 --- a/mixs6/Human-associatedMIGSPlant.md +++ b/mixs6/Human-associatedMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-associatedMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-associated]^-[Human-associatedMIGSPlant],[Human-associated],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-associated]^-[Human-associatedMIGSPlant],[Human-associated],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-as ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-as * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-as * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-as * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -392,22 +400,27 @@ URI: [mixs.vocab:Human-associatedMIGSPlant](https://w3id.org/mixs/vocab/Human-as ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Human-associatedMIGSVirus.md b/mixs6/Human-associatedMIGSVirus.md index 307515c0..0f7274a4 100644 --- a/mixs6/Human-associatedMIGSVirus.md +++ b/mixs6/Human-associatedMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-associatedMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-associated]^-[Human-associatedMIGSVirus],[Human-associated],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-associated]^-[Human-associatedMIGSVirus],[Human-associated],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-as ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-as * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-as * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-as * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -412,22 +420,27 @@ URI: [mixs.vocab:Human-associatedMIGSVirus](https://w3id.org/mixs/vocab/Human-as ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Human-associatedMIMARKSSpecimen.md b/mixs6/Human-associatedMIMARKSSpecimen.md index 0bf183e9..52921041 100644 --- a/mixs6/Human-associatedMIMARKSSpecimen.md +++ b/mixs6/Human-associatedMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-associated]^-[Human-associatedMIMARKSSpecimen],[Human-associated],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-associated]^-[Human-associatedMIMARKSSpecimen],[Human-associated],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hu ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hu * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hu * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hu * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -347,22 +355,27 @@ URI: [mixs.vocab:Human-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Hu ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Human-associatedMIMARKSSurvey.md b/mixs6/Human-associatedMIMARKSSurvey.md index 5e7a87ce..ff7c67a3 100644 --- a/mixs6/Human-associatedMIMARKSSurvey.md +++ b/mixs6/Human-associatedMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-associatedMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-associated]^-[Human-associatedMIMARKSSurvey],[Human-associated],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-associated]^-[Human-associatedMIMARKSSurvey],[Human-associated],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Huma ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Huma * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Huma * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Huma * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -322,22 +330,27 @@ URI: [mixs.vocab:Human-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Huma ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Human-associatedMe.md b/mixs6/Human-associatedMe.md index d1899efa..e90fad30 100644 --- a/mixs6/Human-associatedMe.md +++ b/mixs6/Human-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-associated]^-[Human-associatedME],[Human-associated],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-associated]^-[Human-associatedME],[Human-associated],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associate ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associate * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associate * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associate * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -367,22 +375,27 @@ URI: [mixs.vocab:Human-associatedME](https://w3id.org/mixs/vocab/Human-associate ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Human-associatedMigsBa.md b/mixs6/Human-associatedMigsBa.md deleted file mode 100644 index f4e1f626..00000000 --- a/mixs6/Human-associatedMigsBa.md +++ /dev/null @@ -1,491 +0,0 @@ - -# Class: Human-associatedMigsBa - - -Combinatorial checklist for human-associated with migs_ba - -URI: [mixs.vocab:Human-associatedMigsBa](https://w3id.org/mixs/vocab/Human-associatedMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-associated]^-[Human-associatedMigsBa],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsEu.md b/mixs6/Human-associatedMigsEu.md deleted file mode 100644 index 69ac9b79..00000000 --- a/mixs6/Human-associatedMigsEu.md +++ /dev/null @@ -1,491 +0,0 @@ - -# Class: Human-associatedMigsEu - - -Combinatorial checklist for human-associated with migs_eu - -URI: [mixs.vocab:Human-associatedMigsEu](https://w3id.org/mixs/vocab/Human-associatedMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-associated]^-[Human-associatedMigsEu],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsOrg.md b/mixs6/Human-associatedMigsOrg.md index 72f24c92..670ff68f 100644 --- a/mixs6/Human-associatedMigsOrg.md +++ b/mixs6/Human-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-associated]^-[Human-associatedMIGSOrg],[Human-associated],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-associated]^-[Human-associatedMIGSOrg],[Human-associated],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-asso ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-asso * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-asso * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-asso * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -382,22 +390,27 @@ URI: [mixs.vocab:Human-associatedMIGSOrg](https://w3id.org/mixs/vocab/Human-asso ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Human-associatedMigsPl.md b/mixs6/Human-associatedMigsPl.md deleted file mode 100644 index a59c23a5..00000000 --- a/mixs6/Human-associatedMigsPl.md +++ /dev/null @@ -1,461 +0,0 @@ - -# Class: Human-associatedMigsPl - - -Combinatorial checklist for human-associated with migs_pl - -URI: [mixs.vocab:Human-associatedMigsPl](https://w3id.org/mixs/vocab/Human-associatedMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-associated]^-[Human-associatedMigsPl],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMigsVi.md b/mixs6/Human-associatedMigsVi.md deleted file mode 100644 index 5b3945a0..00000000 --- a/mixs6/Human-associatedMigsVi.md +++ /dev/null @@ -1,486 +0,0 @@ - -# Class: Human-associatedMigsVi - - -Combinatorial checklist for human-associated with migs_vi - -URI: [mixs.vocab:Human-associatedMigsVi](https://w3id.org/mixs/vocab/Human-associatedMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-associated]^-[Human-associatedMigsVi],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Human-associatedMimag.md b/mixs6/Human-associatedMimag.md index 89d666bc..096a8afa 100644 --- a/mixs6/Human-associatedMimag.md +++ b/mixs6/Human-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-associated]^-[Human-associatedMIMAG],[Human-associated],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-associated]^-[Human-associatedMIMAG],[Human-associated],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -422,22 +430,27 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -499,8 +512,3 @@ URI: [mixs.vocab:Human-associatedMIMAG](https://w3id.org/mixs/vocab/Human-associ * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimarksC.md b/mixs6/Human-associatedMimarksC.md deleted file mode 100644 index 5b10e12f..00000000 --- a/mixs6/Human-associatedMimarksC.md +++ /dev/null @@ -1,391 +0,0 @@ - -# Class: Human-associatedMimarksC - - -Combinatorial checklist for human-associated with mimarks_c - -URI: [mixs.vocab:Human-associatedMimarksC](https://w3id.org/mixs/vocab/Human-associatedMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-associated]^-[Human-associatedMimarksC],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMimarksS.md b/mixs6/Human-associatedMimarksS.md deleted file mode 100644 index 78f5d6d8..00000000 --- a/mixs6/Human-associatedMimarksS.md +++ /dev/null @@ -1,411 +0,0 @@ - -# Class: Human-associatedMimarksS - - -Combinatorial checklist for human-associated with mimarks_s - -URI: [mixs.vocab:Human-associatedMimarksS](https://w3id.org/mixs/vocab/Human-associatedMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-associated]^-[Human-associatedMimarksS],[Human-associated]) - -## Parents - - * is_a: [Human-associated](Human-associated.md) - human-associated - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from human-associated: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [amniotic_fluid_color](amniotic_fluid_color.md) OPT - * Description: Specification of the color of the amniotic fluid sample - * range: [String](types/String.md) - * Example: None - * [blood_blood_disord](blood_blood_disord.md) OPT - * Description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diet_last_six_month](diet_last_six_month.md) OPT - * Description: Specification of major diet changes in the last six months, if yes the change should be specified - * range: [String](types/String.md) - * Example: yes;vegetarian diet None - * [drug_usage](drug_usage.md) OPT - * Description: Any drug used by subject and the frequency of usage; can include multiple drugs used - * range: - * Example: Lipitor;2/day None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [foetal_health_stat](foetal_health_stat.md) OPT - * Description: Specification of foetal health status, should also include abortion - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gestation_state](gestation_state.md) OPT - * Description: Specification of the gestation state - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_hiv_stat](host_hiv_stat.md) OPT - * Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] - * range: [String](types/String.md) - * Example: yes;yes None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [maternal_health_stat](maternal_health_stat.md) OPT - * Description: Specification of the maternal health status - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_throat_disord](nose_throat_disord.md) OPT - * Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pet_farm_animal](pet_farm_animal.md) OPT - * Description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present - * range: [String](types/String.md) - * Example: yes; 5 cats None - * [pulmonary_disord](pulmonary_disord.md) OPT - * Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [smoker](smoker.md) OPT - * Description: Specification of smoking status - * range: [String](types/String.md) - * Example: yes None - * [study_complt_stat](study_complt_stat.md) OPT - * Description: Specification of study completion status, if no the reason should be specified - * range: - * Example: no;non-compliance None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [travel_out_six_month](travel_out_six_month.md) OPT - * Description: Specification of the countries travelled in the last six months; can include multiple travels - * range: [String](types/String.md) - * Example: None - * [twin_sibling](twin_sibling.md) OPT - * Description: Specification of twin sibling presence - * range: [String](types/String.md) - * Example: yes None - * [urine_collect_meth](urine_collect_meth.md) OPT - * Description: Specification of urine collection method - * range: [String](types/String.md) - * Example: catheter None - * [urogenit_tract_disor](urogenit_tract_disor.md) OPT - * Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - * [weight_loss_3_month](weight_loss_3_month.md) OPT - * Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss - * range: [String](types/String.md) - * Example: yes;5 kilogram None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMisag.md b/mixs6/Human-associatedMisag.md index 5082bd1b..51557f35 100644 --- a/mixs6/Human-associatedMisag.md +++ b/mixs6/Human-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-associated]^-[Human-associatedMISAG],[Human-associated],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-associated]^-[Human-associatedMISAG],[Human-associated],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -402,22 +410,27 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -504,8 +517,3 @@ URI: [mixs.vocab:Human-associatedMISAG](https://w3id.org/mixs/vocab/Human-associ * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-associatedMiuvig.md b/mixs6/Human-associatedMiuvig.md index c3e9f591..3917a641 100644 --- a/mixs6/Human-associatedMiuvig.md +++ b/mixs6/Human-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-associated]^-[Human-associatedMIUVIG],[Human-associated],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;smoker(i):string%20%3F;host_hiv_stat(i):string%20%3F;drug_usage(i):drug_usage_enum%20%3F;diet_last_six_month(i):string%20%3F;weight_loss_3_month(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;pet_farm_animal(i):string%20%3F;travel_out_six_month(i):string%20%3F;twin_sibling(i):string%20%3F;medic_hist_perform(i):string%20%3F;study_complt_stat(i):study_complt_stat_enum%20%3F;pulmonary_disord(i):string%20%3F;nose_throat_disord(i):string%20%3F;blood_blood_disord(i):string%20%3F;gestation_state(i):string%20%3F;maternal_health_stat(i):string%20%3F;foetal_health_stat(i):string%20%3F;amniotic_fluid_color(i):string%20%3F;kidney_disord(i):string%20%3F;urogenit_tract_disor(i):string%20%3F;urine_collect_meth(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-associated]^-[Human-associatedMIUVIG],[Human-associated],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-assoc ### Inherited from human-associated: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [amniotic_fluid_color](amniotic_fluid_color.md) OPT @@ -40,10 +40,10 @@ URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-assoc * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diet_last_six_month](diet_last_six_month.md) OPT @@ -150,6 +150,10 @@ URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-assoc * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -162,6 +166,10 @@ URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-assoc * Description: Can include multiple medication codes * range: [String](types/String.md) * Example: 810 None + * [kidney_disord](kidney_disord.md) OPT + * Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + * range: [String](types/String.md) + * Example: None * [lat_lon](lat_lon.md) OPT * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * range: [String](types/String.md) @@ -442,22 +450,27 @@ URI: [mixs.vocab:Human-associatedMIUVIG](https://w3id.org/mixs/vocab/Human-assoc ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Human-gut.md b/mixs6/Human-gut.md index fb95a39c..c1e67896 100644 --- a/mixs6/Human-gut.md +++ b/mixs6/Human-gut.md @@ -7,7 +7,7 @@ human-gut URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG],[Human-gutMISAG],[Human-gutMIMARKSSurvey],[Human-gutMIMARKSSpecimen],[Human-gutMIMAG],[Human-gutMIGSVirus],[Human-gutMIGSPlant],[Human-gutMIGSOrg],[Human-gutMIGSEukaryote],[Human-gutMIGSBacteria],[Human-gutME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -41,10 +41,10 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -135,6 +135,10 @@ URI: [mixs.vocab:Human-gut](https://w3id.org/mixs/vocab/Human-gut) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) diff --git a/mixs6/Human-gutMIGSBacteria.md b/mixs6/Human-gutMIGSBacteria.md index fc5d3cd4..91028283 100644 --- a/mixs6/Human-gutMIGSBacteria.md +++ b/mixs6/Human-gutMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-gut]^-[Human-gutMIGSBacteria],[Human-gut],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-gut]^-[Human-gutMIGSBacteria],[Human-gut],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIG ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIG * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIG * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -357,22 +361,27 @@ URI: [mixs.vocab:Human-gutMIGSBacteria](https://w3id.org/mixs/vocab/Human-gutMIG ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Human-gutMIGSEukaryote.md b/mixs6/Human-gutMIGSEukaryote.md index 595740be..e716259e 100644 --- a/mixs6/Human-gutMIGSEukaryote.md +++ b/mixs6/Human-gutMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-gut]^-[Human-gutMIGSEukaryote],[Human-gut],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-gut]^-[Human-gutMIGSEukaryote],[Human-gut],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMI ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMI * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMI * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -357,22 +361,27 @@ URI: [mixs.vocab:Human-gutMIGSEukaryote](https://w3id.org/mixs/vocab/Human-gutMI ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Human-gutMIGSPlant.md b/mixs6/Human-gutMIGSPlant.md index c82bf631..52024785 100644 --- a/mixs6/Human-gutMIGSPlant.md +++ b/mixs6/Human-gutMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-gut]^-[Human-gutMIGSPlant],[Human-gut],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-gut]^-[Human-gutMIGSPlant],[Human-gut],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPl ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPl * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPl * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -332,22 +336,27 @@ URI: [mixs.vocab:Human-gutMIGSPlant](https://w3id.org/mixs/vocab/Human-gutMIGSPl ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Human-gutMIGSVirus.md b/mixs6/Human-gutMIGSVirus.md index 9b3d9077..56c17587 100644 --- a/mixs6/Human-gutMIGSVirus.md +++ b/mixs6/Human-gutMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-gut]^-[Human-gutMIGSVirus],[Human-gut],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-gut]^-[Human-gutMIGSVirus],[Human-gut],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVi ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVi * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVi * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -352,22 +356,27 @@ URI: [mixs.vocab:Human-gutMIGSVirus](https://w3id.org/mixs/vocab/Human-gutMIGSVi ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Human-gutMIMARKSSpecimen.md b/mixs6/Human-gutMIMARKSSpecimen.md index 3cb70198..7c6fb2ae 100644 --- a/mixs6/Human-gutMIMARKSSpecimen.md +++ b/mixs6/Human-gutMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gutMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-gut]^-[Human-gutMIMARKSSpecimen],[Human-gut],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-gut]^-[Human-gutMIMARKSSpecimen],[Human-gut],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gut ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gut * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gut * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -287,22 +291,27 @@ URI: [mixs.vocab:Human-gutMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-gut ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Human-gutMIMARKSSurvey.md b/mixs6/Human-gutMIMARKSSurvey.md index 1e3d22bb..f9ff5f5f 100644 --- a/mixs6/Human-gutMIMARKSSurvey.md +++ b/mixs6/Human-gutMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-gut]^-[Human-gutMIMARKSSurvey],[Human-gut],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-gut]^-[Human-gutMIMARKSSurvey],[Human-gut],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMI ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMI * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMI * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -262,22 +266,27 @@ URI: [mixs.vocab:Human-gutMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-gutMI ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Human-gutMe.md b/mixs6/Human-gutMe.md index 495caf06..45316412 100644 --- a/mixs6/Human-gutMe.md +++ b/mixs6/Human-gutMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-gut]^-[Human-gutME],[Human-gut],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-gut]^-[Human-gutME],[Human-gut],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -307,22 +311,27 @@ URI: [mixs.vocab:Human-gutME](https://w3id.org/mixs/vocab/Human-gutME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Human-gutMigsBa.md b/mixs6/Human-gutMigsBa.md deleted file mode 100644 index 6cb96bd3..00000000 --- a/mixs6/Human-gutMigsBa.md +++ /dev/null @@ -1,431 +0,0 @@ - -# Class: Human-gutMigsBa - - -Combinatorial checklist for human-gut with migs_ba - -URI: [mixs.vocab:Human-gutMigsBa](https://w3id.org/mixs/vocab/Human-gutMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-gutMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-gut]^-[Human-gutMigsBa],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsEu.md b/mixs6/Human-gutMigsEu.md deleted file mode 100644 index b9ef44b5..00000000 --- a/mixs6/Human-gutMigsEu.md +++ /dev/null @@ -1,431 +0,0 @@ - -# Class: Human-gutMigsEu - - -Combinatorial checklist for human-gut with migs_eu - -URI: [mixs.vocab:Human-gutMigsEu](https://w3id.org/mixs/vocab/Human-gutMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-gutMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-gut]^-[Human-gutMigsEu],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsOrg.md b/mixs6/Human-gutMigsOrg.md index fd219851..ddcf75d7 100644 --- a/mixs6/Human-gutMigsOrg.md +++ b/mixs6/Human-gutMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-gut]^-[Human-gutMIGSOrg],[Human-gut],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-gut]^-[Human-gutMIGSOrg],[Human-gut],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -322,22 +326,27 @@ URI: [mixs.vocab:Human-gutMIGSOrg](https://w3id.org/mixs/vocab/Human-gutMIGSOrg) ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Human-gutMigsPl.md b/mixs6/Human-gutMigsPl.md deleted file mode 100644 index 3d56e081..00000000 --- a/mixs6/Human-gutMigsPl.md +++ /dev/null @@ -1,401 +0,0 @@ - -# Class: Human-gutMigsPl - - -Combinatorial checklist for human-gut with migs_pl - -URI: [mixs.vocab:Human-gutMigsPl](https://w3id.org/mixs/vocab/Human-gutMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-gutMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-gut]^-[Human-gutMigsPl],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMigsVi.md b/mixs6/Human-gutMigsVi.md deleted file mode 100644 index cc6888a7..00000000 --- a/mixs6/Human-gutMigsVi.md +++ /dev/null @@ -1,426 +0,0 @@ - -# Class: Human-gutMigsVi - - -Combinatorial checklist for human-gut with migs_vi - -URI: [mixs.vocab:Human-gutMigsVi](https://w3id.org/mixs/vocab/Human-gutMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-gutMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-gut]^-[Human-gutMigsVi],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Human-gutMimag.md b/mixs6/Human-gutMimag.md index bf877e07..1290868f 100644 --- a/mixs6/Human-gutMimag.md +++ b/mixs6/Human-gutMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-gut]^-[Human-gutMIMAG],[Human-gut],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-gut]^-[Human-gutMIMAG],[Human-gut],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -362,22 +366,27 @@ URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -439,8 +448,3 @@ URI: [mixs.vocab:Human-gutMIMAG](https://w3id.org/mixs/vocab/Human-gutMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimarksC.md b/mixs6/Human-gutMimarksC.md deleted file mode 100644 index cdbb39ad..00000000 --- a/mixs6/Human-gutMimarksC.md +++ /dev/null @@ -1,331 +0,0 @@ - -# Class: Human-gutMimarksC - - -Combinatorial checklist for human-gut with mimarks_c - -URI: [mixs.vocab:Human-gutMimarksC](https://w3id.org/mixs/vocab/Human-gutMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-gutMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-gut]^-[Human-gutMimarksC],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMimarksS.md b/mixs6/Human-gutMimarksS.md deleted file mode 100644 index 3082b52d..00000000 --- a/mixs6/Human-gutMimarksS.md +++ /dev/null @@ -1,351 +0,0 @@ - -# Class: Human-gutMimarksS - - -Combinatorial checklist for human-gut with mimarks_s - -URI: [mixs.vocab:Human-gutMimarksS](https://w3id.org/mixs/vocab/Human-gutMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-gutMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-gut]^-[Human-gutMimarksS],[Human-gut]) - -## Parents - - * is_a: [Human-gut](Human-gut.md) - human-gut - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from human-gut: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gastrointest_disord](gastrointest_disord.md) OPT - * Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [liver_disord](liver_disord.md) OPT - * Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). - * range: [String](types/String.md) - * Example: None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [special_diet](special_diet.md) OPT - * Description: Specification of special diet; can include multiple special diets - * range: - * Example: other:vegan None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMisag.md b/mixs6/Human-gutMisag.md index 55ed35a9..26adb92d 100644 --- a/mixs6/Human-gutMisag.md +++ b/mixs6/Human-gutMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-gut]^-[Human-gutMISAG],[Human-gut],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-gut]^-[Human-gutMISAG],[Human-gut],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -342,22 +346,27 @@ URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -444,8 +453,3 @@ URI: [mixs.vocab:Human-gutMISAG](https://w3id.org/mixs/vocab/Human-gutMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-gutMiuvig.md b/mixs6/Human-gutMiuvig.md index d425d6a3..3d6f8aab 100644 --- a/mixs6/Human-gutMiuvig.md +++ b/mixs6/Human-gutMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-gut]^-[Human-gutMIUVIG],[Human-gut],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-gutMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;gastrointest_disord(i):string%20%3F;liver_disord(i):string%20%3F;special_diet(i):special_diet_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-gut]^-[Human-gutMIUVIG],[Human-gut],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) ### Inherited from human-gut: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -126,6 +126,10 @@ URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -382,22 +386,27 @@ URI: [mixs.vocab:Human-gutMIUVIG](https://w3id.org/mixs/vocab/Human-gutMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Human-oral.md b/mixs6/Human-oral.md index 494084b7..c1f87f0e 100644 --- a/mixs6/Human-oral.md +++ b/mixs6/Human-oral.md @@ -7,7 +7,7 @@ human-oral URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG],[Human-oralMISAG],[Human-oralMIMARKSSurvey],[Human-oralMIMARKSSpecimen],[Human-oralMIMAG],[Human-oralMIGSVirus],[Human-oralMIGSPlant],[Human-oralMIGSOrg],[Human-oralMIGSEukaryote],[Human-oralMIGSBacteria],[Human-oralME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -41,10 +41,10 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -131,6 +131,10 @@ URI: [mixs.vocab:Human-oral](https://w3id.org/mixs/vocab/Human-oral) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) diff --git a/mixs6/Human-oralMIGSBacteria.md b/mixs6/Human-oralMIGSBacteria.md index 165fc89b..46bf8fc4 100644 --- a/mixs6/Human-oralMIGSBacteria.md +++ b/mixs6/Human-oralMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-oral]^-[Human-oralMIGSBacteria],[Human-oral],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-oral]^-[Human-oralMIGSBacteria],[Human-oral],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralM ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralM * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralM * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -353,22 +357,27 @@ URI: [mixs.vocab:Human-oralMIGSBacteria](https://w3id.org/mixs/vocab/Human-oralM ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Human-oralMIGSEukaryote.md b/mixs6/Human-oralMIGSEukaryote.md index d86053cc..bb30d3d2 100644 --- a/mixs6/Human-oralMIGSEukaryote.md +++ b/mixs6/Human-oralMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oralMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-oral]^-[Human-oralMIGSEukaryote],[Human-oral],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-oral]^-[Human-oralMIGSEukaryote],[Human-oral],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oral ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oral * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oral * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -353,22 +357,27 @@ URI: [mixs.vocab:Human-oralMIGSEukaryote](https://w3id.org/mixs/vocab/Human-oral ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Human-oralMIGSPlant.md b/mixs6/Human-oralMIGSPlant.md index 057ef81f..e59b706e 100644 --- a/mixs6/Human-oralMIGSPlant.md +++ b/mixs6/Human-oralMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-oral]^-[Human-oralMIGSPlant],[Human-oral],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-oral]^-[Human-oralMIGSPlant],[Human-oral],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGS ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGS * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -328,22 +332,27 @@ URI: [mixs.vocab:Human-oralMIGSPlant](https://w3id.org/mixs/vocab/Human-oralMIGS ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Human-oralMIGSVirus.md b/mixs6/Human-oralMIGSVirus.md index 6e6be11b..13edcace 100644 --- a/mixs6/Human-oralMIGSVirus.md +++ b/mixs6/Human-oralMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-oral]^-[Human-oralMIGSVirus],[Human-oral],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-oral]^-[Human-oralMIGSVirus],[Human-oral],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGS ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGS * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -348,22 +352,27 @@ URI: [mixs.vocab:Human-oralMIGSVirus](https://w3id.org/mixs/vocab/Human-oralMIGS ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Human-oralMIMARKSSpecimen.md b/mixs6/Human-oralMIMARKSSpecimen.md index b7f7c8ff..0aa0b8af 100644 --- a/mixs6/Human-oralMIMARKSSpecimen.md +++ b/mixs6/Human-oralMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-oralMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-oral]^-[Human-oralMIMARKSSpecimen],[Human-oral],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-oral]^-[Human-oralMIMARKSSpecimen],[Human-oral],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-or ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-or * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-or * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -283,22 +287,27 @@ URI: [mixs.vocab:Human-oralMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-or ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Human-oralMIMARKSSurvey.md b/mixs6/Human-oralMIMARKSSurvey.md index d593eb7e..959f5e45 100644 --- a/mixs6/Human-oralMIMARKSSurvey.md +++ b/mixs6/Human-oralMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oralMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-oral]^-[Human-oralMIMARKSSurvey],[Human-oral],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-oral]^-[Human-oralMIMARKSSurvey],[Human-oral],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oral ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oral * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oral * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -258,22 +262,27 @@ URI: [mixs.vocab:Human-oralMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-oral ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Human-oralMe.md b/mixs6/Human-oralMe.md index dc681564..1cc994ff 100644 --- a/mixs6/Human-oralMe.md +++ b/mixs6/Human-oralMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-oral]^-[Human-oralME],[Human-oral],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-oral]^-[Human-oralME],[Human-oral],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -303,22 +307,27 @@ URI: [mixs.vocab:Human-oralME](https://w3id.org/mixs/vocab/Human-oralME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Human-oralMigsBa.md b/mixs6/Human-oralMigsBa.md deleted file mode 100644 index 3c4e251e..00000000 --- a/mixs6/Human-oralMigsBa.md +++ /dev/null @@ -1,427 +0,0 @@ - -# Class: Human-oralMigsBa - - -Combinatorial checklist for human-oral with migs_ba - -URI: [mixs.vocab:Human-oralMigsBa](https://w3id.org/mixs/vocab/Human-oralMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-oralMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-oral]^-[Human-oralMigsBa],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsEu.md b/mixs6/Human-oralMigsEu.md deleted file mode 100644 index f40bb0c9..00000000 --- a/mixs6/Human-oralMigsEu.md +++ /dev/null @@ -1,427 +0,0 @@ - -# Class: Human-oralMigsEu - - -Combinatorial checklist for human-oral with migs_eu - -URI: [mixs.vocab:Human-oralMigsEu](https://w3id.org/mixs/vocab/Human-oralMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-oralMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-oral]^-[Human-oralMigsEu],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsOrg.md b/mixs6/Human-oralMigsOrg.md index 238fac59..f2f43fb2 100644 --- a/mixs6/Human-oralMigsOrg.md +++ b/mixs6/Human-oralMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-oral]^-[Human-oralMIGSOrg],[Human-oral],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-oral]^-[Human-oralMIGSOrg],[Human-oral],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOr ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOr * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOr * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -318,22 +322,27 @@ URI: [mixs.vocab:Human-oralMIGSOrg](https://w3id.org/mixs/vocab/Human-oralMIGSOr ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Human-oralMigsPl.md b/mixs6/Human-oralMigsPl.md deleted file mode 100644 index d72c77be..00000000 --- a/mixs6/Human-oralMigsPl.md +++ /dev/null @@ -1,397 +0,0 @@ - -# Class: Human-oralMigsPl - - -Combinatorial checklist for human-oral with migs_pl - -URI: [mixs.vocab:Human-oralMigsPl](https://w3id.org/mixs/vocab/Human-oralMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-oralMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-oral]^-[Human-oralMigsPl],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMigsVi.md b/mixs6/Human-oralMigsVi.md deleted file mode 100644 index 211f81ac..00000000 --- a/mixs6/Human-oralMigsVi.md +++ /dev/null @@ -1,422 +0,0 @@ - -# Class: Human-oralMigsVi - - -Combinatorial checklist for human-oral with migs_vi - -URI: [mixs.vocab:Human-oralMigsVi](https://w3id.org/mixs/vocab/Human-oralMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-oralMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-oral]^-[Human-oralMigsVi],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Human-oralMimag.md b/mixs6/Human-oralMimag.md index e742203b..0b284360 100644 --- a/mixs6/Human-oralMimag.md +++ b/mixs6/Human-oralMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-oral]^-[Human-oralMIMAG],[Human-oral],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-oral]^-[Human-oralMIMAG],[Human-oral],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -358,22 +362,27 @@ URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -435,8 +444,3 @@ URI: [mixs.vocab:Human-oralMIMAG](https://w3id.org/mixs/vocab/Human-oralMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimarksC.md b/mixs6/Human-oralMimarksC.md deleted file mode 100644 index 7b9b2f58..00000000 --- a/mixs6/Human-oralMimarksC.md +++ /dev/null @@ -1,327 +0,0 @@ - -# Class: Human-oralMimarksC - - -Combinatorial checklist for human-oral with mimarks_c - -URI: [mixs.vocab:Human-oralMimarksC](https://w3id.org/mixs/vocab/Human-oralMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-oralMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-oral]^-[Human-oralMimarksC],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMimarksS.md b/mixs6/Human-oralMimarksS.md deleted file mode 100644 index 7eb12e84..00000000 --- a/mixs6/Human-oralMimarksS.md +++ /dev/null @@ -1,347 +0,0 @@ - -# Class: Human-oralMimarksS - - -Combinatorial checklist for human-oral with mimarks_s - -URI: [mixs.vocab:Human-oralMimarksS](https://w3id.org/mixs/vocab/Human-oralMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-oralMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-oral]^-[Human-oralMimarksS],[Human-oral]) - -## Parents - - * is_a: [Human-oral](Human-oral.md) - human-oral - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from human-oral: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nose_mouth_teeth_throat_disord](nose_mouth_teeth_throat_disord.md) OPT - * Description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_last_toothbrush](time_last_toothbrush.md) OPT - * Description: Specification of the time since last toothbrushing - * range: [String](types/String.md) - * Example: P2H45M None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMisag.md b/mixs6/Human-oralMisag.md index 52b2b00c..12a6c368 100644 --- a/mixs6/Human-oralMisag.md +++ b/mixs6/Human-oralMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-oral]^-[Human-oralMISAG],[Human-oral],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-oral]^-[Human-oralMISAG],[Human-oral],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -338,22 +342,27 @@ URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -440,8 +449,3 @@ URI: [mixs.vocab:Human-oralMISAG](https://w3id.org/mixs/vocab/Human-oralMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-oralMiuvig.md b/mixs6/Human-oralMiuvig.md index 1b4e2fc8..ed3bbd35 100644 --- a/mixs6/Human-oralMiuvig.md +++ b/mixs6/Human-oralMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-oral]^-[Human-oralMIUVIG],[Human-oral],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-oralMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;nose_mouth_teeth_throat_disord(i):string%20%3F;time_last_toothbrush(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-oral]^-[Human-oralMIUVIG],[Human-oral],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) ### Inherited from human-oral: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -122,6 +122,10 @@ URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -378,22 +382,27 @@ URI: [mixs.vocab:Human-oralMIUVIG](https://w3id.org/mixs/vocab/Human-oralMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Human-skin.md b/mixs6/Human-skin.md index ea8f4915..e4b1060c 100644 --- a/mixs6/Human-skin.md +++ b/mixs6/Human-skin.md @@ -7,7 +7,7 @@ human-skin URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG],[Human-skinMISAG],[Human-skinMIMARKSSurvey],[Human-skinMIMARKSSpecimen],[Human-skinMIMAG],[Human-skinMIGSVirus],[Human-skinMIGSPlant],[Human-skinMIGSOrg],[Human-skinMIGSEukaryote],[Human-skinMIGSBacteria],[Human-skinME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -41,10 +41,10 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -139,6 +139,10 @@ URI: [mixs.vocab:Human-skin](https://w3id.org/mixs/vocab/Human-skin) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) diff --git a/mixs6/Human-skinMIGSBacteria.md b/mixs6/Human-skinMIGSBacteria.md index 84d3c471..10572bf0 100644 --- a/mixs6/Human-skinMIGSBacteria.md +++ b/mixs6/Human-skinMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-skin]^-[Human-skinMIGSBacteria],[Human-skin],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-skin]^-[Human-skinMIGSBacteria],[Human-skin],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinM ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinM * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinM * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -357,22 +361,27 @@ URI: [mixs.vocab:Human-skinMIGSBacteria](https://w3id.org/mixs/vocab/Human-skinM ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Human-skinMIGSEukaryote.md b/mixs6/Human-skinMIGSEukaryote.md index d01d6c01..3fac3d8a 100644 --- a/mixs6/Human-skinMIGSEukaryote.md +++ b/mixs6/Human-skinMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skinMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-skin]^-[Human-skinMIGSEukaryote],[Human-skin],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-skin]^-[Human-skinMIGSEukaryote],[Human-skin],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skin ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skin * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skin * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -357,22 +361,27 @@ URI: [mixs.vocab:Human-skinMIGSEukaryote](https://w3id.org/mixs/vocab/Human-skin ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Human-skinMIGSPlant.md b/mixs6/Human-skinMIGSPlant.md index c03995ac..58b7ffbd 100644 --- a/mixs6/Human-skinMIGSPlant.md +++ b/mixs6/Human-skinMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-skin]^-[Human-skinMIGSPlant],[Human-skin],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-skin]^-[Human-skinMIGSPlant],[Human-skin],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGS ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGS * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -332,22 +336,27 @@ URI: [mixs.vocab:Human-skinMIGSPlant](https://w3id.org/mixs/vocab/Human-skinMIGS ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Human-skinMIGSVirus.md b/mixs6/Human-skinMIGSVirus.md index 254b1110..be0e0604 100644 --- a/mixs6/Human-skinMIGSVirus.md +++ b/mixs6/Human-skinMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-skin]^-[Human-skinMIGSVirus],[Human-skin],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-skin]^-[Human-skinMIGSVirus],[Human-skin],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGS ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGS * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGS * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -352,22 +356,27 @@ URI: [mixs.vocab:Human-skinMIGSVirus](https://w3id.org/mixs/vocab/Human-skinMIGS ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Human-skinMIMARKSSpecimen.md b/mixs6/Human-skinMIMARKSSpecimen.md index a8ba6df6..2794412e 100644 --- a/mixs6/Human-skinMIMARKSSpecimen.md +++ b/mixs6/Human-skinMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-skinMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-skin]^-[Human-skinMIMARKSSpecimen],[Human-skin],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-skin]^-[Human-skinMIMARKSSpecimen],[Human-skin],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-sk ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-sk * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-sk * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -287,22 +291,27 @@ URI: [mixs.vocab:Human-skinMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-sk ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Human-skinMIMARKSSurvey.md b/mixs6/Human-skinMIMARKSSurvey.md index c1172644..b4b0ee30 100644 --- a/mixs6/Human-skinMIMARKSSurvey.md +++ b/mixs6/Human-skinMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skinMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-skin]^-[Human-skinMIMARKSSurvey],[Human-skin],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-skin]^-[Human-skinMIMARKSSurvey],[Human-skin],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skin ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skin * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skin * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -262,22 +266,27 @@ URI: [mixs.vocab:Human-skinMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-skin ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Human-skinMe.md b/mixs6/Human-skinMe.md index 37d87ed5..264dd4ec 100644 --- a/mixs6/Human-skinMe.md +++ b/mixs6/Human-skinMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-skin]^-[Human-skinME],[Human-skin],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-skin]^-[Human-skinME],[Human-skin],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -307,22 +311,27 @@ URI: [mixs.vocab:Human-skinME](https://w3id.org/mixs/vocab/Human-skinME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Human-skinMigsBa.md b/mixs6/Human-skinMigsBa.md deleted file mode 100644 index ecf26c74..00000000 --- a/mixs6/Human-skinMigsBa.md +++ /dev/null @@ -1,431 +0,0 @@ - -# Class: Human-skinMigsBa - - -Combinatorial checklist for human-skin with migs_ba - -URI: [mixs.vocab:Human-skinMigsBa](https://w3id.org/mixs/vocab/Human-skinMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-skinMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-skin]^-[Human-skinMigsBa],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsEu.md b/mixs6/Human-skinMigsEu.md deleted file mode 100644 index 775aaeb8..00000000 --- a/mixs6/Human-skinMigsEu.md +++ /dev/null @@ -1,431 +0,0 @@ - -# Class: Human-skinMigsEu - - -Combinatorial checklist for human-skin with migs_eu - -URI: [mixs.vocab:Human-skinMigsEu](https://w3id.org/mixs/vocab/Human-skinMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-skinMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-skin]^-[Human-skinMigsEu],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsOrg.md b/mixs6/Human-skinMigsOrg.md index 9ffda114..f32997ec 100644 --- a/mixs6/Human-skinMigsOrg.md +++ b/mixs6/Human-skinMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-skin]^-[Human-skinMIGSOrg],[Human-skin],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-skin]^-[Human-skinMIGSOrg],[Human-skin],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOr ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOr * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOr * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -322,22 +326,27 @@ URI: [mixs.vocab:Human-skinMIGSOrg](https://w3id.org/mixs/vocab/Human-skinMIGSOr ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Human-skinMigsPl.md b/mixs6/Human-skinMigsPl.md deleted file mode 100644 index fdb939cc..00000000 --- a/mixs6/Human-skinMigsPl.md +++ /dev/null @@ -1,401 +0,0 @@ - -# Class: Human-skinMigsPl - - -Combinatorial checklist for human-skin with migs_pl - -URI: [mixs.vocab:Human-skinMigsPl](https://w3id.org/mixs/vocab/Human-skinMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-skinMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-skin]^-[Human-skinMigsPl],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMigsVi.md b/mixs6/Human-skinMigsVi.md deleted file mode 100644 index f7cf4a4c..00000000 --- a/mixs6/Human-skinMigsVi.md +++ /dev/null @@ -1,426 +0,0 @@ - -# Class: Human-skinMigsVi - - -Combinatorial checklist for human-skin with migs_vi - -URI: [mixs.vocab:Human-skinMigsVi](https://w3id.org/mixs/vocab/Human-skinMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-skinMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-skin]^-[Human-skinMigsVi],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Human-skinMimag.md b/mixs6/Human-skinMimag.md index be36689d..3f44e568 100644 --- a/mixs6/Human-skinMimag.md +++ b/mixs6/Human-skinMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-skin]^-[Human-skinMIMAG],[Human-skin],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-skin]^-[Human-skinMIMAG],[Human-skin],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -362,22 +366,27 @@ URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -439,8 +448,3 @@ URI: [mixs.vocab:Human-skinMIMAG](https://w3id.org/mixs/vocab/Human-skinMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimarksC.md b/mixs6/Human-skinMimarksC.md deleted file mode 100644 index 1cde0bff..00000000 --- a/mixs6/Human-skinMimarksC.md +++ /dev/null @@ -1,331 +0,0 @@ - -# Class: Human-skinMimarksC - - -Combinatorial checklist for human-skin with mimarks_c - -URI: [mixs.vocab:Human-skinMimarksC](https://w3id.org/mixs/vocab/Human-skinMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-skinMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-skin]^-[Human-skinMimarksC],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMimarksS.md b/mixs6/Human-skinMimarksS.md deleted file mode 100644 index 7efef9fe..00000000 --- a/mixs6/Human-skinMimarksS.md +++ /dev/null @@ -1,351 +0,0 @@ - -# Class: Human-skinMimarksS - - -Combinatorial checklist for human-skin with mimarks_s - -URI: [mixs.vocab:Human-skinMimarksS](https://w3id.org/mixs/vocab/Human-skinMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-skinMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-skin]^-[Human-skinMimarksS],[Human-skin]) - -## Parents - - * is_a: [Human-skin](Human-skin.md) - human-skin - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from human-skin: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [dermatology_disord](dermatology_disord.md) OPT - * Description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). - * range: [String](types/String.md) - * Example: None - * [dominant_hand](dominant_hand.md) OPT - * Description: Dominant hand of the subject - * range: - * Example: right None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [time_since_last_wash](time_since_last_wash.md) OPT - * Description: Specification of the time since last wash - * range: [String](types/String.md) - * Example: P1D None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMisag.md b/mixs6/Human-skinMisag.md index 03a35d80..e49a32cf 100644 --- a/mixs6/Human-skinMisag.md +++ b/mixs6/Human-skinMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-skin]^-[Human-skinMISAG],[Human-skin],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-skin]^-[Human-skinMISAG],[Human-skin],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -342,22 +346,27 @@ URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -444,8 +453,3 @@ URI: [mixs.vocab:Human-skinMISAG](https://w3id.org/mixs/vocab/Human-skinMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-skinMiuvig.md b/mixs6/Human-skinMiuvig.md index 5a87a7bd..c0b07e9c 100644 --- a/mixs6/Human-skinMiuvig.md +++ b/mixs6/Human-skinMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-skin]^-[Human-skinMIUVIG],[Human-skin],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-skinMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;dermatology_disord(i):string%20%3F;time_since_last_wash(i):string%20%3F;dominant_hand(i):dominant_hand_enum%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-skin]^-[Human-skinMIUVIG],[Human-skin],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) ### Inherited from human-skin: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [chem_administration](chem_administration.md) OPT @@ -32,10 +32,10 @@ URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [dermatology_disord](dermatology_disord.md) OPT @@ -130,6 +130,10 @@ URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) @@ -382,22 +386,27 @@ URI: [mixs.vocab:Human-skinMIUVIG](https://w3id.org/mixs/vocab/Human-skinMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Human-vaginal.md b/mixs6/Human-vaginal.md index e1e8a7da..f4a6815c 100644 --- a/mixs6/Human-vaginal.md +++ b/mixs6/Human-vaginal.md @@ -7,7 +7,7 @@ human-vaginal URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG],[Human-vaginalMISAG],[Human-vaginalMIMARKSSurvey],[Human-vaginalMIMARKSSpecimen],[Human-vaginalMIMAG],[Human-vaginalMIGSVirus],[Human-vaginalMIGSPlant],[Human-vaginalMIGSOrg],[Human-vaginalMIGSEukaryote],[Human-vaginalMIGSBacteria],[Human-vaginalME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -45,15 +45,15 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -143,13 +143,17 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -173,11 +177,11 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -197,7 +201,7 @@ URI: [mixs.vocab:Human-vaginal](https://w3id.org/mixs/vocab/Human-vaginal) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater diff --git a/mixs6/Human-vaginalMIGSBacteria.md b/mixs6/Human-vaginalMIGSBacteria.md index 49605242..a1c1683c 100644 --- a/mixs6/Human-vaginalMIGSBacteria.md +++ b/mixs6/Human-vaginalMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-vaginalMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-vaginal]^-[Human-vaginalMIGSBacteria],[Human-vaginal],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Human-vaginal]^-[Human-vaginalMIGSBacteria],[Human-vaginal],[MIGSBacteria]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -385,22 +389,27 @@ URI: [mixs.vocab:Human-vaginalMIGSBacteria](https://w3id.org/mixs/vocab/Human-va ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Human-vaginalMIGSEukaryote.md b/mixs6/Human-vaginalMIGSEukaryote.md index ffc385cf..43feb6c8 100644 --- a/mixs6/Human-vaginalMIGSEukaryote.md +++ b/mixs6/Human-vaginalMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-vaginalMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-vaginal]^-[Human-vaginalMIGSEukaryote],[Human-vaginal],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Human-vaginal]^-[Human-vaginalMIGSEukaryote],[Human-vaginal],[MIGSEukaryote]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -385,22 +389,27 @@ URI: [mixs.vocab:Human-vaginalMIGSEukaryote](https://w3id.org/mixs/vocab/Human-v ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Human-vaginalMIGSPlant.md b/mixs6/Human-vaginalMIGSPlant.md index 1a14ee95..e4e194c1 100644 --- a/mixs6/Human-vaginalMIGSPlant.md +++ b/mixs6/Human-vaginalMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vaginalMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-vaginal]^-[Human-vaginalMIGSPlant],[Human-vaginal],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Human-vaginal]^-[Human-vaginalMIGSPlant],[Human-vaginal],[MIGSPlant]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -360,22 +364,27 @@ URI: [mixs.vocab:Human-vaginalMIGSPlant](https://w3id.org/mixs/vocab/Human-vagin ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Human-vaginalMIGSVirus.md b/mixs6/Human-vaginalMIGSVirus.md index 9721fc60..0b7797dd 100644 --- a/mixs6/Human-vaginalMIGSVirus.md +++ b/mixs6/Human-vaginalMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vaginalMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-vaginal]^-[Human-vaginalMIGSVirus],[Human-vaginal],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Human-vaginal]^-[Human-vaginalMIGSVirus],[Human-vaginal],[MIGSVirus]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -380,22 +384,27 @@ URI: [mixs.vocab:Human-vaginalMIGSVirus](https://w3id.org/mixs/vocab/Human-vagin ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Human-vaginalMIMARKSSpecimen.md b/mixs6/Human-vaginalMIMARKSSpecimen.md index 3fea70e3..ec40fba1 100644 --- a/mixs6/Human-vaginalMIMARKSSpecimen.md +++ b/mixs6/Human-vaginalMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-vaginal]^-[Human-vaginalMIMARKSSpecimen],[Human-vaginal],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Human-vaginal]^-[Human-vaginalMIMARKSSpecimen],[Human-vaginal],[MIMARKSSpecimen]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -315,22 +319,27 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSpecimen](https://w3id.org/mixs/vocab/Human ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Human-vaginalMIMARKSSurvey.md b/mixs6/Human-vaginalMIMARKSSurvey.md index c72d8a9d..dcb71676 100644 --- a/mixs6/Human-vaginalMIMARKSSurvey.md +++ b/mixs6/Human-vaginalMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-vaginalMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-vaginal]^-[Human-vaginalMIMARKSSurvey],[Human-vaginal],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Human-vaginal]^-[Human-vaginalMIMARKSSurvey],[Human-vaginal],[MIMARKSSurvey]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -290,22 +294,27 @@ URI: [mixs.vocab:Human-vaginalMIMARKSSurvey](https://w3id.org/mixs/vocab/Human-v ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Human-vaginalMe.md b/mixs6/Human-vaginalMe.md index e223eff2..9223b69e 100644 --- a/mixs6/Human-vaginalMe.md +++ b/mixs6/Human-vaginalMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-vaginal]^-[Human-vaginalME],[Human-vaginal],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Human-vaginal]^-[Human-vaginalME],[Human-vaginal],[ME]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -335,22 +339,27 @@ URI: [mixs.vocab:Human-vaginalME](https://w3id.org/mixs/vocab/Human-vaginalME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Human-vaginalMigsBa.md b/mixs6/Human-vaginalMigsBa.md deleted file mode 100644 index 96a70a1b..00000000 --- a/mixs6/Human-vaginalMigsBa.md +++ /dev/null @@ -1,459 +0,0 @@ - -# Class: Human-vaginalMigsBa - - -Combinatorial checklist for human-vaginal with migs_ba - -URI: [mixs.vocab:Human-vaginalMigsBa](https://w3id.org/mixs/vocab/Human-vaginalMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[Human-vaginalMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Human-vaginal]^-[Human-vaginalMigsBa],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsEu.md b/mixs6/Human-vaginalMigsEu.md deleted file mode 100644 index d3b1241e..00000000 --- a/mixs6/Human-vaginalMigsEu.md +++ /dev/null @@ -1,459 +0,0 @@ - -# Class: Human-vaginalMigsEu - - -Combinatorial checklist for human-vaginal with migs_eu - -URI: [mixs.vocab:Human-vaginalMigsEu](https://w3id.org/mixs/vocab/Human-vaginalMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[Human-vaginalMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Human-vaginal]^-[Human-vaginalMigsEu],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsOrg.md b/mixs6/Human-vaginalMigsOrg.md index 4a7b14a0..c26c49f9 100644 --- a/mixs6/Human-vaginalMigsOrg.md +++ b/mixs6/Human-vaginalMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginalMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-vaginal]^-[Human-vaginalMIGSOrg],[Human-vaginal],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Human-vaginal]^-[Human-vaginalMIGSOrg],[Human-vaginal],[MIGSOrg]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -350,22 +354,27 @@ URI: [mixs.vocab:Human-vaginalMIGSOrg](https://w3id.org/mixs/vocab/Human-vaginal ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Human-vaginalMigsPl.md b/mixs6/Human-vaginalMigsPl.md deleted file mode 100644 index 9a00bba3..00000000 --- a/mixs6/Human-vaginalMigsPl.md +++ /dev/null @@ -1,429 +0,0 @@ - -# Class: Human-vaginalMigsPl - - -Combinatorial checklist for human-vaginal with migs_pl - -URI: [mixs.vocab:Human-vaginalMigsPl](https://w3id.org/mixs/vocab/Human-vaginalMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[Human-vaginalMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Human-vaginal]^-[Human-vaginalMigsPl],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMigsVi.md b/mixs6/Human-vaginalMigsVi.md deleted file mode 100644 index 86c5abcc..00000000 --- a/mixs6/Human-vaginalMigsVi.md +++ /dev/null @@ -1,454 +0,0 @@ - -# Class: Human-vaginalMigsVi - - -Combinatorial checklist for human-vaginal with migs_vi - -URI: [mixs.vocab:Human-vaginalMigsVi](https://w3id.org/mixs/vocab/Human-vaginalMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[Human-vaginalMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Human-vaginal]^-[Human-vaginalMigsVi],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Human-vaginalMimag.md b/mixs6/Human-vaginalMimag.md index 4302412f..f6c9ae6c 100644 --- a/mixs6/Human-vaginalMimag.md +++ b/mixs6/Human-vaginalMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-vaginal]^-[Human-vaginalMIMAG],[Human-vaginal],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Human-vaginal]^-[Human-vaginalMIMAG],[Human-vaginal],[MIMAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -390,22 +394,27 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -467,8 +476,3 @@ URI: [mixs.vocab:Human-vaginalMIMAG](https://w3id.org/mixs/vocab/Human-vaginalMI * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimarksC.md b/mixs6/Human-vaginalMimarksC.md deleted file mode 100644 index 03e168f1..00000000 --- a/mixs6/Human-vaginalMimarksC.md +++ /dev/null @@ -1,359 +0,0 @@ - -# Class: Human-vaginalMimarksC - - -Combinatorial checklist for human-vaginal with mimarks_c - -URI: [mixs.vocab:Human-vaginalMimarksC](https://w3id.org/mixs/vocab/Human-vaginalMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[Human-vaginalMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Human-vaginal]^-[Human-vaginalMimarksC],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMimarksS.md b/mixs6/Human-vaginalMimarksS.md deleted file mode 100644 index 2750fe70..00000000 --- a/mixs6/Human-vaginalMimarksS.md +++ /dev/null @@ -1,379 +0,0 @@ - -# Class: Human-vaginalMimarksS - - -Combinatorial checklist for human-vaginal with mimarks_s - -URI: [mixs.vocab:Human-vaginalMimarksS](https://w3id.org/mixs/vocab/Human-vaginalMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[Human-vaginalMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Human-vaginal]^-[Human-vaginalMimarksS],[Human-vaginal]) - -## Parents - - * is_a: [Human-vaginal](Human-vaginal.md) - human-vaginal - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from human-vaginal: - - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [birth_control](birth_control.md) OPT - * Description: Specification of birth control medication used - * range: [String](types/String.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [douche](douche.md) OPT - * Description: Date of most recent douche - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gynecologic_disord](gynecologic_disord.md) OPT - * Description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - * range: [String](types/String.md) - * Example: None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_body_mass_index](host_body_mass_index.md) OPT - * Description: Body mass index, calculated as weight/(height)squared - * range: [QuantityValue](QuantityValue.md) - * Example: 22 kilogram per square meter None - * [host_body_product](host_body_product.md) OPT - * Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon - * range: [String](types/String.md) - * Example: Portion of mucus [fma66938] None - * [host_body_site](host_body_site.md) OPT - * Description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - * range: [String](types/String.md) - * Example: gill [UBERON:0002535] None - * [host_body_temp](host_body_temp.md) OPT - * Description: Core body temperature of the host when sample was collected - * range: [QuantityValue](QuantityValue.md) - * Example: 15 degree Celsius None - * [host_diet](host_diet.md) OPT - * Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types - * range: [String](types/String.md) - * Example: herbivore None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_family_relationship](host_family_relationship.md) OPT - * Description: Relationships to other hosts in the same study; can include multiple relationships - * range: [String](types/String.md) - * Example: offspring;Mussel25 None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_last_meal](host_last_meal.md) OPT - * Description: Content of last meal and time since feeding; can include multiple values - * range: [String](types/String.md) - * Example: corn feed;P2H None - * [host_occupation](host_occupation.md) OPT - * Description: Most frequent job performed by subject - * range: [String](types/String.md) - * Example: veterinary None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_pulse](host_pulse.md) OPT - * Description: Resting pulse, measured as beats per minute - * range: [QuantityValue](QuantityValue.md) - * Example: 65 beats per minute None - * [host_sex](host_sex.md) OPT - * Description: Physical sex of the host - * range: - * Example: female None - * [host_subject_id](host_subject_id.md) OPT - * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 - * range: [String](types/String.md) - * Example: MPI123 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [hrt](hrt.md) OPT - * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [hysterectomy](hysterectomy.md) OPT - * Description: Specification of whether hysterectomy was performed - * range: [String](types/String.md) - * Example: no None - * [ihmc_ethnicity](ihmc_ethnicity.md) OPT - * Description: Ethnicity of the subject - * range: [String](types/String.md) - * Example: caucasian None - * [ihmc_medication_code](ihmc_medication_code.md) OPT - * Description: Can include multiple medication codes - * range: [String](types/String.md) - * Example: 810 None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [medic_hist_perform](medic_hist_perform.md) OPT - * Description: Whether full medical history was collected - * range: [String](types/String.md) - * Example: TRUE None - * [menarche](menarche.md) OPT - * Description: Date of most recent menstruation - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [menopause](menopause.md) OPT - * Description: Date of onset of menopause - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pregnancy](pregnancy.md) OPT - * Description: Date due of pregnancy - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sexual_act](sexual_act.md) OPT - * Description: Current sexual partner and frequency of sex - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [urogenit_disord](urogenit_disord.md) OPT - * Description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18). - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMisag.md b/mixs6/Human-vaginalMisag.md index 417f4119..77e4271b 100644 --- a/mixs6/Human-vaginalMisag.md +++ b/mixs6/Human-vaginalMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-vaginal]^-[Human-vaginalMISAG],[Human-vaginal],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Human-vaginal]^-[Human-vaginalMISAG],[Human-vaginal],[MISAG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -370,22 +374,27 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -472,8 +481,3 @@ URI: [mixs.vocab:Human-vaginalMISAG](https://w3id.org/mixs/vocab/Human-vaginalMI * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Human-vaginalMiuvig.md b/mixs6/Human-vaginalMiuvig.md index ae693081..ff8c79b1 100644 --- a/mixs6/Human-vaginalMiuvig.md +++ b/mixs6/Human-vaginalMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):string%20%3F;sexual_act(i):string%20%3F;pregnancy(i):string%20%3F;douche(i):string%20%3F;birth_control(i):string%20%3F;menopause(i):string%20%3F;hrt(i):string%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-vaginal]^-[Human-vaginalMIUVIG],[Human-vaginal],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Human-vaginalMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;menarche(i):date%20%3F;sexual_act(i):string%20%3F;pregnancy(i):date%20%3F;douche(i):date%20%3F;birth_control(i):string%20%3F;menopause(i):date%20%3F;hrt(i):date%20%3F;hysterectomy(i):string%20%3F;gynecologic_disord(i):string%20%3F;urogenit_disord(i):string%20%3F;host_subject_id(i):string%20%3F;host_sex(i):host_sex_enum%20%3F;host_disease_stat(i):string%20%3F;ihmc_medication_code(i):string%20%3F;chem_administration(i):string%20%3F;host_body_site(i):string%20%3F;host_body_product(i):string%20%3F;host_diet(i):string%20%3F;host_last_meal(i):string%20%3F;host_family_relationship(i):string%20%3F;host_genotype(i):string%20%3F;host_phenotype(i):string%20%3F;ihmc_ethnicity(i):string%20%3F;host_occupation(i):string%20%3F;medic_hist_perform(i):string%20%3F;perturbation(i):string%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;organism_count(i):organism_count_enum%20%3F;samp_store_loc(i):string%20%3F;samp_store_dur(i):string%20%3F;host_symbiont(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Human-vaginal]^-[Human-vaginalMIUVIG],[Human-vaginal],[MIUVIG]) ## Parents @@ -23,7 +23,7 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM ### Inherited from human-vaginal: * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [birth_control](birth_control.md) OPT @@ -36,15 +36,15 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM * Example: agar [CHEBI:2509];2018-05-11T20:00Z None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [douche](douche.md) OPT * Description: Date of most recent douche - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [elev](elev.md) OPT * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit @@ -134,13 +134,17 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM * Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * range: [String](types/String.md) * Example: MPI123 None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_tot_mass](host_tot_mass.md) OPT * Description: Total mass of the host at collection, the unit depends on host * range: [QuantityValue](QuantityValue.md) * Example: 2500 gram None * [hrt](hrt.md) OPT * Description: Whether subject had hormone replacement theraphy, and if yes start date - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [hysterectomy](hysterectomy.md) OPT * Description: Specification of whether hysterectomy was performed @@ -164,11 +168,11 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM * Example: TRUE None * [menarche](menarche.md) OPT * Description: Date of most recent menstruation - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [menopause](menopause.md) OPT * Description: Date of onset of menopause - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [misc_param](misc_param.md) OPT * Description: Any other measurement performed or parameter collected, that is not listed here @@ -188,7 +192,7 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None * [pregnancy](pregnancy.md) OPT * Description: Date due of pregnancy - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -410,22 +414,27 @@ URI: [mixs.vocab:Human-vaginalMIUVIG](https://w3id.org/mixs/vocab/Human-vaginalM ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/HydrocarbonResources-cores.md b/mixs6/HydrocarbonResources-cores.md index d9e848fc..43d45b7a 100644 --- a/mixs6/HydrocarbonResources-cores.md +++ b/mixs6/HydrocarbonResources-cores.md @@ -7,7 +7,7 @@ hydrocarbon resources-cores URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/HydrocarbonResources-cores) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-coresMISAG],[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-coresME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -81,7 +81,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -356,11 +356,11 @@ URI: [mixs.vocab:HydrocarbonResources-cores](https://w3id.org/mixs/vocab/Hydroca * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT diff --git a/mixs6/HydrocarbonResources-coresMIGSBacteria.md b/mixs6/HydrocarbonResources-coresMIGSBacteria.md index 4a03e317..fab846f1 100644 --- a/mixs6/HydrocarbonResources-coresMIGSBacteria.md +++ b/mixs6/HydrocarbonResources-coresMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-cores],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSBacteria],[HydrocarbonResources-cores],[MIGSBacteria]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/v * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/v * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/v * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/v * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -537,22 +537,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSBacteria](https://w3id.org/mixs/v ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/HydrocarbonResources-coresMIGSEukaryote.md b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md index 93acfdc3..d8f04085 100644 --- a/mixs6/HydrocarbonResources-coresMIGSEukaryote.md +++ b/mixs6/HydrocarbonResources-coresMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-cores],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSEukaryote],[HydrocarbonResources-cores],[MIGSEukaryote]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/ * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/ * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/ * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/ * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -537,22 +537,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSEukaryote](https://w3id.org/mixs/ ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/HydrocarbonResources-coresMIGSPlant.md b/mixs6/HydrocarbonResources-coresMIGSPlant.md index fa429282..ae26c134 100644 --- a/mixs6/HydrocarbonResources-coresMIGSPlant.md +++ b/mixs6/HydrocarbonResources-coresMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-cores],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSPlant],[HydrocarbonResources-cores],[MIGSPlant]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/voca * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/voca * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/voca * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/voca * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -512,22 +512,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSPlant](https://w3id.org/mixs/voca ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/HydrocarbonResources-coresMIGSVirus.md b/mixs6/HydrocarbonResources-coresMIGSVirus.md index 0755dac1..09190183 100644 --- a/mixs6/HydrocarbonResources-coresMIGSVirus.md +++ b/mixs6/HydrocarbonResources-coresMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-cores],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSVirus],[HydrocarbonResources-cores],[MIGSVirus]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/voca * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/voca * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/voca * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/voca * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -532,22 +532,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSVirus](https://w3id.org/mixs/voca ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md index cc5db42c..f6e3b20a 100644 --- a/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md +++ b/mixs6/HydrocarbonResources-coresMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-cores],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSpecimen],[HydrocarbonResources-cores],[MIMARKSSpecimen]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mix * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mix * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mix * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mix * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -467,22 +467,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSpecimen](https://w3id.org/mix ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md index 7b52aead..a7751730 100644 --- a/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md +++ b/mixs6/HydrocarbonResources-coresMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-cores],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMARKSSurvey],[HydrocarbonResources-cores],[MIMARKSSurvey]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/ * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/ * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/ * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/ * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -442,22 +442,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMARKSSurvey](https://w3id.org/mixs/ ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/HydrocarbonResources-coresMe.md b/mixs6/HydrocarbonResources-coresMe.md index 4baecfc7..74ea6ccd 100644 --- a/mixs6/HydrocarbonResources-coresMe.md +++ b/mixs6/HydrocarbonResources-coresMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/HydrocarbonResources-coresME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresME],[HydrocarbonResources-cores],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresME],[HydrocarbonResources-cores],[ME]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/Hydro * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/Hydro * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/Hydro * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/Hydro * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -487,22 +487,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresME](https://w3id.org/mixs/vocab/Hydro ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/HydrocarbonResources-coresMigsBa.md b/mixs6/HydrocarbonResources-coresMigsBa.md deleted file mode 100644 index be15c999..00000000 --- a/mixs6/HydrocarbonResources-coresMigsBa.md +++ /dev/null @@ -1,611 +0,0 @@ - -# Class: HydrocarbonResources-coresMigsBa - - -Combinatorial checklist for hydrocarbon resources-cores with migs_ba - -URI: [mixs.vocab:HydrocarbonResources-coresMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[HydrocarbonResources-coresMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsBa],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsEu.md b/mixs6/HydrocarbonResources-coresMigsEu.md deleted file mode 100644 index 810d29c7..00000000 --- a/mixs6/HydrocarbonResources-coresMigsEu.md +++ /dev/null @@ -1,611 +0,0 @@ - -# Class: HydrocarbonResources-coresMigsEu - - -Combinatorial checklist for hydrocarbon resources-cores with migs_eu - -URI: [mixs.vocab:HydrocarbonResources-coresMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[HydrocarbonResources-coresMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsEu],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsOrg.md b/mixs6/HydrocarbonResources-coresMigsOrg.md index 551bf9d2..a0389207 100644 --- a/mixs6/HydrocarbonResources-coresMigsOrg.md +++ b/mixs6/HydrocarbonResources-coresMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-cores],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIGSOrg],[HydrocarbonResources-cores],[MIGSOrg]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/ * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/ * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/ * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/ * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -502,22 +502,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIGSOrg](https://w3id.org/mixs/vocab/ ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/HydrocarbonResources-coresMigsPl.md b/mixs6/HydrocarbonResources-coresMigsPl.md deleted file mode 100644 index 17d74dfc..00000000 --- a/mixs6/HydrocarbonResources-coresMigsPl.md +++ /dev/null @@ -1,581 +0,0 @@ - -# Class: HydrocarbonResources-coresMigsPl - - -Combinatorial checklist for hydrocarbon resources-cores with migs_pl - -URI: [mixs.vocab:HydrocarbonResources-coresMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[HydrocarbonResources-coresMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsPl],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMigsVi.md b/mixs6/HydrocarbonResources-coresMigsVi.md deleted file mode 100644 index 350509ff..00000000 --- a/mixs6/HydrocarbonResources-coresMigsVi.md +++ /dev/null @@ -1,606 +0,0 @@ - -# Class: HydrocarbonResources-coresMigsVi - - -Combinatorial checklist for hydrocarbon resources-cores with migs_vi - -URI: [mixs.vocab:HydrocarbonResources-coresMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[HydrocarbonResources-coresMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMigsVi],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/HydrocarbonResources-coresMimag.md b/mixs6/HydrocarbonResources-coresMimag.md index 91b80179..c7df31cd 100644 --- a/mixs6/HydrocarbonResources-coresMimag.md +++ b/mixs6/HydrocarbonResources-coresMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-cores],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIMAG],[HydrocarbonResources-cores],[MIMAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -542,22 +542,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -619,8 +624,3 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIMAG](https://w3id.org/mixs/vocab/Hy * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimarksC.md b/mixs6/HydrocarbonResources-coresMimarksC.md deleted file mode 100644 index a0555025..00000000 --- a/mixs6/HydrocarbonResources-coresMimarksC.md +++ /dev/null @@ -1,511 +0,0 @@ - -# Class: HydrocarbonResources-coresMimarksC - - -Combinatorial checklist for hydrocarbon resources-cores with mimarks_c - -URI: [mixs.vocab:HydrocarbonResources-coresMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[HydrocarbonResources-coresMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksC],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMimarksS.md b/mixs6/HydrocarbonResources-coresMimarksS.md deleted file mode 100644 index bfecefce..00000000 --- a/mixs6/HydrocarbonResources-coresMimarksS.md +++ /dev/null @@ -1,531 +0,0 @@ - -# Class: HydrocarbonResources-coresMimarksS - - -Combinatorial checklist for hydrocarbon resources-cores with mimarks_s - -URI: [mixs.vocab:HydrocarbonResources-coresMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[HydrocarbonResources-coresMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMimarksS],[HydrocarbonResources-cores]) - -## Parents - - * is_a: [HydrocarbonResources-cores](HydrocarbonResources-cores.md) - hydrocarbon resources-cores - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-cores: - - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [owc_tvdss](owc_tvdss.md) OPT - * Description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [permeability](permeability.md) OPT - * Description: Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) - * range: [String](types/String.md) - * Example: None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_md](samp_md.md) OPT - * Description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: 1534 meter;MSL None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_tvdss](samp_tvdss.md) OPT - * Description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m - * range: [String](types/String.md) - * Example: None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sr_dep_env](sr_dep_env.md) OPT - * Description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Marine None - * [sr_geol_age](sr_geol_age.md) OPT - * Description: Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [sr_kerog_type](sr_kerog_type.md) OPT - * Description: Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Type IV None - * [sr_lithology](sr_lithology.md) OPT - * Description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Coal None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMisag.md b/mixs6/HydrocarbonResources-coresMisag.md index 1d73cdf3..ff32bcce 100644 --- a/mixs6/HydrocarbonResources-coresMisag.md +++ b/mixs6/HydrocarbonResources-coresMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMISAG],[HydrocarbonResources-cores],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMISAG],[HydrocarbonResources-cores],[MISAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -522,22 +522,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -624,8 +629,3 @@ URI: [mixs.vocab:HydrocarbonResources-coresMISAG](https://w3id.org/mixs/vocab/Hy * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-coresMiuvig.md b/mixs6/HydrocarbonResources-coresMiuvig.md index 37ece903..4e6e13ce 100644 --- a/mixs6/HydrocarbonResources-coresMiuvig.md +++ b/mixs6/HydrocarbonResources-coresMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-coresMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-cores],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-coresMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;permeability(i):string%20%3F;porosity(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;sr_kerog_type(i):sr_kerog_type_enum%20%3F;sr_lithology(i):sr_lithology_enum%20%3F;sr_dep_env(i):sr_dep_env_enum%20%3F;sr_geol_age(i):sr_geol_age_enum%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_tvdss(i):string%20%3F;samp_md(i):samp_md_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-cores]^-[HydrocarbonResources-coresMIUVIG],[HydrocarbonResources-cores],[MIUVIG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/H * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -72,7 +72,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/H * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -83,7 +83,7 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/H * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -347,11 +347,11 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/H * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -562,22 +562,27 @@ URI: [mixs.vocab:HydrocarbonResources-coresMIUVIG](https://w3id.org/mixs/vocab/H ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/HydrocarbonResources-fluidsSwabs.md b/mixs6/HydrocarbonResources-fluidsSwabs.md index 5cf4ceda..3d005358 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabs.md +++ b/mixs6/HydrocarbonResources-fluidsSwabs.md @@ -7,7 +7,7 @@ hydrocarbon resources-fluids/swabs URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabs) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabsME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -101,7 +101,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -112,7 +112,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -193,7 +193,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -257,7 +257,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -368,11 +368,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabs](https://w3id.org/mixs/vocab/H * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md index 111cde34..2904aa2e 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabs],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-fluidsSwabs],[MIGSBacteria]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -557,22 +557,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria](https://w3id.org/ ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md index 31cfff37..0ccd0bee 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabs],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-fluidsSwabs],[MIGSEukaryote]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -557,22 +557,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSEukaryote](https://w3id.org ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md index 2bc7867e..65133b69 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabs],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-fluidsSwabs],[MIGSPlant]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -532,22 +532,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSPlant](https://w3id.org/mix ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md index e29a98fd..15275a35 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabs],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-fluidsSwabs],[MIGSVirus]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -552,22 +552,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSVirus](https://w3id.org/mix ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md index 86e209c8..10ecf5f1 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabs],[MIMARKSSpecimen]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -487,22 +487,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](https://w3id.o ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md index 85fb4d46..1d8ebd20 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabs],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-fluidsSwabs],[MIMARKSSurvey]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -462,22 +462,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMARKSSurvey](https://w3id.org ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMe.md b/mixs6/HydrocarbonResources-fluidsSwabsMe.md index 5fe771c0..3b518363 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMe.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package h URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-fluidsSwabs],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-fluidsSwabs],[ME]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -507,22 +507,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsME](https://w3id.org/mixs/vocab ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md deleted file mode 100644 index bcff39ea..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsBa.md +++ /dev/null @@ -1,631 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMigsBa - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsBa](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md deleted file mode 100644 index decfdce9..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsEu.md +++ /dev/null @@ -1,631 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMigsEu - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsEu](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md index 5eb54cd7..f58c9d62 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabs],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-fluidsSwabs],[MIGSOrg]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -522,22 +522,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSOrg](https://w3id.org/mixs/ ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md deleted file mode 100644 index ee801ccb..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsPl.md +++ /dev/null @@ -1,601 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMigsPl - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsPl](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md b/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md deleted file mode 100644 index 3f1ffa7c..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMigsVi.md +++ /dev/null @@ -1,626 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMigsVi - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMigsVi](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md index 70a887fe..2ef0932e 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabs],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-fluidsSwabs],[MIMAG]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -562,22 +562,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -639,8 +644,3 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIMAG](https://w3id.org/mixs/vo * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md deleted file mode 100644 index bb3878b5..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimarksC.md +++ /dev/null @@ -1,531 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMimarksC - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksC](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md b/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md deleted file mode 100644 index 6567e263..00000000 --- a/mixs6/HydrocarbonResources-fluidsSwabsMimarksS.md +++ /dev/null @@ -1,551 +0,0 @@ - -# Class: HydrocarbonResources-fluidsSwabsMimarksS - - -Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s - -URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMimarksS](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-fluidsSwabs]) - -## Parents - - * is_a: [HydrocarbonResources-fluidsSwabs](HydrocarbonResources-fluidsSwabs.md) - hydrocarbon resources-fluids/swabs - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from hydrocarbon resources-fluids_swabs: - - * [add_recov_method](add_recov_method.md) OPT - * Description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Polymer Addition;2018-06-21T14:30Z None - * [additional_info](additional_info.md) OPT - * Description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary - * range: [String](types/String.md) - * Example: None - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [api](api.md) OPT - * Description: API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [aromatics_pc](aromatics_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [asphaltenes_pc](asphaltenes_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [basin](basin.md) OPT - * Description: Name of the basin (e.g. Campos) - * range: [String](types/String.md) - * Example: None - * [benzene](benzene.md) OPT - * Description: Concentration of benzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [biocide](biocide.md) OPT - * Description: List of biocides (commercial name of product and supplier) and date of administration - * range: [String](types/String.md) - * Example: ALPHA 1427;Baker Hughes;2008-01-23 None - * [biocide_admin_method](biocide_admin_method.md) OPT - * Description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * range: [String](types/String.md) - * Example: None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_treatment](chem_treatment.md) OPT - * Description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included - * range: [String](types/String.md) - * Example: ACCENT 1125;DOW;2010-11-17 None - * [chem_treatment_method](chem_treatment_method.md) OPT - * Description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) - * range: [String](types/String.md) - * Example: None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depos_env](depos_env.md) OPT - * Description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Continental - Alluvial None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_iron](diss_iron.md) OPT - * Description: Concentration of dissolved iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_oxygen_fluid](diss_oxygen_fluid.md) OPT - * Description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [ethylbenzene](ethylbenzene.md) OPT - * Description: Concentration of ethylbenzene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [field](field.md) OPT - * Description: Name of the hydrocarbon field (e.g. Albacora) - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [hc_produced](hc_produced.md) OPT - * Description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Gas None - * [hcr](hcr.md) OPT - * Description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Oil Sand None - * [hcr_fw_salinity](hcr_fw_salinity.md) OPT - * Description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [hcr_geol_age](hcr_geol_age.md) OPT - * Description: Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Silurian None - * [hcr_pressure](hcr_pressure.md) OPT - * Description: Original pressure of the hydrocarbon resource - * range: [String](types/String.md) - * Example: None - * [hcr_temp](hcr_temp.md) OPT - * Description: Original temperature of the hydrocarbon resource - * range: [String](types/String.md) - * Example: 150-295 degree Celsius None - * [iw_bt_date_well](iw_bt_date_well.md) OPT - * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [iwf](iwf.md) OPT - * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [lithology](lithology.md) OPT - * Description: Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: Volcanic None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [organism_count_qpcr_info](organism_count_qpcr_info.md) OPT - * Description: If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) - * range: [String](types/String.md) - * Example: None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pour_point](pour_point.md) OPT - * Description: Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [prod_rate](prod_rate.md) OPT - * Description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [prod_start_date](prod_start_date.md) OPT - * Description: Date of field's first production - * range: [String](types/String.md) - * Example: 2018-05-11 None - * [reservoir](reservoir.md) OPT - * Description: Name of the reservoir (e.g. Carapebus) - * range: [String](types/String.md) - * Example: None - * [resins_pc](resins_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [samp_collection_point](samp_collection_point.md) OPT - * Description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field - * range: - * Example: well None - * [samp_loc_corr_rate](samp_loc_corr_rate.md) OPT - * Description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays - * range: [String](types/String.md) - * Example: None - * [samp_preserv](samp_preserv.md) OPT - * Description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_subtype](samp_subtype.md) OPT - * Description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field - * range: - * Example: biofilm None - * [samp_transport_cond](samp_transport_cond.md) OPT - * Description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) - * range: [String](types/String.md) - * Example: 5 days;-20 degree Celsius None - * [samp_type](samp_type.md) OPT - * Description: Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field - * range: - * Example: solid deposit None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [samp_well_name](samp_well_name.md) OPT - * Description: Name of the well (e.g. BXA1123) where sample was taken - * range: [String](types/String.md) - * Example: None - * [saturates_pc](saturates_pc.md) OPT - * Description: Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) - * range: [String](types/String.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfate_fw](sulfate_fw.md) OPT - * Description: Original sulfate concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [tan](tan.md) OPT - * Description: Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [toluene](toluene.md) OPT - * Description: Concentration of toluene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_iron](tot_iron.md) OPT - * Description: Concentration of total iron in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [tot_sulfur](tot_sulfur.md) OPT - * Description: Concentration of total sulfur in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa](vfa.md) OPT - * Description: Concentration of Volatile Fatty Acids in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [vfa_fw](vfa_fw.md) OPT - * Description: Original volatile fatty acid concentration in the hydrocarbon resource - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [viscosity](viscosity.md) OPT - * Description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) - * range: [String](types/String.md) - * Example: None - * [water_cut](water_cut.md) OPT - * Description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_production_rate](water_production_rate.md) OPT - * Description: Water production rates per well (e.g. 987 m3 / day) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [win](win.md) OPT - * Description: A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) - * range: [String](types/String.md) - * Example: None - * [xylene](xylene.md) OPT - * Description: Concentration of xylene in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md index f193ea6e..5f89ef72 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMisag.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabs],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-fluidsSwabs],[MISAG]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -542,22 +542,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -644,8 +649,3 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMISAG](https://w3id.org/mixs/vo * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md index 01959d2a..ba00f372 100644 --- a/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md +++ b/mixs6/HydrocarbonResources-fluidsSwabsMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/vocab/HydrocarbonResources-fluidsSwabsMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):string%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):string%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabs],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[HydrocarbonResources-fluidsSwabsMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;hcr(i):hcr_enum%20%3F;hc_produced(i):hc_produced_enum%20%3F;basin(i):string%20%3F;field(i):string%20%3F;reservoir(i):string%20%3F;hcr_temp(i):string%20%3F;hcr_pressure(i):string%20%3F;lithology(i):lithology_enum%20%3F;depos_env(i):depos_env_enum%20%3F;hcr_geol_age(i):hcr_geol_age_enum%20%3F;prod_start_date(i):date%20%3F;add_recov_method(i):add_recov_method_enum%20%3F;iw_bt_date_well(i):date%20%3F;biocide(i):string%20%3F;biocide_admin_method(i):string%20%3F;chem_treatment(i):string%20%3F;chem_treatment_method(i):string%20%3F;samp_loc_corr_rate(i):string%20%3F;samp_well_name(i):string%20%3F;win(i):string%20%3F;samp_type(i):samp_type_enum%20%3F;samp_subtype(i):samp_subtype_enum%20%3F;samp_collection_point(i):samp_collection_point_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;samp_preserv(i):string%20%3F;samp_transport_cond(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;organism_count_qpcr_info(i):string%20%3F;ph(i):double%20%3F;alkalinity_method(i):string%20%3F;suspend_solids(i):string%20%3F;viscosity(i):string%20%3F;saturates_pc(i):string%20%3F;aromatics_pc(i):string%20%3F;resins_pc(i):string%20%3F;asphaltenes_pc(i):string%20%3F;misc_param(i):string%20%3F;additional_info(i):string%20%3F]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabs]^-[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-fluidsSwabs],[MIUVIG]) ## Parents @@ -39,7 +39,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * range: [String](types/String.md) * Example: titration None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * Example: 5000 milligram per liter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) @@ -103,7 +103,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * range: * Example: Continental - Alluvial None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diss_carb_dioxide](diss_carb_dioxide.md) OPT @@ -184,7 +184,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * Example: 150-295 degree Celsius None * [iw_bt_date_well](iw_bt_date_well.md) OPT * Description: Injection water breakthrough date per well following a secondary and/or tertiary recovery - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [iwf](iwf.md) OPT * Description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) @@ -248,7 +248,7 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * Example: None * [prod_start_date](prod_start_date.md) OPT * Description: Date of field's first production - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11 None * [reservoir](reservoir.md) OPT * Description: Name of the reservoir (e.g. Carapebus) @@ -359,11 +359,11 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) OPT - * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * Description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * range: [QuantityValue](QuantityValue.md) * Example: None * [vfa](vfa.md) OPT @@ -582,22 +582,27 @@ URI: [mixs.vocab:HydrocarbonResources-fluidsSwabsMIUVIG](https://w3id.org/mixs/v ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/IndoorSpaceEnum.md b/mixs6/IndoorSpaceEnum.md new file mode 100644 index 00000000..7b26fd99 --- /dev/null +++ b/mixs6/IndoorSpaceEnum.md @@ -0,0 +1,19 @@ + +# Enum: indoor_space_enum + + + + +URI: [mixs.vocab:indoor_space_enum](https://w3id.org/mixs/vocab/indoor_space_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/IndoorSurfEnum.md b/mixs6/IndoorSurfEnum.md new file mode 100644 index 00000000..726d4e28 --- /dev/null +++ b/mixs6/IndoorSurfEnum.md @@ -0,0 +1,19 @@ + +# Enum: indoor_surf_enum + + + + +URI: [mixs.vocab:indoor_surf_enum](https://w3id.org/mixs/vocab/indoor_surf_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/IntWallCondEnum.md b/mixs6/IntWallCondEnum.md new file mode 100644 index 00000000..43294c18 --- /dev/null +++ b/mixs6/IntWallCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: int_wall_cond_enum + + + + +URI: [mixs.vocab:int_wall_cond_enum](https://w3id.org/mixs/vocab/int_wall_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/InvestigationTypeEnum.md b/mixs6/InvestigationTypeEnum.md new file mode 100644 index 00000000..cbb53e4c --- /dev/null +++ b/mixs6/InvestigationTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: investigation_type_enum + + + + +URI: [mixs.vocab:investigation_type_enum](https://w3id.org/mixs/vocab/investigation_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LibLayoutEnum.md b/mixs6/LibLayoutEnum.md new file mode 100644 index 00000000..f0f31110 --- /dev/null +++ b/mixs6/LibLayoutEnum.md @@ -0,0 +1,19 @@ + +# Enum: lib_layout_enum + + + + +URI: [mixs.vocab:lib_layout_enum](https://w3id.org/mixs/vocab/lib_layout_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LightTypeEnum.md b/mixs6/LightTypeEnum.md new file mode 100644 index 00000000..82eb06e8 --- /dev/null +++ b/mixs6/LightTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: light_type_enum + + + + +URI: [mixs.vocab:light_type_enum](https://w3id.org/mixs/vocab/light_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/LithologyEnum.md b/mixs6/LithologyEnum.md new file mode 100644 index 00000000..1c2a5288 --- /dev/null +++ b/mixs6/LithologyEnum.md @@ -0,0 +1,19 @@ + +# Enum: lithology_enum + + + + +URI: [mixs.vocab:lithology_enum](https://w3id.org/mixs/vocab/lithology_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/me_samp_collect_device.md b/mixs6/ME_sample_collect_device.md similarity index 84% rename from mixs6/me_samp_collect_device.md rename to mixs6/ME_sample_collect_device.md index 03911d20..8f525232 100644 --- a/mixs6/me_samp_collect_device.md +++ b/mixs6/ME_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: ME_samp_collect_device +# Slot: ME_sample_collect_device -URI: [mixs.vocab:ME_samp_collect_device](https://w3id.org/mixs/vocab/ME_samp_collect_device) +URI: [mixs.vocab:ME_sample_collect_device](https://w3id.org/mixs/vocab/ME_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:ME_samp_collect_device](https://w3id.org/mixs/vocab/ME_samp_col ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/ME_sample_collect_method.md b/mixs6/ME_sample_collect_method.md new file mode 100644 index 00000000..99ff8992 --- /dev/null +++ b/mixs6/ME_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: ME_sample_collect_method + + + + +URI: [mixs.vocab:ME_sample_collect_method](https://w3id.org/mixs/vocab/ME_sample_collect_method) + + +## Domain and Range + +[ME](ME.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [ME](ME.md) + * [AirME](AirME.md) + * [BuiltEnvironmentME](BuiltEnvironmentME.md) + * [Host-associatedME](Host-associatedME.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-gutME](Human-gutME.md) + * [Human-oralME](Human-oralME.md) + * [Human-skinME](Human-skinME.md) + * [Human-vaginalME](Human-vaginalME.md) + * [HydrocarbonResources-coresME](HydrocarbonResources-coresME.md) + * [HydrocarbonResources-fluidsSwabsME](HydrocarbonResources-fluidsSwabsME.md) + * [MicrobialMatBiofilmME](MicrobialMatBiofilmME.md) + * [MiscellaneousNaturalOrArtificialEnvironmentME](MiscellaneousNaturalOrArtificialEnvironmentME.md) + * [Plant-associatedME](Plant-associatedME.md) + * [SedimentME](SedimentME.md) + * [SoilME](SoilME.md) + * [WastewaterSludgeME](WastewaterSludgeME.md) + * [WaterME](WaterME.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIGSBacteria.md b/mixs6/MIGSBacteria.md index e37ee90d..c3519267 100644 --- a/mixs6/MIGSBacteria.md +++ b/mixs6/MIGSBacteria.md @@ -7,7 +7,7 @@ Minimal Information about a Genome Sequence: cultured bacteria/archaea URI: [mixs.vocab:MIGSBacteria](https://w3id.org/mixs/vocab/MIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSBacteria],[WastewaterSludgeMIGSBacteria]uses%20-.->[MIGSBacteria],[SoilMIGSBacteria]uses%20-.->[MIGSBacteria],[SedimentMIGSBacteria]uses%20-.->[MIGSBacteria],[Plant-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilmMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-coresMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-vaginalMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-skinMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-oralMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-gutMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[Host-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[BuiltEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[AirMIGSBacteria]uses%20-.->[MIGSBacteria],[WaterMIGSBacteria],[WastewaterSludgeMIGSBacteria],[SoilMIGSBacteria],[SedimentMIGSBacteria],[Plant-associatedMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MicrobialMatBiofilmMIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-coresMIGSBacteria],[Human-vaginalMIGSBacteria],[Human-skinMIGSBacteria],[Human-oralMIGSBacteria],[Human-gutMIGSBacteria],[Human-associatedMIGSBacteria],[Host-associatedMIGSBacteria],[BuiltEnvironmentMIGSBacteria],[AirMIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSBacteria],[WastewaterSludgeMIGSBacteria]uses%20-.->[MIGSBacteria],[SoilMIGSBacteria]uses%20-.->[MIGSBacteria],[SedimentMIGSBacteria]uses%20-.->[MIGSBacteria],[Plant-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilmMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria]uses%20-.->[MIGSBacteria],[HydrocarbonResources-coresMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-vaginalMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-skinMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-oralMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-gutMIGSBacteria]uses%20-.->[MIGSBacteria],[Human-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[Host-associatedMIGSBacteria]uses%20-.->[MIGSBacteria],[BuiltEnvironmentMIGSBacteria]uses%20-.->[MIGSBacteria],[AirMIGSBacteria]uses%20-.->[MIGSBacteria],[WaterMIGSBacteria],[WastewaterSludgeMIGSBacteria],[SoilMIGSBacteria],[SedimentMIGSBacteria],[Plant-associatedMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MicrobialMatBiofilmMIGSBacteria],[HydrocarbonResources-fluidsSwabsMIGSBacteria],[HydrocarbonResources-coresMIGSBacteria],[Human-vaginalMIGSBacteria],[Human-skinMIGSBacteria],[Human-oralMIGSBacteria],[Human-gutMIGSBacteria],[Human-associatedMIGSBacteria],[Host-associatedMIGSBacteria],[BuiltEnvironmentMIGSBacteria],[AirMIGSBacteria]) ## Mixin for @@ -50,7 +50,7 @@ URI: [mixs.vocab:MIGSBacteria](https://w3id.org/mixs/vocab/MIGSBacteria) * [MIGS bacteria➞biotic_relationship](MIGS_bacteria_biotic_relationship.md) OPT * range: * [MIGS bacteria➞collection_date](MIGS_bacteria_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIGS bacteria➞compl_score](MIGS_bacteria_compl_score.md) OPT * range: * [MIGS bacteria➞compl_software](MIGS_bacteria_compl_software.md) OPT @@ -113,13 +113,15 @@ URI: [mixs.vocab:MIGSBacteria](https://w3id.org/mixs/vocab/MIGSBacteria) * range: [String](types/String.md) * [MIGS bacteria➞rel_to_oxygen](MIGS_bacteria_rel_to_oxygen.md) OPT * range: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) * [MIGS bacteria➞seq_meth](MIGS_bacteria_seq_meth.md) REQ * range: diff --git a/mixs6/MIGSEukaryote.md b/mixs6/MIGSEukaryote.md index a55e5022..2f820aa2 100644 --- a/mixs6/MIGSEukaryote.md +++ b/mixs6/MIGSEukaryote.md @@ -7,7 +7,7 @@ Minimal Information about a Genome Sequence: eukaryote URI: [mixs.vocab:MIGSEukaryote](https://w3id.org/mixs/vocab/MIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSEukaryote],[WastewaterSludgeMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SoilMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SedimentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Plant-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-vaginalMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-skinMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-oralMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-gutMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Host-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[BuiltEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[AirMIGSEukaryote]uses%20-.->[MIGSEukaryote],[WaterMIGSEukaryote],[WastewaterSludgeMIGSEukaryote],[SoilMIGSEukaryote],[SedimentMIGSEukaryote],[Plant-associatedMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote],[Human-vaginalMIGSEukaryote],[Human-skinMIGSEukaryote],[Human-oralMIGSEukaryote],[Human-gutMIGSEukaryote],[Human-associatedMIGSEukaryote],[Host-associatedMIGSEukaryote],[BuiltEnvironmentMIGSEukaryote],[AirMIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSEukaryote],[WastewaterSludgeMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SoilMIGSEukaryote]uses%20-.->[MIGSEukaryote],[SedimentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Plant-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote]uses%20-.->[MIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-vaginalMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-skinMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-oralMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-gutMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Human-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[Host-associatedMIGSEukaryote]uses%20-.->[MIGSEukaryote],[BuiltEnvironmentMIGSEukaryote]uses%20-.->[MIGSEukaryote],[AirMIGSEukaryote]uses%20-.->[MIGSEukaryote],[WaterMIGSEukaryote],[WastewaterSludgeMIGSEukaryote],[SoilMIGSEukaryote],[SedimentMIGSEukaryote],[Plant-associatedMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MicrobialMatBiofilmMIGSEukaryote],[HydrocarbonResources-fluidsSwabsMIGSEukaryote],[HydrocarbonResources-coresMIGSEukaryote],[Human-vaginalMIGSEukaryote],[Human-skinMIGSEukaryote],[Human-oralMIGSEukaryote],[Human-gutMIGSEukaryote],[Human-associatedMIGSEukaryote],[Host-associatedMIGSEukaryote],[BuiltEnvironmentMIGSEukaryote],[AirMIGSEukaryote]) ## Mixin for @@ -50,7 +50,7 @@ URI: [mixs.vocab:MIGSEukaryote](https://w3id.org/mixs/vocab/MIGSEukaryote) * [MIGS eukaryote➞biotic_relationship](MIGS_eukaryote_biotic_relationship.md) OPT * range: * [MIGS eukaryote➞collection_date](MIGS_eukaryote_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIGS eukaryote➞compl_score](MIGS_eukaryote_compl_score.md) OPT * range: * [MIGS eukaryote➞compl_software](MIGS_eukaryote_compl_software.md) OPT @@ -113,13 +113,15 @@ URI: [mixs.vocab:MIGSEukaryote](https://w3id.org/mixs/vocab/MIGSEukaryote) * range: [String](types/String.md) * [MIGS eukaryote➞ref_db](MIGS_eukaryote_ref_db.md) OPT * range: [String](types/String.md) - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) * [MIGS eukaryote➞seq_meth](MIGS_eukaryote_seq_meth.md) REQ * range: diff --git a/mixs6/MIGSPlant.md b/mixs6/MIGSPlant.md index e8d9992e..ed32693e 100644 --- a/mixs6/MIGSPlant.md +++ b/mixs6/MIGSPlant.md @@ -7,7 +7,7 @@ Minimal Information about a Genome Sequence: plant URI: [mixs.vocab:MIGSPlant](https://w3id.org/mixs/vocab/MIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSPlant],[WastewaterSludgeMIGSPlant]uses%20-.->[MIGSPlant],[SoilMIGSPlant]uses%20-.->[MIGSPlant],[SedimentMIGSPlant]uses%20-.->[MIGSPlant],[Plant-associatedMIGSPlant]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[MicrobialMatBiofilmMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-coresMIGSPlant]uses%20-.->[MIGSPlant],[Human-vaginalMIGSPlant]uses%20-.->[MIGSPlant],[Human-skinMIGSPlant]uses%20-.->[MIGSPlant],[Human-oralMIGSPlant]uses%20-.->[MIGSPlant],[Human-gutMIGSPlant]uses%20-.->[MIGSPlant],[Human-associatedMIGSPlant]uses%20-.->[MIGSPlant],[Host-associatedMIGSPlant]uses%20-.->[MIGSPlant],[BuiltEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[AirMIGSPlant]uses%20-.->[MIGSPlant],[WaterMIGSPlant],[WastewaterSludgeMIGSPlant],[SoilMIGSPlant],[SedimentMIGSPlant],[Plant-associatedMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MicrobialMatBiofilmMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-coresMIGSPlant],[Human-vaginalMIGSPlant],[Human-skinMIGSPlant],[Human-oralMIGSPlant],[Human-gutMIGSPlant],[Human-associatedMIGSPlant],[Host-associatedMIGSPlant],[BuiltEnvironmentMIGSPlant],[AirMIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSPlant],[WastewaterSludgeMIGSPlant]uses%20-.->[MIGSPlant],[SoilMIGSPlant]uses%20-.->[MIGSPlant],[SedimentMIGSPlant]uses%20-.->[MIGSPlant],[Plant-associatedMIGSPlant]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[MicrobialMatBiofilmMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant]uses%20-.->[MIGSPlant],[HydrocarbonResources-coresMIGSPlant]uses%20-.->[MIGSPlant],[Human-vaginalMIGSPlant]uses%20-.->[MIGSPlant],[Human-skinMIGSPlant]uses%20-.->[MIGSPlant],[Human-oralMIGSPlant]uses%20-.->[MIGSPlant],[Human-gutMIGSPlant]uses%20-.->[MIGSPlant],[Human-associatedMIGSPlant]uses%20-.->[MIGSPlant],[Host-associatedMIGSPlant]uses%20-.->[MIGSPlant],[BuiltEnvironmentMIGSPlant]uses%20-.->[MIGSPlant],[AirMIGSPlant]uses%20-.->[MIGSPlant],[WaterMIGSPlant],[WastewaterSludgeMIGSPlant],[SoilMIGSPlant],[SedimentMIGSPlant],[Plant-associatedMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MicrobialMatBiofilmMIGSPlant],[HydrocarbonResources-fluidsSwabsMIGSPlant],[HydrocarbonResources-coresMIGSPlant],[Human-vaginalMIGSPlant],[Human-skinMIGSPlant],[Human-oralMIGSPlant],[Human-gutMIGSPlant],[Human-associatedMIGSPlant],[Host-associatedMIGSPlant],[BuiltEnvironmentMIGSPlant],[AirMIGSPlant]) ## Mixin for @@ -48,7 +48,7 @@ URI: [mixs.vocab:MIGSPlant](https://w3id.org/mixs/vocab/MIGSPlant) * [MIGS plant➞assembly_software](MIGS_plant_assembly_software.md) REQ * range: [String](types/String.md) * [MIGS plant➞collection_date](MIGS_plant_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIGS plant➞compl_score](MIGS_plant_compl_score.md) OPT * range: * [MIGS plant➞compl_software](MIGS_plant_compl_software.md) OPT @@ -103,13 +103,15 @@ URI: [mixs.vocab:MIGSPlant](https://w3id.org/mixs/vocab/MIGSPlant) * range: [String](types/String.md) * [MIGS plant➞ref_db](MIGS_plant_ref_db.md) OPT * range: [String](types/String.md) - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) * [MIGS plant➞seq_meth](MIGS_plant_seq_meth.md) REQ * range: diff --git a/mixs6/MIGSVirus.md b/mixs6/MIGSVirus.md index 74641603..7513e059 100644 --- a/mixs6/MIGSVirus.md +++ b/mixs6/MIGSVirus.md @@ -7,7 +7,7 @@ Minimal Information about a Genome Sequence: cultured bacteria/archaea URI: [mixs.vocab:MIGSVirus](https://w3id.org/mixs/vocab/MIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSVirus],[WastewaterSludgeMIGSVirus]uses%20-.->[MIGSVirus],[SoilMIGSVirus]uses%20-.->[MIGSVirus],[SedimentMIGSVirus]uses%20-.->[MIGSVirus],[Plant-associatedMIGSVirus]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[MicrobialMatBiofilmMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-coresMIGSVirus]uses%20-.->[MIGSVirus],[Human-vaginalMIGSVirus]uses%20-.->[MIGSVirus],[Human-skinMIGSVirus]uses%20-.->[MIGSVirus],[Human-oralMIGSVirus]uses%20-.->[MIGSVirus],[Human-gutMIGSVirus]uses%20-.->[MIGSVirus],[Human-associatedMIGSVirus]uses%20-.->[MIGSVirus],[Host-associatedMIGSVirus]uses%20-.->[MIGSVirus],[BuiltEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[AirMIGSVirus]uses%20-.->[MIGSVirus],[WaterMIGSVirus],[WastewaterSludgeMIGSVirus],[SoilMIGSVirus],[SedimentMIGSVirus],[Plant-associatedMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MicrobialMatBiofilmMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-coresMIGSVirus],[Human-vaginalMIGSVirus],[Human-skinMIGSVirus],[Human-oralMIGSVirus],[Human-gutMIGSVirus],[Human-associatedMIGSVirus],[Host-associatedMIGSVirus],[BuiltEnvironmentMIGSVirus],[AirMIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSVirus],[WastewaterSludgeMIGSVirus]uses%20-.->[MIGSVirus],[SoilMIGSVirus]uses%20-.->[MIGSVirus],[SedimentMIGSVirus]uses%20-.->[MIGSVirus],[Plant-associatedMIGSVirus]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[MicrobialMatBiofilmMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus]uses%20-.->[MIGSVirus],[HydrocarbonResources-coresMIGSVirus]uses%20-.->[MIGSVirus],[Human-vaginalMIGSVirus]uses%20-.->[MIGSVirus],[Human-skinMIGSVirus]uses%20-.->[MIGSVirus],[Human-oralMIGSVirus]uses%20-.->[MIGSVirus],[Human-gutMIGSVirus]uses%20-.->[MIGSVirus],[Human-associatedMIGSVirus]uses%20-.->[MIGSVirus],[Host-associatedMIGSVirus]uses%20-.->[MIGSVirus],[BuiltEnvironmentMIGSVirus]uses%20-.->[MIGSVirus],[AirMIGSVirus]uses%20-.->[MIGSVirus],[WaterMIGSVirus],[WastewaterSludgeMIGSVirus],[SoilMIGSVirus],[SedimentMIGSVirus],[Plant-associatedMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MicrobialMatBiofilmMIGSVirus],[HydrocarbonResources-fluidsSwabsMIGSVirus],[HydrocarbonResources-coresMIGSVirus],[Human-vaginalMIGSVirus],[Human-skinMIGSVirus],[Human-oralMIGSVirus],[Human-gutMIGSVirus],[Human-associatedMIGSVirus],[Host-associatedMIGSVirus],[BuiltEnvironmentMIGSVirus],[AirMIGSVirus]) ## Mixin for @@ -50,7 +50,7 @@ URI: [mixs.vocab:MIGSVirus](https://w3id.org/mixs/vocab/MIGSVirus) * [MIGS virus➞biotic_relationship](MIGS_virus_biotic_relationship.md) OPT * range: * [MIGS virus➞collection_date](MIGS_virus_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIGS virus➞compl_score](MIGS_virus_compl_score.md) OPT * range: * [MIGS virus➞compl_software](MIGS_virus_compl_software.md) OPT @@ -111,13 +111,15 @@ URI: [mixs.vocab:MIGSVirus](https://w3id.org/mixs/vocab/MIGSVirus) * range: [String](types/String.md) * [MIGS virus➞ref_db](MIGS_virus_ref_db.md) OPT * range: [String](types/String.md) - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) * [MIGS virus➞seq_meth](MIGS_virus_seq_meth.md) REQ * range: diff --git a/mixs6/MIGS_bacteria_collection_date.md b/mixs6/MIGS_bacteria_collection_date.md index 949a5a6f..bb003eaf 100644 --- a/mixs6/MIGS_bacteria_collection_date.md +++ b/mixs6/MIGS_bacteria_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_bacteria_collection_date](https://w3id.org/mixs/vocab/MIGS ## Domain and Range -[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) +[MIGSBacteria](MIGSBacteria.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIGS_bacteria_samp_collect_device.md b/mixs6/MIGS_bacteria_sample_collect_device.md similarity index 85% rename from mixs6/MIGS_bacteria_samp_collect_device.md rename to mixs6/MIGS_bacteria_sample_collect_device.md index df27ec0a..c87d7b80 100644 --- a/mixs6/MIGS_bacteria_samp_collect_device.md +++ b/mixs6/MIGS_bacteria_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIGS_bacteria_samp_collect_device +# Slot: MIGS_bacteria_sample_collect_device -URI: [mixs.vocab:MIGS_bacteria_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_bacteria_samp_collect_device) +URI: [mixs.vocab:MIGS_bacteria_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIGS_bacteria_samp_collect_device](https://w3id.org/mixs/vocab/ ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIGS_bacteria_sample_collect_method.md b/mixs6/MIGS_bacteria_sample_collect_method.md new file mode 100644 index 00000000..1eaee283 --- /dev/null +++ b/mixs6/MIGS_bacteria_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_bacteria_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_bacteria_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_bacteria_sample_collect_method) + + +## Domain and Range + +[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSBacteria](MIGSBacteria.md) + * [AirMIGSBacteria](AirMIGSBacteria.md) + * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md) + * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md) + * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [SedimentMIGSBacteria](SedimentMIGSBacteria.md) + * [SoilMIGSBacteria](SoilMIGSBacteria.md) + * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md) + * [WaterMIGSBacteria](WaterMIGSBacteria.md) diff --git a/mixs6/MIGS_bacteria_sample_name.md b/mixs6/MIGS_bacteria_sample_name.md index b26a9d24..59b30f9e 100644 --- a/mixs6/MIGS_bacteria_sample_name.md +++ b/mixs6/MIGS_bacteria_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_bacteria_sample_name](https://w3id.org/mixs/vocab/MIGS_bac ## Domain and Range -[MIGSBacteria](MIGSBacteria.md) -> OPT [String](types/String.md) +[MIGSBacteria](MIGSBacteria.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/MIGS_eukaryote_collection_date.md b/mixs6/MIGS_eukaryote_collection_date.md index 567b02ff..7c0b4e08 100644 --- a/mixs6/MIGS_eukaryote_collection_date.md +++ b/mixs6/MIGS_eukaryote_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_eukaryote_collection_date](https://w3id.org/mixs/vocab/MIG ## Domain and Range -[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIGS_eukaryote_samp_collect_device.md b/mixs6/MIGS_eukaryote_sample_collect_device.md similarity index 85% rename from mixs6/MIGS_eukaryote_samp_collect_device.md rename to mixs6/MIGS_eukaryote_sample_collect_device.md index 87e93bee..1362ed1c 100644 --- a/mixs6/MIGS_eukaryote_samp_collect_device.md +++ b/mixs6/MIGS_eukaryote_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIGS_eukaryote_samp_collect_device +# Slot: MIGS_eukaryote_sample_collect_device -URI: [mixs.vocab:MIGS_eukaryote_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_eukaryote_samp_collect_device) +URI: [mixs.vocab:MIGS_eukaryote_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIGS_eukaryote_samp_collect_device](https://w3id.org/mixs/vocab ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIGS_eukaryote_sample_collect_method.md b/mixs6/MIGS_eukaryote_sample_collect_method.md new file mode 100644 index 00000000..03b5f30e --- /dev/null +++ b/mixs6/MIGS_eukaryote_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_eukaryote_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_eukaryote_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_eukaryote_sample_collect_method) + + +## Domain and Range + +[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSEukaryote](MIGSEukaryote.md) + * [AirMIGSEukaryote](AirMIGSEukaryote.md) + * [BuiltEnvironmentMIGSEukaryote](BuiltEnvironmentMIGSEukaryote.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [HydrocarbonResources-coresMIGSEukaryote](HydrocarbonResources-coresMIGSEukaryote.md) + * [HydrocarbonResources-fluidsSwabsMIGSEukaryote](HydrocarbonResources-fluidsSwabsMIGSEukaryote.md) + * [MicrobialMatBiofilmMIGSEukaryote](MicrobialMatBiofilmMIGSEukaryote.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [SedimentMIGSEukaryote](SedimentMIGSEukaryote.md) + * [SoilMIGSEukaryote](SoilMIGSEukaryote.md) + * [WastewaterSludgeMIGSEukaryote](WastewaterSludgeMIGSEukaryote.md) + * [WaterMIGSEukaryote](WaterMIGSEukaryote.md) diff --git a/mixs6/MIGS_eukaryote_sample_name.md b/mixs6/MIGS_eukaryote_sample_name.md index 570ab29f..7647d8a8 100644 --- a/mixs6/MIGS_eukaryote_sample_name.md +++ b/mixs6/MIGS_eukaryote_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_eukaryote_sample_name](https://w3id.org/mixs/vocab/MIGS_eu ## Domain and Range -[MIGSEukaryote](MIGSEukaryote.md) -> OPT [String](types/String.md) +[MIGSEukaryote](MIGSEukaryote.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/migs_org_samp_collect_device.md b/mixs6/MIGS_org_sample_collect_device.md similarity index 84% rename from mixs6/migs_org_samp_collect_device.md rename to mixs6/MIGS_org_sample_collect_device.md index 00baf73d..fb357582 100644 --- a/mixs6/migs_org_samp_collect_device.md +++ b/mixs6/MIGS_org_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIGS_org_samp_collect_device +# Slot: MIGS_org_sample_collect_device -URI: [mixs.vocab:MIGS_org_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_org_samp_collect_device) +URI: [mixs.vocab:MIGS_org_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_org_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIGS_org_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_ ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIGS_org_sample_collect_method.md b/mixs6/MIGS_org_sample_collect_method.md new file mode 100644 index 00000000..00ddacfb --- /dev/null +++ b/mixs6/MIGS_org_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_org_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_org_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_org_sample_collect_method) + + +## Domain and Range + +[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSOrg](MIGSOrg.md) + * [AirMIGSOrg](AirMIGSOrg.md) + * [BuiltEnvironmentMIGSOrg](BuiltEnvironmentMIGSOrg.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [HydrocarbonResources-coresMIGSOrg](HydrocarbonResources-coresMIGSOrg.md) + * [HydrocarbonResources-fluidsSwabsMIGSOrg](HydrocarbonResources-fluidsSwabsMIGSOrg.md) + * [MicrobialMatBiofilmMIGSOrg](MicrobialMatBiofilmMIGSOrg.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [SedimentMIGSOrg](SedimentMIGSOrg.md) + * [SoilMIGSOrg](SoilMIGSOrg.md) + * [WastewaterSludgeMIGSOrg](WastewaterSludgeMIGSOrg.md) + * [WaterMIGSOrg](WaterMIGSOrg.md) diff --git a/mixs6/MIGS_plant_collection_date.md b/mixs6/MIGS_plant_collection_date.md index b8b90631..6c3a079e 100644 --- a/mixs6/MIGS_plant_collection_date.md +++ b/mixs6/MIGS_plant_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_plant_collection_date](https://w3id.org/mixs/vocab/MIGS_pl ## Domain and Range -[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) +[MIGSPlant](MIGSPlant.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIGS_plant_samp_collect_device.md b/mixs6/MIGS_plant_sample_collect_device.md similarity index 84% rename from mixs6/MIGS_plant_samp_collect_device.md rename to mixs6/MIGS_plant_sample_collect_device.md index bc4a1ab6..053e90b0 100644 --- a/mixs6/MIGS_plant_samp_collect_device.md +++ b/mixs6/MIGS_plant_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIGS_plant_samp_collect_device +# Slot: MIGS_plant_sample_collect_device -URI: [mixs.vocab:MIGS_plant_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_plant_samp_collect_device) +URI: [mixs.vocab:MIGS_plant_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_plant_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIGS_plant_samp_collect_device](https://w3id.org/mixs/vocab/MIG ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIGS_plant_sample_collect_method.md b/mixs6/MIGS_plant_sample_collect_method.md new file mode 100644 index 00000000..aad27a5d --- /dev/null +++ b/mixs6/MIGS_plant_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_plant_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_plant_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_plant_sample_collect_method) + + +## Domain and Range + +[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSPlant](MIGSPlant.md) + * [AirMIGSPlant](AirMIGSPlant.md) + * [BuiltEnvironmentMIGSPlant](BuiltEnvironmentMIGSPlant.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [HydrocarbonResources-coresMIGSPlant](HydrocarbonResources-coresMIGSPlant.md) + * [HydrocarbonResources-fluidsSwabsMIGSPlant](HydrocarbonResources-fluidsSwabsMIGSPlant.md) + * [MicrobialMatBiofilmMIGSPlant](MicrobialMatBiofilmMIGSPlant.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [SedimentMIGSPlant](SedimentMIGSPlant.md) + * [SoilMIGSPlant](SoilMIGSPlant.md) + * [WastewaterSludgeMIGSPlant](WastewaterSludgeMIGSPlant.md) + * [WaterMIGSPlant](WaterMIGSPlant.md) diff --git a/mixs6/MIGS_plant_sample_name.md b/mixs6/MIGS_plant_sample_name.md index b0389a89..dbf67ad6 100644 --- a/mixs6/MIGS_plant_sample_name.md +++ b/mixs6/MIGS_plant_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_plant_sample_name](https://w3id.org/mixs/vocab/MIGS_plant_ ## Domain and Range -[MIGSPlant](MIGSPlant.md) -> OPT [String](types/String.md) +[MIGSPlant](MIGSPlant.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/MIGS_virus_collection_date.md b/mixs6/MIGS_virus_collection_date.md index 6d76d920..a81cfb4d 100644 --- a/mixs6/MIGS_virus_collection_date.md +++ b/mixs6/MIGS_virus_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_virus_collection_date](https://w3id.org/mixs/vocab/MIGS_vi ## Domain and Range -[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) +[MIGSVirus](MIGSVirus.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIGS_virus_samp_collect_device.md b/mixs6/MIGS_virus_sample_collect_device.md similarity index 84% rename from mixs6/MIGS_virus_samp_collect_device.md rename to mixs6/MIGS_virus_sample_collect_device.md index 2cd087b8..7fc3bbfa 100644 --- a/mixs6/MIGS_virus_samp_collect_device.md +++ b/mixs6/MIGS_virus_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIGS_virus_samp_collect_device +# Slot: MIGS_virus_sample_collect_device -URI: [mixs.vocab:MIGS_virus_samp_collect_device](https://w3id.org/mixs/vocab/MIGS_virus_samp_collect_device) +URI: [mixs.vocab:MIGS_virus_sample_collect_device](https://w3id.org/mixs/vocab/MIGS_virus_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIGS_virus_samp_collect_device](https://w3id.org/mixs/vocab/MIG ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIGS_virus_sample_collect_method.md b/mixs6/MIGS_virus_sample_collect_method.md new file mode 100644 index 00000000..8c362c89 --- /dev/null +++ b/mixs6/MIGS_virus_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIGS_virus_sample_collect_method + + + + +URI: [mixs.vocab:MIGS_virus_sample_collect_method](https://w3id.org/mixs/vocab/MIGS_virus_sample_collect_method) + + +## Domain and Range + +[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIGSVirus](MIGSVirus.md) + * [AirMIGSVirus](AirMIGSVirus.md) + * [BuiltEnvironmentMIGSVirus](BuiltEnvironmentMIGSVirus.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [HydrocarbonResources-coresMIGSVirus](HydrocarbonResources-coresMIGSVirus.md) + * [HydrocarbonResources-fluidsSwabsMIGSVirus](HydrocarbonResources-fluidsSwabsMIGSVirus.md) + * [MicrobialMatBiofilmMIGSVirus](MicrobialMatBiofilmMIGSVirus.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [SedimentMIGSVirus](SedimentMIGSVirus.md) + * [SoilMIGSVirus](SoilMIGSVirus.md) + * [WastewaterSludgeMIGSVirus](WastewaterSludgeMIGSVirus.md) + * [WaterMIGSVirus](WaterMIGSVirus.md) diff --git a/mixs6/MIGS_virus_sample_name.md b/mixs6/MIGS_virus_sample_name.md index 2072300e..278617b5 100644 --- a/mixs6/MIGS_virus_sample_name.md +++ b/mixs6/MIGS_virus_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_virus_sample_name](https://w3id.org/mixs/vocab/MIGS_virus_ ## Domain and Range -[MIGSVirus](MIGSVirus.md) -> OPT [String](types/String.md) +[MIGSVirus](MIGSVirus.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/mimag_samp_collect_device.md b/mixs6/MIMAG_sample_collect_device.md similarity index 85% rename from mixs6/mimag_samp_collect_device.md rename to mixs6/MIMAG_sample_collect_device.md index ef2d4b48..3b9f9ea8 100644 --- a/mixs6/mimag_samp_collect_device.md +++ b/mixs6/MIMAG_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIMAG_samp_collect_device +# Slot: MIMAG_sample_collect_device -URI: [mixs.vocab:MIMAG_samp_collect_device](https://w3id.org/mixs/vocab/MIMAG_samp_collect_device) +URI: [mixs.vocab:MIMAG_sample_collect_device](https://w3id.org/mixs/vocab/MIMAG_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIMAG_samp_collect_device](https://w3id.org/mixs/vocab/MIMAG_sa ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/mimag_x_16s_recover_software.md b/mixs6/MIMAG_sample_collect_method.md similarity index 77% rename from mixs6/mimag_x_16s_recover_software.md rename to mixs6/MIMAG_sample_collect_method.md index 3b488185..742757c4 100644 --- a/mixs6/mimag_x_16s_recover_software.md +++ b/mixs6/MIMAG_sample_collect_method.md @@ -1,10 +1,10 @@ -# Slot: MIMAG_x_16s_recover_software +# Slot: MIMAG_sample_collect_method -URI: [mixs.vocab:MIMAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MIMAG_x_16s_recover_software) +URI: [mixs.vocab:MIMAG_sample_collect_method](https://w3id.org/mixs/vocab/MIMAG_sample_collect_method) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIMAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MIMAG ## Parents - * is_a: [x_16s_recover_software](x_16s_recover_software.md) + * is_a: [sample_collect_method](sample_collect_method.md) ## Children @@ -38,3 +38,10 @@ URI: [mixs.vocab:MIMAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MIMAG * [SoilMIMAG](SoilMIMAG.md) * [WastewaterSludgeMIMAG](WastewaterSludgeMIMAG.md) * [WaterMIMAG](WaterMIMAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKSSpecimen.md b/mixs6/MIMARKSSpecimen.md index c8beab73..8f61465c 100644 --- a/mixs6/MIMARKSSpecimen.md +++ b/mixs6/MIMARKSSpecimen.md @@ -7,7 +7,7 @@ Minimal Information about a Marker Specimen: specimen URI: [mixs.vocab:MIMARKSSpecimen](https://w3id.org/mixs/vocab/MIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SoilMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SedimentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-skinMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-oralMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-gutMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Host-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[AirMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[WaterMIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen],[SoilMIMARKSSpecimen],[SedimentMIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen],[Human-skinMIMARKSSpecimen],[Human-oralMIMARKSSpecimen],[Human-gutMIMARKSSpecimen],[Human-associatedMIMARKSSpecimen],[Host-associatedMIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen],[AirMIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SoilMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[SedimentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-skinMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-oralMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-gutMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Human-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[Host-associatedMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[AirMIMARKSSpecimen]uses%20-.->[MIMARKSSpecimen],[WaterMIMARKSSpecimen],[WastewaterSludgeMIMARKSSpecimen],[SoilMIMARKSSpecimen],[SedimentMIMARKSSpecimen],[Plant-associatedMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MicrobialMatBiofilmMIMARKSSpecimen],[HydrocarbonResources-fluidsSwabsMIMARKSSpecimen],[HydrocarbonResources-coresMIMARKSSpecimen],[Human-vaginalMIMARKSSpecimen],[Human-skinMIMARKSSpecimen],[Human-oralMIMARKSSpecimen],[Human-gutMIMARKSSpecimen],[Human-associatedMIMARKSSpecimen],[Host-associatedMIMARKSSpecimen],[BuiltEnvironmentMIMARKSSpecimen],[AirMIMARKSSpecimen]) ## Mixin for @@ -44,7 +44,7 @@ URI: [mixs.vocab:MIMARKSSpecimen](https://w3id.org/mixs/vocab/MIMARKSSpecimen) * [MIMARKS specimen➞chimera_check](MIMARKS_specimen_chimera_check.md) OPT * range: [String](types/String.md) * [MIMARKS specimen➞collection_date](MIMARKS_specimen_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIMARKS specimen➞env_broad_scale](MIMARKS_specimen_env_broad_scale.md) REQ * range: [String](types/String.md) * [MIMARKS specimen➞env_local_scale](MIMARKS_specimen_env_local_scale.md) REQ @@ -85,13 +85,15 @@ URI: [mixs.vocab:MIMARKSSpecimen](https://w3id.org/mixs/vocab/MIMARKSSpecimen) * range: [String](types/String.md) * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) OPT * range: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) * [MIMARKS specimen➞seq_meth](MIMARKS_specimen_seq_meth.md) REQ * range: diff --git a/mixs6/MIMARKSSurvey.md b/mixs6/MIMARKSSurvey.md index d751e522..b57a5821 100644 --- a/mixs6/MIMARKSSurvey.md +++ b/mixs6/MIMARKSSurvey.md @@ -7,7 +7,7 @@ Minimal Information about a Marker Specimen: survey URI: [mixs.vocab:MIMARKSSurvey](https://w3id.org/mixs/vocab/MIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SoilMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SedimentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Plant-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-vaginalMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-skinMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-oralMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-gutMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Host-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[AirMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[WaterMIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey],[SoilMIMARKSSurvey],[SedimentMIMARKSSurvey],[Plant-associatedMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey],[Human-vaginalMIMARKSSurvey],[Human-skinMIMARKSSurvey],[Human-oralMIMARKSSurvey],[Human-gutMIMARKSSurvey],[Human-associatedMIMARKSSurvey],[Host-associatedMIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey],[AirMIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SoilMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[SedimentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Plant-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-vaginalMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-skinMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-oralMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-gutMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Human-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[Host-associatedMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[AirMIMARKSSurvey]uses%20-.->[MIMARKSSurvey],[WaterMIMARKSSurvey],[WastewaterSludgeMIMARKSSurvey],[SoilMIMARKSSurvey],[SedimentMIMARKSSurvey],[Plant-associatedMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSurvey],[HydrocarbonResources-fluidsSwabsMIMARKSSurvey],[HydrocarbonResources-coresMIMARKSSurvey],[Human-vaginalMIMARKSSurvey],[Human-skinMIMARKSSurvey],[Human-oralMIMARKSSurvey],[Human-gutMIMARKSSurvey],[Human-associatedMIMARKSSurvey],[Host-associatedMIMARKSSurvey],[BuiltEnvironmentMIMARKSSurvey],[AirMIMARKSSurvey]) ## Mixin for @@ -42,7 +42,7 @@ URI: [mixs.vocab:MIMARKSSurvey](https://w3id.org/mixs/vocab/MIMARKSSurvey) * [MIMARKS survey➞chimera_check](MIMARKS_survey_chimera_check.md) OPT * range: [String](types/String.md) * [MIMARKS survey➞collection_date](MIMARKS_survey_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIMARKS survey➞env_broad_scale](MIMARKS_survey_env_broad_scale.md) REQ * range: [String](types/String.md) * [MIMARKS survey➞env_local_scale](MIMARKS_survey_env_local_scale.md) REQ @@ -75,13 +75,15 @@ URI: [mixs.vocab:MIMARKSSurvey](https://w3id.org/mixs/vocab/MIMARKSSurvey) * range: [String](types/String.md) * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) OPT * range: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) * [MIMARKS survey➞seq_meth](MIMARKS_survey_seq_meth.md) REQ * range: diff --git a/mixs6/MIMARKS_specimen_collection_date.md b/mixs6/MIMARKS_specimen_collection_date.md index a56c3488..2a056cd5 100644 --- a/mixs6/MIMARKS_specimen_collection_date.md +++ b/mixs6/MIMARKS_specimen_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMARKS_specimen_collection_date](https://w3id.org/mixs/vocab/M ## Domain and Range -[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIMARKS_specimen_samp_collect_device.md b/mixs6/MIMARKS_specimen_sample_collect_device.md similarity index 86% rename from mixs6/MIMARKS_specimen_samp_collect_device.md rename to mixs6/MIMARKS_specimen_sample_collect_device.md index 27485d9b..e484264e 100644 --- a/mixs6/MIMARKS_specimen_samp_collect_device.md +++ b/mixs6/MIMARKS_specimen_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIMARKS_specimen_samp_collect_device +# Slot: MIMARKS_specimen_sample_collect_device -URI: [mixs.vocab:MIMARKS_specimen_samp_collect_device](https://w3id.org/mixs/vocab/MIMARKS_specimen_samp_collect_device) +URI: [mixs.vocab:MIMARKS_specimen_sample_collect_device](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIMARKS_specimen_samp_collect_device](https://w3id.org/mixs/voc ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIMARKS_specimen_sample_collect_method.md b/mixs6/MIMARKS_specimen_sample_collect_method.md new file mode 100644 index 00000000..0596f7bc --- /dev/null +++ b/mixs6/MIMARKS_specimen_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MIMARKS_specimen_sample_collect_method + + + + +URI: [mixs.vocab:MIMARKS_specimen_sample_collect_method](https://w3id.org/mixs/vocab/MIMARKS_specimen_sample_collect_method) + + +## Domain and Range + +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIMARKSSpecimen](MIMARKSSpecimen.md) + * [AirMIMARKSSpecimen](AirMIMARKSSpecimen.md) + * [BuiltEnvironmentMIMARKSSpecimen](BuiltEnvironmentMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [HydrocarbonResources-coresMIMARKSSpecimen](HydrocarbonResources-coresMIMARKSSpecimen.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSpecimen](HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md) + * [MicrobialMatBiofilmMIMARKSSpecimen](MicrobialMatBiofilmMIMARKSSpecimen.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [SedimentMIMARKSSpecimen](SedimentMIMARKSSpecimen.md) + * [SoilMIMARKSSpecimen](SoilMIMARKSSpecimen.md) + * [WastewaterSludgeMIMARKSSpecimen](WastewaterSludgeMIMARKSSpecimen.md) + * [WaterMIMARKSSpecimen](WaterMIMARKSSpecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MIMARKS_specimen_sample_name.md b/mixs6/MIMARKS_specimen_sample_name.md index f6c48943..df5f4364 100644 --- a/mixs6/MIMARKS_specimen_sample_name.md +++ b/mixs6/MIMARKS_specimen_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMARKS_specimen_sample_name](https://w3id.org/mixs/vocab/MIMAR ## Domain and Range -[MIMARKSSpecimen](MIMARKSSpecimen.md) -> OPT [String](types/String.md) +[MIMARKSSpecimen](MIMARKSSpecimen.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/MIMARKS_survey_collection_date.md b/mixs6/MIMARKS_survey_collection_date.md index ec191cac..89300003 100644 --- a/mixs6/MIMARKS_survey_collection_date.md +++ b/mixs6/MIMARKS_survey_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMARKS_survey_collection_date](https://w3id.org/mixs/vocab/MIM ## Domain and Range -[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/MIMARKS_survey_samp_collect_device.md b/mixs6/MIMARKS_survey_sample_collect_device.md similarity index 85% rename from mixs6/MIMARKS_survey_samp_collect_device.md rename to mixs6/MIMARKS_survey_sample_collect_device.md index d4bae0c1..724689ed 100644 --- a/mixs6/MIMARKS_survey_samp_collect_device.md +++ b/mixs6/MIMARKS_survey_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIMARKS_survey_samp_collect_device +# Slot: MIMARKS_survey_sample_collect_device -URI: [mixs.vocab:MIMARKS_survey_samp_collect_device](https://w3id.org/mixs/vocab/MIMARKS_survey_samp_collect_device) +URI: [mixs.vocab:MIMARKS_survey_sample_collect_device](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIMARKS_survey_samp_collect_device](https://w3id.org/mixs/vocab ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIMARKS_survey_sample_collect_method.md b/mixs6/MIMARKS_survey_sample_collect_method.md new file mode 100644 index 00000000..1d02ffaf --- /dev/null +++ b/mixs6/MIMARKS_survey_sample_collect_method.md @@ -0,0 +1,40 @@ + +# Slot: MIMARKS_survey_sample_collect_method + + + + +URI: [mixs.vocab:MIMARKS_survey_sample_collect_method](https://w3id.org/mixs/vocab/MIMARKS_survey_sample_collect_method) + + +## Domain and Range + +[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIMARKSSurvey](MIMARKSSurvey.md) + * [AirMIMARKSSurvey](AirMIMARKSSurvey.md) + * [BuiltEnvironmentMIMARKSSurvey](BuiltEnvironmentMIMARKSSurvey.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [HydrocarbonResources-coresMIMARKSSurvey](HydrocarbonResources-coresMIMARKSSurvey.md) + * [HydrocarbonResources-fluidsSwabsMIMARKSSurvey](HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md) + * [MicrobialMatBiofilmMIMARKSSurvey](MicrobialMatBiofilmMIMARKSSurvey.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [SedimentMIMARKSSurvey](SedimentMIMARKSSurvey.md) + * [SoilMIMARKSSurvey](SoilMIMARKSSurvey.md) + * [WastewaterSludgeMIMARKSSurvey](WastewaterSludgeMIMARKSSurvey.md) + * [WaterMIMARKSSurvey](WaterMIMARKSSurvey.md) diff --git a/mixs6/MIMARKS_survey_sample_name.md b/mixs6/MIMARKS_survey_sample_name.md index 35a0b888..f54c0368 100644 --- a/mixs6/MIMARKS_survey_sample_name.md +++ b/mixs6/MIMARKS_survey_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMARKS_survey_sample_name](https://w3id.org/mixs/vocab/MIMARKS ## Domain and Range -[MIMARKSSurvey](MIMARKSSurvey.md) -> OPT [String](types/String.md) +[MIMARKSSurvey](MIMARKSSurvey.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/misag_samp_collect_device.md b/mixs6/MISAG_sample_collect_device.md similarity index 85% rename from mixs6/misag_samp_collect_device.md rename to mixs6/MISAG_sample_collect_device.md index 55e704ea..f976e5ad 100644 --- a/mixs6/misag_samp_collect_device.md +++ b/mixs6/MISAG_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MISAG_samp_collect_device +# Slot: MISAG_sample_collect_device -URI: [mixs.vocab:MISAG_samp_collect_device](https://w3id.org/mixs/vocab/MISAG_samp_collect_device) +URI: [mixs.vocab:MISAG_sample_collect_device](https://w3id.org/mixs/vocab/MISAG_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MISAG_samp_collect_device](https://w3id.org/mixs/vocab/MISAG_sa ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/misag_x_16s_recover_software.md b/mixs6/MISAG_sample_collect_method.md similarity index 77% rename from mixs6/misag_x_16s_recover_software.md rename to mixs6/MISAG_sample_collect_method.md index f9658c21..27bc27aa 100644 --- a/mixs6/misag_x_16s_recover_software.md +++ b/mixs6/MISAG_sample_collect_method.md @@ -1,10 +1,10 @@ -# Slot: MISAG_x_16s_recover_software +# Slot: MISAG_sample_collect_method -URI: [mixs.vocab:MISAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MISAG_x_16s_recover_software) +URI: [mixs.vocab:MISAG_sample_collect_method](https://w3id.org/mixs/vocab/MISAG_sample_collect_method) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MISAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MISAG ## Parents - * is_a: [x_16s_recover_software](x_16s_recover_software.md) + * is_a: [sample_collect_method](sample_collect_method.md) ## Children @@ -38,3 +38,10 @@ URI: [mixs.vocab:MISAG_x_16s_recover_software](https://w3id.org/mixs/vocab/MISAG * [SoilMISAG](SoilMISAG.md) * [WastewaterSludgeMISAG](WastewaterSludgeMISAG.md) * [WaterMISAG](WaterMISAG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/miuvig_samp_collect_device.md b/mixs6/MIUVIG_sample_collect_device.md similarity index 85% rename from mixs6/miuvig_samp_collect_device.md rename to mixs6/MIUVIG_sample_collect_device.md index c0fef2c1..56d0cbc3 100644 --- a/mixs6/miuvig_samp_collect_device.md +++ b/mixs6/MIUVIG_sample_collect_device.md @@ -1,10 +1,10 @@ -# Slot: MIUVIG_samp_collect_device +# Slot: MIUVIG_sample_collect_device -URI: [mixs.vocab:MIUVIG_samp_collect_device](https://w3id.org/mixs/vocab/MIUVIG_samp_collect_device) +URI: [mixs.vocab:MIUVIG_sample_collect_device](https://w3id.org/mixs/vocab/MIUVIG_sample_collect_device) ## Domain and Range @@ -13,7 +13,7 @@ URI: [mixs.vocab:MIUVIG_samp_collect_device](https://w3id.org/mixs/vocab/MIUVIG_ ## Parents - * is_a: [samp_collect_device](samp_collect_device.md) + * is_a: [sample_collect_device](sample_collect_device.md) ## Children diff --git a/mixs6/MIUVIG_sample_collect_method.md b/mixs6/MIUVIG_sample_collect_method.md new file mode 100644 index 00000000..c4828d8d --- /dev/null +++ b/mixs6/MIUVIG_sample_collect_method.md @@ -0,0 +1,47 @@ + +# Slot: MIUVIG_sample_collect_method + + + + +URI: [mixs.vocab:MIUVIG_sample_collect_method](https://w3id.org/mixs/vocab/MIUVIG_sample_collect_method) + + +## Domain and Range + +[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) + +## Parents + + * is_a: [sample_collect_method](sample_collect_method.md) + +## Children + + +## Used by + + * [MIUVIG](MIUVIG.md) + * [AirMIUVIG](AirMIUVIG.md) + * [BuiltEnvironmentMIUVIG](BuiltEnvironmentMIUVIG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [HydrocarbonResources-coresMIUVIG](HydrocarbonResources-coresMIUVIG.md) + * [HydrocarbonResources-fluidsSwabsMIUVIG](HydrocarbonResources-fluidsSwabsMIUVIG.md) + * [MicrobialMatBiofilmMIUVIG](MicrobialMatBiofilmMIUVIG.md) + * [MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](MiscellaneousNaturalOrArtificialEnvironmentMIUVIG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + * [SedimentMIUVIG](SedimentMIUVIG.md) + * [SoilMIUVIG](SoilMIUVIG.md) + * [WastewaterSludgeMIUVIG](WastewaterSludgeMIUVIG.md) + * [WaterMIUVIG](WaterMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Comments:** | | conditional mandatory | + diff --git a/mixs6/MagCovSoftwareEnum.md b/mixs6/MagCovSoftwareEnum.md new file mode 100644 index 00000000..fac2da39 --- /dev/null +++ b/mixs6/MagCovSoftwareEnum.md @@ -0,0 +1,19 @@ + +# Enum: mag_cov_software_enum + + + + +URI: [mixs.vocab:mag_cov_software_enum](https://w3id.org/mixs/vocab/mag_cov_software_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Me.md b/mixs6/Me.md index 44c25296..22e4f75b 100644 --- a/mixs6/Me.md +++ b/mixs6/Me.md @@ -7,7 +7,7 @@ Metagenome or Environmental URI: [mixs.vocab:ME](https://w3id.org/mixs/vocab/ME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][ME],[WastewaterSludgeME]uses%20-.->[ME],[SoilME]uses%20-.->[ME],[SedimentME]uses%20-.->[ME],[Plant-associatedME]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironmentME]uses%20-.->[ME],[MicrobialMatBiofilmME]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabsME]uses%20-.->[ME],[HydrocarbonResources-coresME]uses%20-.->[ME],[Human-vaginalME]uses%20-.->[ME],[Human-skinME]uses%20-.->[ME],[Human-oralME]uses%20-.->[ME],[Human-gutME]uses%20-.->[ME],[Human-associatedME]uses%20-.->[ME],[Host-associatedME]uses%20-.->[ME],[BuiltEnvironmentME]uses%20-.->[ME],[AirME]uses%20-.->[ME],[WaterME],[WastewaterSludgeME],[SoilME],[SedimentME],[Plant-associatedME],[MiscellaneousNaturalOrArtificialEnvironmentME],[MicrobialMatBiofilmME],[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-coresME],[Human-vaginalME],[Human-skinME],[Human-oralME],[Human-gutME],[Human-associatedME],[Host-associatedME],[BuiltEnvironmentME],[AirME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][ME],[WastewaterSludgeME]uses%20-.->[ME],[SoilME]uses%20-.->[ME],[SedimentME]uses%20-.->[ME],[Plant-associatedME]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironmentME]uses%20-.->[ME],[MicrobialMatBiofilmME]uses%20-.->[ME],[HydrocarbonResources-fluidsSwabsME]uses%20-.->[ME],[HydrocarbonResources-coresME]uses%20-.->[ME],[Human-vaginalME]uses%20-.->[ME],[Human-skinME]uses%20-.->[ME],[Human-oralME]uses%20-.->[ME],[Human-gutME]uses%20-.->[ME],[Human-associatedME]uses%20-.->[ME],[Host-associatedME]uses%20-.->[ME],[BuiltEnvironmentME]uses%20-.->[ME],[AirME]uses%20-.->[ME],[WaterME],[WastewaterSludgeME],[SoilME],[SedimentME],[Plant-associatedME],[MiscellaneousNaturalOrArtificialEnvironmentME],[MicrobialMatBiofilmME],[HydrocarbonResources-fluidsSwabsME],[HydrocarbonResources-coresME],[Human-vaginalME],[Human-skinME],[Human-oralME],[Human-gutME],[Human-associatedME],[Host-associatedME],[BuiltEnvironmentME],[AirME]) ## Mixin for @@ -48,7 +48,7 @@ URI: [mixs.vocab:ME](https://w3id.org/mixs/vocab/ME) * [ME➞assembly_software](ME_assembly_software.md) OPT * range: [String](types/String.md) * [ME➞collection_date](ME_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [ME➞env_broad_scale](ME_env_broad_scale.md) REQ * range: [String](types/String.md) * [ME➞env_local_scale](ME_env_local_scale.md) REQ @@ -93,13 +93,15 @@ URI: [mixs.vocab:ME](https://w3id.org/mixs/vocab/ME) * range: [String](types/String.md) * [ME➞rel_to_oxygen](ME_rel_to_oxygen.md) OPT * range: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT - * range: [String](types/String.md) * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) * [ME➞samp_size](ME_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) * [ME➞seq_meth](ME_seq_meth.md) REQ * range: diff --git a/mixs6/MechStrucEnum.md b/mixs6/MechStrucEnum.md new file mode 100644 index 00000000..e68f8427 --- /dev/null +++ b/mixs6/MechStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: mech_struc_enum + + + + +URI: [mixs.vocab:mech_struc_enum](https://w3id.org/mixs/vocab/mech_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/MicrobialMatBiofilm.md b/mixs6/MicrobialMatBiofilm.md index 090b4aee..5ec0fe7d 100644 --- a/mixs6/MicrobialMatBiofilm.md +++ b/mixs6/MicrobialMatBiofilm.md @@ -7,7 +7,7 @@ microbial mat/biofilm URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBiofilm) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilmME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -89,10 +89,10 @@ URI: [mixs.vocab:MicrobialMatBiofilm](https://w3id.org/mixs/vocab/MicrobialMatBi * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT diff --git a/mixs6/MicrobialMatBiofilmMIGSBacteria.md b/mixs6/MicrobialMatBiofilmMIGSBacteria.md index 0df0a826..c79f39f6 100644 --- a/mixs6/MicrobialMatBiofilmMIGSBacteria.md +++ b/mixs6/MicrobialMatBiofilmMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:MicrobialMatBiofilmMIGSBacteria](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilm],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSBacteria],[MicrobialMatBiofilm],[MIGSBacteria]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSBacteria](https://w3id.org/mixs/vocab/Mi * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSBacteria](https://w3id.org/mixs/vocab/Mi * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -461,22 +461,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSBacteria](https://w3id.org/mixs/vocab/Mi ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/MicrobialMatBiofilmMIGSEukaryote.md b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md index 30c7a098..5467b332 100644 --- a/mixs6/MicrobialMatBiofilmMIGSEukaryote.md +++ b/mixs6/MicrobialMatBiofilmMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilm],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSEukaryote],[MicrobialMatBiofilm],[MIGSEukaryote]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/M * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/M * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -461,22 +461,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSEukaryote](https://w3id.org/mixs/vocab/M ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/MicrobialMatBiofilmMIGSPlant.md b/mixs6/MicrobialMatBiofilmMIGSPlant.md index d2abc406..7b65f843 100644 --- a/mixs6/MicrobialMatBiofilmMIGSPlant.md +++ b/mixs6/MicrobialMatBiofilmMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilm],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSPlant],[MicrobialMatBiofilm],[MIGSPlant]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/Micro * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/Micro * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -436,22 +436,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSPlant](https://w3id.org/mixs/vocab/Micro ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/MicrobialMatBiofilmMIGSVirus.md b/mixs6/MicrobialMatBiofilmMIGSVirus.md index 28c9b27e..6a3b87f4 100644 --- a/mixs6/MicrobialMatBiofilmMIGSVirus.md +++ b/mixs6/MicrobialMatBiofilmMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilm],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSVirus],[MicrobialMatBiofilm],[MIGSVirus]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/Micro * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/Micro * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -456,22 +456,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSVirus](https://w3id.org/mixs/vocab/Micro ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md index 542bc844..c229462d 100644 --- a/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md +++ b/mixs6/MicrobialMatBiofilmMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilm],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSpecimen],[MicrobialMatBiofilm],[MIMARKSSpecimen]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -391,22 +391,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen](https://w3id.org/mixs/vocab ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md index ba7a937e..ff07e96a 100644 --- a/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md +++ b/mixs6/MicrobialMatBiofilmMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilm],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMARKSSurvey],[MicrobialMatBiofilm],[MIMARKSSurvey]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/M * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/M * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -366,22 +366,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMARKSSurvey](https://w3id.org/mixs/vocab/M ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/MicrobialMatBiofilmMe.md b/mixs6/MicrobialMatBiofilmMe.md index e0309f5a..4627bc31 100644 --- a/mixs6/MicrobialMatBiofilmMe.md +++ b/mixs6/MicrobialMatBiofilmMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package m URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMatBiofilmME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmME],[MicrobialMatBiofilm],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmME],[MicrobialMatBiofilm],[ME]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMat * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMat * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -411,22 +411,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmME](https://w3id.org/mixs/vocab/MicrobialMat ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/MicrobialMatBiofilmMigsBa.md b/mixs6/MicrobialMatBiofilmMigsBa.md deleted file mode 100644 index 58276d97..00000000 --- a/mixs6/MicrobialMatBiofilmMigsBa.md +++ /dev/null @@ -1,535 +0,0 @@ - -# Class: MicrobialMatBiofilmMigsBa - - -Combinatorial checklist for microbial mat_biofilm with migs_ba - -URI: [mixs.vocab:MicrobialMatBiofilmMigsBa](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsBa],[MicrobialMatBiofilmMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsBa],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsBa],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsEu.md b/mixs6/MicrobialMatBiofilmMigsEu.md deleted file mode 100644 index 605a7bf8..00000000 --- a/mixs6/MicrobialMatBiofilmMigsEu.md +++ /dev/null @@ -1,535 +0,0 @@ - -# Class: MicrobialMatBiofilmMigsEu - - -Combinatorial checklist for microbial mat_biofilm with migs_eu - -URI: [mixs.vocab:MicrobialMatBiofilmMigsEu](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsEu],[MicrobialMatBiofilmMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsEu],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsEu],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsOrg.md b/mixs6/MicrobialMatBiofilmMigsOrg.md index 717d86c4..e9f72f32 100644 --- a/mixs6/MicrobialMatBiofilmMigsOrg.md +++ b/mixs6/MicrobialMatBiofilmMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilm],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIGSOrg],[MicrobialMatBiofilm],[MIGSOrg]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/Microbi * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/Microbi * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -426,22 +426,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIGSOrg](https://w3id.org/mixs/vocab/Microbi ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/MicrobialMatBiofilmMigsPl.md b/mixs6/MicrobialMatBiofilmMigsPl.md deleted file mode 100644 index 01caf50c..00000000 --- a/mixs6/MicrobialMatBiofilmMigsPl.md +++ /dev/null @@ -1,505 +0,0 @@ - -# Class: MicrobialMatBiofilmMigsPl - - -Combinatorial checklist for microbial mat_biofilm with migs_pl - -URI: [mixs.vocab:MicrobialMatBiofilmMigsPl](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsPl],[MicrobialMatBiofilmMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsPl],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsPl],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMigsVi.md b/mixs6/MicrobialMatBiofilmMigsVi.md deleted file mode 100644 index 96a174b1..00000000 --- a/mixs6/MicrobialMatBiofilmMigsVi.md +++ /dev/null @@ -1,530 +0,0 @@ - -# Class: MicrobialMatBiofilmMigsVi - - -Combinatorial checklist for microbial mat_biofilm with migs_vi - -URI: [mixs.vocab:MicrobialMatBiofilmMigsVi](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MigsVi],[MicrobialMatBiofilmMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsVi],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMigsVi],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/MicrobialMatBiofilmMimag.md b/mixs6/MicrobialMatBiofilmMimag.md index 6934ef85..45309fff 100644 --- a/mixs6/MicrobialMatBiofilmMimag.md +++ b/mixs6/MicrobialMatBiofilmMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilm],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIMAG],[MicrobialMatBiofilm],[MIMAG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/Microbial * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/Microbial * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -466,22 +466,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/Microbial ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -543,8 +548,3 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIMAG](https://w3id.org/mixs/vocab/Microbial * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimarksC.md b/mixs6/MicrobialMatBiofilmMimarksC.md deleted file mode 100644 index 32203a20..00000000 --- a/mixs6/MicrobialMatBiofilmMimarksC.md +++ /dev/null @@ -1,435 +0,0 @@ - -# Class: MicrobialMatBiofilmMimarksC - - -Combinatorial checklist for microbial mat_biofilm with mimarks_c - -URI: [mixs.vocab:MicrobialMatBiofilmMimarksC](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksC],[MicrobialMatBiofilmMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksC],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksC],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMimarksS.md b/mixs6/MicrobialMatBiofilmMimarksS.md deleted file mode 100644 index 10b03a91..00000000 --- a/mixs6/MicrobialMatBiofilmMimarksS.md +++ /dev/null @@ -1,455 +0,0 @@ - -# Class: MicrobialMatBiofilmMimarksS - - -Combinatorial checklist for microbial mat_biofilm with mimarks_s - -URI: [mixs.vocab:MicrobialMatBiofilmMimarksS](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MimarksS],[MicrobialMatBiofilmMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksS],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMimarksS],[MicrobialMatBiofilm]) - -## Parents - - * is_a: [MicrobialMatBiofilm](MicrobialMatBiofilm.md) - microbial mat/biofilm - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from microbial mat_biofilm: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMisag.md b/mixs6/MicrobialMatBiofilmMisag.md index 3f34e8e1..9c310e5a 100644 --- a/mixs6/MicrobialMatBiofilmMisag.md +++ b/mixs6/MicrobialMatBiofilmMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilm],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMISAG],[MicrobialMatBiofilm],[MISAG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/Microbial * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/Microbial * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -446,22 +446,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/Microbial ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -548,8 +553,3 @@ URI: [mixs.vocab:MicrobialMatBiofilmMISAG](https://w3id.org/mixs/vocab/Microbial * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MicrobialMatBiofilmMiuvig.md b/mixs6/MicrobialMatBiofilmMiuvig.md index 45a9dab4..e298dc9b 100644 --- a/mixs6/MicrobialMatBiofilmMiuvig.md +++ b/mixs6/MicrobialMatBiofilmMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/MicrobialMatBiofilmMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilm],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MicrobialMatBiofilmMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MicrobialMatBiofilm]^-[MicrobialMatBiofilmMIUVIG],[MicrobialMatBiofilm],[MIUVIG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/Microbia * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,10 +80,10 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/Microbia * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -486,22 +486,27 @@ URI: [mixs.vocab:MicrobialMatBiofilmMIUVIG](https://w3id.org/mixs/vocab/Microbia ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/MigsBa.md b/mixs6/MigsBa.md deleted file mode 100644 index 7f65e1ed..00000000 --- a/mixs6/MigsBa.md +++ /dev/null @@ -1,145 +0,0 @@ - -# Class: MigsBa - - -migs_ba Checklist - -URI: [mixs.vocab:MigsBa](https://w3id.org/mixs/vocab/MigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsBa],[WastewaterSludgeMigsBa]uses%20-.->[MigsBa],[SoilMigsBa]uses%20-.->[MigsBa],[SedimentMigsBa]uses%20-.->[MigsBa],[Plant-associatedMigsBa]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa]uses%20-.->[MigsBa],[MicrobialMatBiofilmMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-fluidsSwabsMigsBa]uses%20-.->[MigsBa],[HydrocarbonResources-coresMigsBa]uses%20-.->[MigsBa],[Human-vaginalMigsBa]uses%20-.->[MigsBa],[Human-skinMigsBa]uses%20-.->[MigsBa],[Human-oralMigsBa]uses%20-.->[MigsBa],[Human-gutMigsBa]uses%20-.->[MigsBa],[Human-associatedMigsBa]uses%20-.->[MigsBa],[Host-associatedMigsBa]uses%20-.->[MigsBa],[BuiltEnvironmentMigsBa]uses%20-.->[MigsBa],[AirMigsBa]uses%20-.->[MigsBa],[WaterMigsBa],[WastewaterSludgeMigsBa],[SoilMigsBa],[SedimentMigsBa],[Plant-associatedMigsBa],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MicrobialMatBiofilmMigsBa],[HydrocarbonResources-fluidsSwabsMigsBa],[HydrocarbonResources-coresMigsBa],[Human-vaginalMigsBa],[Human-skinMigsBa],[Human-oralMigsBa],[Human-gutMigsBa],[Human-associatedMigsBa],[Host-associatedMigsBa],[BuiltEnvironmentMigsBa],[AirMigsBa]) - -## Mixin for - - * [AirMigsBa](AirMigsBa.md) (mixin) - Combinatorial checklist for air with migs_ba - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) (mixin) - Combinatorial checklist for built environment with migs_ba - * [Host-associatedMigsBa](Host-associatedMigsBa.md) (mixin) - Combinatorial checklist for host-associated with migs_ba - * [Human-associatedMigsBa](Human-associatedMigsBa.md) (mixin) - Combinatorial checklist for human-associated with migs_ba - * [Human-gutMigsBa](Human-gutMigsBa.md) (mixin) - Combinatorial checklist for human-gut with migs_ba - * [Human-oralMigsBa](Human-oralMigsBa.md) (mixin) - Combinatorial checklist for human-oral with migs_ba - * [Human-skinMigsBa](Human-skinMigsBa.md) (mixin) - Combinatorial checklist for human-skin with migs_ba - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) (mixin) - Combinatorial checklist for human-vaginal with migs_ba - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_ba - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_ba - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_ba - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) (mixin) - Combinatorial checklist for plant-associated with migs_ba - * [SedimentMigsBa](SedimentMigsBa.md) (mixin) - Combinatorial checklist for sediment with migs_ba - * [SoilMigsBa](SoilMigsBa.md) (mixin) - Combinatorial checklist for soil with migs_ba - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_ba - * [WaterMigsBa](WaterMigsBa.md) (mixin) - Combinatorial checklist for water with migs_ba - -## Referenced by class - - -## Attributes - - -### Own - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - * [migs_ba➞collection_date](migs_ba_collection_date.md) REQ - * range: [String](types/String.md) - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - * [migs_ba➞env_broad_scale](migs_ba_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [migs_ba➞env_local_scale](migs_ba_env_local_scale.md) REQ - * range: [String](types/String.md) - * [migs_ba➞env_medium](migs_ba_env_medium.md) REQ - * range: [String](types/String.md) - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - * [migs_ba➞geo_loc_name](migs_ba_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - * [migs_ba➞lat_lon](migs_ba_lat_lon.md) REQ - * range: [String](types/String.md) - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MigsEu.md b/mixs6/MigsEu.md deleted file mode 100644 index 6c1aad1b..00000000 --- a/mixs6/MigsEu.md +++ /dev/null @@ -1,145 +0,0 @@ - -# Class: MigsEu - - -migs_eu Checklist - -URI: [mixs.vocab:MigsEu](https://w3id.org/mixs/vocab/MigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsEu],[WastewaterSludgeMigsEu]uses%20-.->[MigsEu],[SoilMigsEu]uses%20-.->[MigsEu],[SedimentMigsEu]uses%20-.->[MigsEu],[Plant-associatedMigsEu]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu]uses%20-.->[MigsEu],[MicrobialMatBiofilmMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-fluidsSwabsMigsEu]uses%20-.->[MigsEu],[HydrocarbonResources-coresMigsEu]uses%20-.->[MigsEu],[Human-vaginalMigsEu]uses%20-.->[MigsEu],[Human-skinMigsEu]uses%20-.->[MigsEu],[Human-oralMigsEu]uses%20-.->[MigsEu],[Human-gutMigsEu]uses%20-.->[MigsEu],[Human-associatedMigsEu]uses%20-.->[MigsEu],[Host-associatedMigsEu]uses%20-.->[MigsEu],[BuiltEnvironmentMigsEu]uses%20-.->[MigsEu],[AirMigsEu]uses%20-.->[MigsEu],[WaterMigsEu],[WastewaterSludgeMigsEu],[SoilMigsEu],[SedimentMigsEu],[Plant-associatedMigsEu],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MicrobialMatBiofilmMigsEu],[HydrocarbonResources-fluidsSwabsMigsEu],[HydrocarbonResources-coresMigsEu],[Human-vaginalMigsEu],[Human-skinMigsEu],[Human-oralMigsEu],[Human-gutMigsEu],[Human-associatedMigsEu],[Host-associatedMigsEu],[BuiltEnvironmentMigsEu],[AirMigsEu]) - -## Mixin for - - * [AirMigsEu](AirMigsEu.md) (mixin) - Combinatorial checklist for air with migs_eu - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) (mixin) - Combinatorial checklist for built environment with migs_eu - * [Host-associatedMigsEu](Host-associatedMigsEu.md) (mixin) - Combinatorial checklist for host-associated with migs_eu - * [Human-associatedMigsEu](Human-associatedMigsEu.md) (mixin) - Combinatorial checklist for human-associated with migs_eu - * [Human-gutMigsEu](Human-gutMigsEu.md) (mixin) - Combinatorial checklist for human-gut with migs_eu - * [Human-oralMigsEu](Human-oralMigsEu.md) (mixin) - Combinatorial checklist for human-oral with migs_eu - * [Human-skinMigsEu](Human-skinMigsEu.md) (mixin) - Combinatorial checklist for human-skin with migs_eu - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) (mixin) - Combinatorial checklist for human-vaginal with migs_eu - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_eu - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_eu - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_eu - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) (mixin) - Combinatorial checklist for plant-associated with migs_eu - * [SedimentMigsEu](SedimentMigsEu.md) (mixin) - Combinatorial checklist for sediment with migs_eu - * [SoilMigsEu](SoilMigsEu.md) (mixin) - Combinatorial checklist for soil with migs_eu - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_eu - * [WaterMigsEu](WaterMigsEu.md) (mixin) - Combinatorial checklist for water with migs_eu - -## Referenced by class - - -## Attributes - - -### Own - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - * [migs_eu➞collection_date](migs_eu_collection_date.md) REQ - * range: [String](types/String.md) - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - * [migs_eu➞env_broad_scale](migs_eu_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [migs_eu➞env_local_scale](migs_eu_env_local_scale.md) REQ - * range: [String](types/String.md) - * [migs_eu➞env_medium](migs_eu_env_medium.md) REQ - * range: [String](types/String.md) - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - * [migs_eu➞geo_loc_name](migs_eu_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - * [migs_eu➞lat_lon](migs_eu_lat_lon.md) REQ - * range: [String](types/String.md) - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MigsOrg.md b/mixs6/MigsOrg.md index 0db6b760..4474d17a 100644 --- a/mixs6/MigsOrg.md +++ b/mixs6/MigsOrg.md @@ -7,7 +7,7 @@ Minimal Information about a Genome Sequence: org URI: [mixs.vocab:MIGSOrg](https://w3id.org/mixs/vocab/MIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSOrg],[WastewaterSludgeMIGSOrg]uses%20-.->[MIGSOrg],[SoilMIGSOrg]uses%20-.->[MIGSOrg],[SedimentMIGSOrg]uses%20-.->[MIGSOrg],[Plant-associatedMIGSOrg]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[MicrobialMatBiofilmMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-coresMIGSOrg]uses%20-.->[MIGSOrg],[Human-vaginalMIGSOrg]uses%20-.->[MIGSOrg],[Human-skinMIGSOrg]uses%20-.->[MIGSOrg],[Human-oralMIGSOrg]uses%20-.->[MIGSOrg],[Human-gutMIGSOrg]uses%20-.->[MIGSOrg],[Human-associatedMIGSOrg]uses%20-.->[MIGSOrg],[Host-associatedMIGSOrg]uses%20-.->[MIGSOrg],[BuiltEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[AirMIGSOrg]uses%20-.->[MIGSOrg],[WaterMIGSOrg],[WastewaterSludgeMIGSOrg],[SoilMIGSOrg],[SedimentMIGSOrg],[Plant-associatedMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MicrobialMatBiofilmMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-coresMIGSOrg],[Human-vaginalMIGSOrg],[Human-skinMIGSOrg],[Human-oralMIGSOrg],[Human-gutMIGSOrg],[Human-associatedMIGSOrg],[Host-associatedMIGSOrg],[BuiltEnvironmentMIGSOrg],[AirMIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIGSOrg],[WastewaterSludgeMIGSOrg]uses%20-.->[MIGSOrg],[SoilMIGSOrg]uses%20-.->[MIGSOrg],[SedimentMIGSOrg]uses%20-.->[MIGSOrg],[Plant-associatedMIGSOrg]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[MicrobialMatBiofilmMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg]uses%20-.->[MIGSOrg],[HydrocarbonResources-coresMIGSOrg]uses%20-.->[MIGSOrg],[Human-vaginalMIGSOrg]uses%20-.->[MIGSOrg],[Human-skinMIGSOrg]uses%20-.->[MIGSOrg],[Human-oralMIGSOrg]uses%20-.->[MIGSOrg],[Human-gutMIGSOrg]uses%20-.->[MIGSOrg],[Human-associatedMIGSOrg]uses%20-.->[MIGSOrg],[Host-associatedMIGSOrg]uses%20-.->[MIGSOrg],[BuiltEnvironmentMIGSOrg]uses%20-.->[MIGSOrg],[AirMIGSOrg]uses%20-.->[MIGSOrg],[WaterMIGSOrg],[WastewaterSludgeMIGSOrg],[SoilMIGSOrg],[SedimentMIGSOrg],[Plant-associatedMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MicrobialMatBiofilmMIGSOrg],[HydrocarbonResources-fluidsSwabsMIGSOrg],[HydrocarbonResources-coresMIGSOrg],[Human-vaginalMIGSOrg],[Human-skinMIGSOrg],[Human-oralMIGSOrg],[Human-gutMIGSOrg],[Human-associatedMIGSOrg],[Host-associatedMIGSOrg],[BuiltEnvironmentMIGSOrg],[AirMIGSOrg]) ## Mixin for @@ -48,7 +48,7 @@ URI: [mixs.vocab:MIGSOrg](https://w3id.org/mixs/vocab/MIGSOrg) * [MIGS org➞assembly_software](MIGS_org_assembly_software.md) REQ * range: [String](types/String.md) * [MIGS org➞collection_date](MIGS_org_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIGS org➞compl_score](MIGS_org_compl_score.md) OPT * range: * [MIGS org➞compl_software](MIGS_org_compl_software.md) OPT @@ -99,13 +99,15 @@ URI: [mixs.vocab:MIGSOrg](https://w3id.org/mixs/vocab/MIGSOrg) * range: [String](types/String.md) * [MIGS org➞ref_db](MIGS_org_ref_db.md) OPT * range: [String](types/String.md) - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) * [MIGS org➞seq_meth](MIGS_org_seq_meth.md) REQ * range: diff --git a/mixs6/MigsPl.md b/mixs6/MigsPl.md deleted file mode 100644 index 93b47854..00000000 --- a/mixs6/MigsPl.md +++ /dev/null @@ -1,133 +0,0 @@ - -# Class: MigsPl - - -migs_pl Checklist - -URI: [mixs.vocab:MigsPl](https://w3id.org/mixs/vocab/MigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsPl],[WastewaterSludgeMigsPl]uses%20-.->[MigsPl],[SoilMigsPl]uses%20-.->[MigsPl],[SedimentMigsPl]uses%20-.->[MigsPl],[Plant-associatedMigsPl]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl]uses%20-.->[MigsPl],[MicrobialMatBiofilmMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-fluidsSwabsMigsPl]uses%20-.->[MigsPl],[HydrocarbonResources-coresMigsPl]uses%20-.->[MigsPl],[Human-vaginalMigsPl]uses%20-.->[MigsPl],[Human-skinMigsPl]uses%20-.->[MigsPl],[Human-oralMigsPl]uses%20-.->[MigsPl],[Human-gutMigsPl]uses%20-.->[MigsPl],[Human-associatedMigsPl]uses%20-.->[MigsPl],[Host-associatedMigsPl]uses%20-.->[MigsPl],[BuiltEnvironmentMigsPl]uses%20-.->[MigsPl],[AirMigsPl]uses%20-.->[MigsPl],[WaterMigsPl],[WastewaterSludgeMigsPl],[SoilMigsPl],[SedimentMigsPl],[Plant-associatedMigsPl],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MicrobialMatBiofilmMigsPl],[HydrocarbonResources-fluidsSwabsMigsPl],[HydrocarbonResources-coresMigsPl],[Human-vaginalMigsPl],[Human-skinMigsPl],[Human-oralMigsPl],[Human-gutMigsPl],[Human-associatedMigsPl],[Host-associatedMigsPl],[BuiltEnvironmentMigsPl],[AirMigsPl]) - -## Mixin for - - * [AirMigsPl](AirMigsPl.md) (mixin) - Combinatorial checklist for air with migs_pl - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) (mixin) - Combinatorial checklist for built environment with migs_pl - * [Host-associatedMigsPl](Host-associatedMigsPl.md) (mixin) - Combinatorial checklist for host-associated with migs_pl - * [Human-associatedMigsPl](Human-associatedMigsPl.md) (mixin) - Combinatorial checklist for human-associated with migs_pl - * [Human-gutMigsPl](Human-gutMigsPl.md) (mixin) - Combinatorial checklist for human-gut with migs_pl - * [Human-oralMigsPl](Human-oralMigsPl.md) (mixin) - Combinatorial checklist for human-oral with migs_pl - * [Human-skinMigsPl](Human-skinMigsPl.md) (mixin) - Combinatorial checklist for human-skin with migs_pl - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) (mixin) - Combinatorial checklist for human-vaginal with migs_pl - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_pl - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_pl - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_pl - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) (mixin) - Combinatorial checklist for plant-associated with migs_pl - * [SedimentMigsPl](SedimentMigsPl.md) (mixin) - Combinatorial checklist for sediment with migs_pl - * [SoilMigsPl](SoilMigsPl.md) (mixin) - Combinatorial checklist for soil with migs_pl - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_pl - * [WaterMigsPl](WaterMigsPl.md) (mixin) - Combinatorial checklist for water with migs_pl - -## Referenced by class - - -## Attributes - - -### Own - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - * [migs_pl➞collection_date](migs_pl_collection_date.md) REQ - * range: [String](types/String.md) - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - * [migs_pl➞env_broad_scale](migs_pl_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [migs_pl➞env_local_scale](migs_pl_env_local_scale.md) REQ - * range: [String](types/String.md) - * [migs_pl➞env_medium](migs_pl_env_medium.md) REQ - * range: [String](types/String.md) - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - * [migs_pl➞geo_loc_name](migs_pl_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - * [migs_pl➞lat_lon](migs_pl_lat_lon.md) REQ - * range: [String](types/String.md) - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MigsVi.md b/mixs6/MigsVi.md deleted file mode 100644 index c45db5cb..00000000 --- a/mixs6/MigsVi.md +++ /dev/null @@ -1,143 +0,0 @@ - -# Class: MigsVi - - -migs_vi Checklist - -URI: [mixs.vocab:MigsVi](https://w3id.org/mixs/vocab/MigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MigsVi],[WastewaterSludgeMigsVi]uses%20-.->[MigsVi],[SoilMigsVi]uses%20-.->[MigsVi],[SedimentMigsVi]uses%20-.->[MigsVi],[Plant-associatedMigsVi]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi]uses%20-.->[MigsVi],[MicrobialMatBiofilmMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-fluidsSwabsMigsVi]uses%20-.->[MigsVi],[HydrocarbonResources-coresMigsVi]uses%20-.->[MigsVi],[Human-vaginalMigsVi]uses%20-.->[MigsVi],[Human-skinMigsVi]uses%20-.->[MigsVi],[Human-oralMigsVi]uses%20-.->[MigsVi],[Human-gutMigsVi]uses%20-.->[MigsVi],[Human-associatedMigsVi]uses%20-.->[MigsVi],[Host-associatedMigsVi]uses%20-.->[MigsVi],[BuiltEnvironmentMigsVi]uses%20-.->[MigsVi],[AirMigsVi]uses%20-.->[MigsVi],[WaterMigsVi],[WastewaterSludgeMigsVi],[SoilMigsVi],[SedimentMigsVi],[Plant-associatedMigsVi],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MicrobialMatBiofilmMigsVi],[HydrocarbonResources-fluidsSwabsMigsVi],[HydrocarbonResources-coresMigsVi],[Human-vaginalMigsVi],[Human-skinMigsVi],[Human-oralMigsVi],[Human-gutMigsVi],[Human-associatedMigsVi],[Host-associatedMigsVi],[BuiltEnvironmentMigsVi],[AirMigsVi]) - -## Mixin for - - * [AirMigsVi](AirMigsVi.md) (mixin) - Combinatorial checklist for air with migs_vi - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) (mixin) - Combinatorial checklist for built environment with migs_vi - * [Host-associatedMigsVi](Host-associatedMigsVi.md) (mixin) - Combinatorial checklist for host-associated with migs_vi - * [Human-associatedMigsVi](Human-associatedMigsVi.md) (mixin) - Combinatorial checklist for human-associated with migs_vi - * [Human-gutMigsVi](Human-gutMigsVi.md) (mixin) - Combinatorial checklist for human-gut with migs_vi - * [Human-oralMigsVi](Human-oralMigsVi.md) (mixin) - Combinatorial checklist for human-oral with migs_vi - * [Human-skinMigsVi](Human-skinMigsVi.md) (mixin) - Combinatorial checklist for human-skin with migs_vi - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) (mixin) - Combinatorial checklist for human-vaginal with migs_vi - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with migs_vi - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with migs_vi - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with migs_vi - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) (mixin) - Combinatorial checklist for plant-associated with migs_vi - * [SedimentMigsVi](SedimentMigsVi.md) (mixin) - Combinatorial checklist for sediment with migs_vi - * [SoilMigsVi](SoilMigsVi.md) (mixin) - Combinatorial checklist for soil with migs_vi - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) (mixin) - Combinatorial checklist for wastewater_sludge with migs_vi - * [WaterMigsVi](WaterMigsVi.md) (mixin) - Combinatorial checklist for water with migs_vi - -## Referenced by class - - -## Attributes - - -### Own - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - * [migs_vi➞collection_date](migs_vi_collection_date.md) REQ - * range: [String](types/String.md) - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - * [migs_vi➞env_broad_scale](migs_vi_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [migs_vi➞env_local_scale](migs_vi_env_local_scale.md) REQ - * range: [String](types/String.md) - * [migs_vi➞env_medium](migs_vi_env_medium.md) REQ - * range: [String](types/String.md) - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - * [migs_vi➞geo_loc_name](migs_vi_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - * [migs_vi➞lat_lon](migs_vi_lat_lon.md) REQ - * range: [String](types/String.md) - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Mimag.md b/mixs6/Mimag.md index 477feccd..55defb40 100644 --- a/mixs6/Mimag.md +++ b/mixs6/Mimag.md @@ -7,7 +7,7 @@ Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMAG],[WastewaterSludgeMIMAG]uses%20-.->[MIMAG],[SoilMIMAG]uses%20-.->[MIMAG],[SedimentMIMAG]uses%20-.->[MIMAG],[Plant-associatedMIMAG]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG]uses%20-.->[MIMAG],[MicrobialMatBiofilmMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabsMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-coresMIMAG]uses%20-.->[MIMAG],[Human-vaginalMIMAG]uses%20-.->[MIMAG],[Human-skinMIMAG]uses%20-.->[MIMAG],[Human-oralMIMAG]uses%20-.->[MIMAG],[Human-gutMIMAG]uses%20-.->[MIMAG],[Human-associatedMIMAG]uses%20-.->[MIMAG],[Host-associatedMIMAG]uses%20-.->[MIMAG],[BuiltEnvironmentMIMAG]uses%20-.->[MIMAG],[AirMIMAG]uses%20-.->[MIMAG],[WaterMIMAG],[WastewaterSludgeMIMAG],[SoilMIMAG],[SedimentMIMAG],[Plant-associatedMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MicrobialMatBiofilmMIMAG],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-coresMIMAG],[Human-vaginalMIMAG],[Human-skinMIMAG],[Human-oralMIMAG],[Human-gutMIMAG],[Human-associatedMIMAG],[Host-associatedMIMAG],[BuiltEnvironmentMIMAG],[AirMIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIMAG],[WastewaterSludgeMIMAG]uses%20-.->[MIMAG],[SoilMIMAG]uses%20-.->[MIMAG],[SedimentMIMAG]uses%20-.->[MIMAG],[Plant-associatedMIMAG]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG]uses%20-.->[MIMAG],[MicrobialMatBiofilmMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-fluidsSwabsMIMAG]uses%20-.->[MIMAG],[HydrocarbonResources-coresMIMAG]uses%20-.->[MIMAG],[Human-vaginalMIMAG]uses%20-.->[MIMAG],[Human-skinMIMAG]uses%20-.->[MIMAG],[Human-oralMIMAG]uses%20-.->[MIMAG],[Human-gutMIMAG]uses%20-.->[MIMAG],[Human-associatedMIMAG]uses%20-.->[MIMAG],[Host-associatedMIMAG]uses%20-.->[MIMAG],[BuiltEnvironmentMIMAG]uses%20-.->[MIMAG],[AirMIMAG]uses%20-.->[MIMAG],[WaterMIMAG],[WastewaterSludgeMIMAG],[SoilMIMAG],[SedimentMIMAG],[Plant-associatedMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MicrobialMatBiofilmMIMAG],[HydrocarbonResources-fluidsSwabsMIMAG],[HydrocarbonResources-coresMIMAG],[Human-vaginalMIMAG],[Human-skinMIMAG],[Human-oralMIMAG],[Human-gutMIMAG],[Human-associatedMIMAG],[Host-associatedMIMAG],[BuiltEnvironmentMIMAG],[AirMIMAG]) ## Mixin for @@ -52,7 +52,7 @@ URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) * [MIMAG➞bin_software](MIMAG_bin_software.md) REQ * range: * [MIMAG➞collection_date](MIMAG_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIMAG➞compl_appr](MIMAG_compl_appr.md) OPT * range: * [MIMAG➞compl_score](MIMAG_compl_score.md) REQ @@ -115,13 +115,15 @@ URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) * range: [String](types/String.md) * [MIMAG➞rel_to_oxygen](MIMAG_rel_to_oxygen.md) OPT * range: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) * [MIMAG➞seq_meth](MIMAG_seq_meth.md) REQ * range: @@ -147,8 +149,6 @@ URI: [mixs.vocab:MIMAG](https://w3id.org/mixs/vocab/MIMAG) * range: [String](types/String.md) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) ## Other properties diff --git a/mixs6/MimarksC.md b/mixs6/MimarksC.md deleted file mode 100644 index 4a96e8a1..00000000 --- a/mixs6/MimarksC.md +++ /dev/null @@ -1,105 +0,0 @@ - -# Class: MimarksC - - -mimarks_c Checklist - -URI: [mixs.vocab:MimarksC](https://w3id.org/mixs/vocab/MimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MimarksC],[WastewaterSludgeMimarksC]uses%20-.->[MimarksC],[SoilMimarksC]uses%20-.->[MimarksC],[SedimentMimarksC]uses%20-.->[MimarksC],[Plant-associatedMimarksC]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC]uses%20-.->[MimarksC],[MicrobialMatBiofilmMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-fluidsSwabsMimarksC]uses%20-.->[MimarksC],[HydrocarbonResources-coresMimarksC]uses%20-.->[MimarksC],[Human-vaginalMimarksC]uses%20-.->[MimarksC],[Human-skinMimarksC]uses%20-.->[MimarksC],[Human-oralMimarksC]uses%20-.->[MimarksC],[Human-gutMimarksC]uses%20-.->[MimarksC],[Human-associatedMimarksC]uses%20-.->[MimarksC],[Host-associatedMimarksC]uses%20-.->[MimarksC],[BuiltEnvironmentMimarksC]uses%20-.->[MimarksC],[AirMimarksC]uses%20-.->[MimarksC],[WaterMimarksC],[WastewaterSludgeMimarksC],[SoilMimarksC],[SedimentMimarksC],[Plant-associatedMimarksC],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MicrobialMatBiofilmMimarksC],[HydrocarbonResources-fluidsSwabsMimarksC],[HydrocarbonResources-coresMimarksC],[Human-vaginalMimarksC],[Human-skinMimarksC],[Human-oralMimarksC],[Human-gutMimarksC],[Human-associatedMimarksC],[Host-associatedMimarksC],[BuiltEnvironmentMimarksC],[AirMimarksC]) - -## Mixin for - - * [AirMimarksC](AirMimarksC.md) (mixin) - Combinatorial checklist for air with mimarks_c - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) (mixin) - Combinatorial checklist for built environment with mimarks_c - * [Host-associatedMimarksC](Host-associatedMimarksC.md) (mixin) - Combinatorial checklist for host-associated with mimarks_c - * [Human-associatedMimarksC](Human-associatedMimarksC.md) (mixin) - Combinatorial checklist for human-associated with mimarks_c - * [Human-gutMimarksC](Human-gutMimarksC.md) (mixin) - Combinatorial checklist for human-gut with mimarks_c - * [Human-oralMimarksC](Human-oralMimarksC.md) (mixin) - Combinatorial checklist for human-oral with mimarks_c - * [Human-skinMimarksC](Human-skinMimarksC.md) (mixin) - Combinatorial checklist for human-skin with mimarks_c - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) (mixin) - Combinatorial checklist for human-vaginal with mimarks_c - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_c - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_c - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimarks_c - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) (mixin) - Combinatorial checklist for plant-associated with mimarks_c - * [SedimentMimarksC](SedimentMimarksC.md) (mixin) - Combinatorial checklist for sediment with mimarks_c - * [SoilMimarksC](SoilMimarksC.md) (mixin) - Combinatorial checklist for soil with mimarks_c - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimarks_c - * [WaterMimarksC](WaterMimarksC.md) (mixin) - Combinatorial checklist for water with mimarks_c - -## Referenced by class - - -## Attributes - - -### Own - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞collection_date](mimarks_c_collection_date.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞env_broad_scale](mimarks_c_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞env_local_scale](mimarks_c_env_local_scale.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞env_medium](mimarks_c_env_medium.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞geo_loc_name](mimarks_c_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞lat_lon](mimarks_c_lat_lon.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MimarksS.md b/mixs6/MimarksS.md deleted file mode 100644 index a03c0cbd..00000000 --- a/mixs6/MimarksS.md +++ /dev/null @@ -1,113 +0,0 @@ - -# Class: MimarksS - - -mimarks_s Checklist - -URI: [mixs.vocab:MimarksS](https://w3id.org/mixs/vocab/MimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MimarksS],[WastewaterSludgeMimarksS]uses%20-.->[MimarksS],[SoilMimarksS]uses%20-.->[MimarksS],[SedimentMimarksS]uses%20-.->[MimarksS],[Plant-associatedMimarksS]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS]uses%20-.->[MimarksS],[MicrobialMatBiofilmMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-fluidsSwabsMimarksS]uses%20-.->[MimarksS],[HydrocarbonResources-coresMimarksS]uses%20-.->[MimarksS],[Human-vaginalMimarksS]uses%20-.->[MimarksS],[Human-skinMimarksS]uses%20-.->[MimarksS],[Human-oralMimarksS]uses%20-.->[MimarksS],[Human-gutMimarksS]uses%20-.->[MimarksS],[Human-associatedMimarksS]uses%20-.->[MimarksS],[Host-associatedMimarksS]uses%20-.->[MimarksS],[BuiltEnvironmentMimarksS]uses%20-.->[MimarksS],[AirMimarksS]uses%20-.->[MimarksS],[WaterMimarksS],[WastewaterSludgeMimarksS],[SoilMimarksS],[SedimentMimarksS],[Plant-associatedMimarksS],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MicrobialMatBiofilmMimarksS],[HydrocarbonResources-fluidsSwabsMimarksS],[HydrocarbonResources-coresMimarksS],[Human-vaginalMimarksS],[Human-skinMimarksS],[Human-oralMimarksS],[Human-gutMimarksS],[Human-associatedMimarksS],[Host-associatedMimarksS],[BuiltEnvironmentMimarksS],[AirMimarksS]) - -## Mixin for - - * [AirMimarksS](AirMimarksS.md) (mixin) - Combinatorial checklist for air with mimarks_s - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) (mixin) - Combinatorial checklist for built environment with mimarks_s - * [Host-associatedMimarksS](Host-associatedMimarksS.md) (mixin) - Combinatorial checklist for host-associated with mimarks_s - * [Human-associatedMimarksS](Human-associatedMimarksS.md) (mixin) - Combinatorial checklist for human-associated with mimarks_s - * [Human-gutMimarksS](Human-gutMimarksS.md) (mixin) - Combinatorial checklist for human-gut with mimarks_s - * [Human-oralMimarksS](Human-oralMimarksS.md) (mixin) - Combinatorial checklist for human-oral with mimarks_s - * [Human-skinMimarksS](Human-skinMimarksS.md) (mixin) - Combinatorial checklist for human-skin with mimarks_s - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) (mixin) - Combinatorial checklist for human-vaginal with mimarks_s - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) (mixin) - Combinatorial checklist for hydrocarbon resources-cores with mimarks_s - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) (mixin) - Combinatorial checklist for hydrocarbon resources-fluids_swabs with mimarks_s - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) (mixin) - Combinatorial checklist for microbial mat_biofilm with mimarks_s - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) (mixin) - Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) (mixin) - Combinatorial checklist for plant-associated with mimarks_s - * [SedimentMimarksS](SedimentMimarksS.md) (mixin) - Combinatorial checklist for sediment with mimarks_s - * [SoilMimarksS](SoilMimarksS.md) (mixin) - Combinatorial checklist for soil with mimarks_s - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) (mixin) - Combinatorial checklist for wastewater_sludge with mimarks_s - * [WaterMimarksS](WaterMimarksS.md) (mixin) - Combinatorial checklist for water with mimarks_s - -## Referenced by class - - -## Attributes - - -### Own - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞collection_date](mimarks_s_collection_date.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞env_broad_scale](mimarks_s_env_broad_scale.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞env_local_scale](mimarks_s_env_local_scale.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞env_medium](mimarks_s_env_medium.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞geo_loc_name](mimarks_s_geo_loc_name.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - * [mimarks_s➞lat_lon](mimarks_s_lat_lon.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Misag.md b/mixs6/Misag.md index 8dafcb1e..0ca75ea5 100644 --- a/mixs6/Misag.md +++ b/mixs6/Misag.md @@ -7,7 +7,7 @@ Minimum Information About a Single Amplified Genome URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MISAG],[WastewaterSludgeMISAG]uses%20-.->[MISAG],[SoilMISAG]uses%20-.->[MISAG],[SedimentMISAG]uses%20-.->[MISAG],[Plant-associatedMISAG]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG]uses%20-.->[MISAG],[MicrobialMatBiofilmMISAG]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabsMISAG]uses%20-.->[MISAG],[HydrocarbonResources-coresMISAG]uses%20-.->[MISAG],[Human-vaginalMISAG]uses%20-.->[MISAG],[Human-skinMISAG]uses%20-.->[MISAG],[Human-oralMISAG]uses%20-.->[MISAG],[Human-gutMISAG]uses%20-.->[MISAG],[Human-associatedMISAG]uses%20-.->[MISAG],[Host-associatedMISAG]uses%20-.->[MISAG],[BuiltEnvironmentMISAG]uses%20-.->[MISAG],[AirMISAG]uses%20-.->[MISAG],[WaterMISAG],[WastewaterSludgeMISAG],[SoilMISAG],[SedimentMISAG],[Plant-associatedMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MicrobialMatBiofilmMISAG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-coresMISAG],[Human-vaginalMISAG],[Human-skinMISAG],[Human-oralMISAG],[Human-gutMISAG],[Human-associatedMISAG],[Host-associatedMISAG],[BuiltEnvironmentMISAG],[AirMISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MISAG],[WastewaterSludgeMISAG]uses%20-.->[MISAG],[SoilMISAG]uses%20-.->[MISAG],[SedimentMISAG]uses%20-.->[MISAG],[Plant-associatedMISAG]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG]uses%20-.->[MISAG],[MicrobialMatBiofilmMISAG]uses%20-.->[MISAG],[HydrocarbonResources-fluidsSwabsMISAG]uses%20-.->[MISAG],[HydrocarbonResources-coresMISAG]uses%20-.->[MISAG],[Human-vaginalMISAG]uses%20-.->[MISAG],[Human-skinMISAG]uses%20-.->[MISAG],[Human-oralMISAG]uses%20-.->[MISAG],[Human-gutMISAG]uses%20-.->[MISAG],[Human-associatedMISAG]uses%20-.->[MISAG],[Host-associatedMISAG]uses%20-.->[MISAG],[BuiltEnvironmentMISAG]uses%20-.->[MISAG],[AirMISAG]uses%20-.->[MISAG],[WaterMISAG],[WastewaterSludgeMISAG],[SoilMISAG],[SedimentMISAG],[Plant-associatedMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MicrobialMatBiofilmMISAG],[HydrocarbonResources-fluidsSwabsMISAG],[HydrocarbonResources-coresMISAG],[Human-vaginalMISAG],[Human-skinMISAG],[Human-oralMISAG],[Human-gutMISAG],[Human-associatedMISAG],[Host-associatedMISAG],[BuiltEnvironmentMISAG],[AirMISAG]) ## Mixin for @@ -48,7 +48,7 @@ URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) * [MISAG➞assembly_software](MISAG_assembly_software.md) REQ * range: [String](types/String.md) * [MISAG➞collection_date](MISAG_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MISAG➞compl_appr](MISAG_compl_appr.md) OPT * range: * [MISAG➞compl_score](MISAG_compl_score.md) REQ @@ -107,13 +107,15 @@ URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) * range: [String](types/String.md) * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) OPT * range: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) * [MISAG➞samp_size](MISAG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) * [MISAG➞seq_meth](MISAG_seq_meth.md) REQ * range: @@ -149,8 +151,6 @@ URI: [mixs.vocab:MISAG](https://w3id.org/mixs/vocab/MISAG) * range: [String](types/String.md) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) ## Other properties diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md index 527bc0d4..a4850e21 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironment.md @@ -7,7 +7,7 @@ miscellaneous natural or artificial environment URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironmentME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -69,14 +69,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment](https://w3id.org/m * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md index 54f65c14..7a65287d 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSBacteria]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](https: * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](https: * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -385,22 +385,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](https: ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md index f962fb99..62aa6d2d 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSEukaryote]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -385,22 +385,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote](https ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md index bb6b145e..df5159fa 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSPlant]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -360,22 +360,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant](https://w ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md index 2e0d175d..9a72a280 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSVirus]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -380,22 +380,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus](https://w ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md index 24c0eded..34d8e121 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSpecimen]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](htt * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](htt * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -315,22 +315,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen](htt ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md index c90ede6c..e75cacd7 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey],[MiscellaneousNaturalOrArtificialEnvironment],[MIMARKSSurvey]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -290,22 +290,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey](https ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md index 501fec88..ad7c9958 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package m URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentME],[MiscellaneousNaturalOrArtificialEnvironment],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[ME],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentME],[MiscellaneousNaturalOrArtificialEnvironment],[ME]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -335,22 +335,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentME](https://w3id.org ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md deleted file mode 100644 index a8b55543..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md +++ /dev/null @@ -1,459 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsBa - - -Combinatorial checklist for miscellaneous natural or artificial environment with migs_ba - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsBa](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsBa],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsBa],[MiscellaneousNaturalOrArtificialEnvironment],[MigsBa]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md deleted file mode 100644 index 07182c20..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md +++ /dev/null @@ -1,459 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsEu - - -Combinatorial checklist for miscellaneous natural or artificial environment with migs_eu - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsEu](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsEu],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsEu],[MiscellaneousNaturalOrArtificialEnvironment],[MigsEu]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md index e2d40c62..ef122edc 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg],[MiscellaneousNaturalOrArtificialEnvironment],[MIGSOrg]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3i * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3i * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -350,22 +350,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg](https://w3i ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md deleted file mode 100644 index 915cce32..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md +++ /dev/null @@ -1,429 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsPl - - -Combinatorial checklist for miscellaneous natural or artificial environment with migs_pl - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsPl](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsPl],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsPl],[MiscellaneousNaturalOrArtificialEnvironment],[MigsPl]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md deleted file mode 100644 index e5833c4b..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md +++ /dev/null @@ -1,454 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMigsVi - - -Combinatorial checklist for miscellaneous natural or artificial environment with migs_vi - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMigsVi](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MigsVi],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMigsVi],[MiscellaneousNaturalOrArtificialEnvironment],[MigsVi]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md index e06f2529..c884dbf8 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironment],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIMAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIMAG],[MiscellaneousNaturalOrArtificialEnvironment],[MIMAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id. * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id. * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -390,22 +390,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id. ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -467,8 +472,3 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMAG](https://w3id. * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md deleted file mode 100644 index 279c3fe9..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md +++ /dev/null @@ -1,359 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMimarksC - - -Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_c - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksC](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksC],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksC],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksC]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md deleted file mode 100644 index 76fa6617..00000000 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md +++ /dev/null @@ -1,379 +0,0 @@ - -# Class: MiscellaneousNaturalOrArtificialEnvironmentMimarksS - - -Combinatorial checklist for miscellaneous natural or artificial environment with mimarks_s - -URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMimarksS](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MimarksS],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMimarksS],[MiscellaneousNaturalOrArtificialEnvironment],[MimarksS]) - -## Parents - - * is_a: [MiscellaneousNaturalOrArtificialEnvironment](MiscellaneousNaturalOrArtificialEnvironment.md) - miscellaneous natural or artificial environment - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from miscellaneous natural or artificial environment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md index 527980f7..5cca3a9e 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironment],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MISAG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMISAG],[MiscellaneousNaturalOrArtificialEnvironment],[MISAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id. * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id. * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -370,22 +370,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id. ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -472,8 +477,3 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMISAG](https://w3id. * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md index 897ead64..a6726458 100644 --- a/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md +++ b/mixs6/MiscellaneousNaturalOrArtificialEnvironmentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id.org/mixs/vocab/MiscellaneousNaturalOrArtificialEnvironmentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironment],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironment]^-[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MiscellaneousNaturalOrArtificialEnvironment],[MIUVIG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ammonium](ammonium.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -410,22 +410,27 @@ URI: [mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG](https://w3id ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Miuvig.md b/mixs6/Miuvig.md index 2fc63fcb..0ae415e2 100644 --- a/mixs6/Miuvig.md +++ b/mixs6/Miuvig.md @@ -7,7 +7,7 @@ Minimum Information About an Uncultivated Virus Genome URI: [mixs.vocab:MIUVIG](https://w3id.org/mixs/vocab/MIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIUVIG],[WastewaterSludgeMIUVIG]uses%20-.->[MIUVIG],[SoilMIUVIG]uses%20-.->[MIUVIG],[SedimentMIUVIG]uses%20-.->[MIUVIG],[Plant-associatedMIUVIG]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG]uses%20-.->[MIUVIG],[MicrobialMatBiofilmMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-coresMIUVIG]uses%20-.->[MIUVIG],[Human-vaginalMIUVIG]uses%20-.->[MIUVIG],[Human-skinMIUVIG]uses%20-.->[MIUVIG],[Human-oralMIUVIG]uses%20-.->[MIUVIG],[Human-gutMIUVIG]uses%20-.->[MIUVIG],[Human-associatedMIUVIG]uses%20-.->[MIUVIG],[Host-associatedMIUVIG]uses%20-.->[MIUVIG],[BuiltEnvironmentMIUVIG]uses%20-.->[MIUVIG],[AirMIUVIG]uses%20-.->[MIUVIG],[WaterMIUVIG],[WastewaterSludgeMIUVIG],[SoilMIUVIG],[SedimentMIUVIG],[Plant-associatedMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MicrobialMatBiofilmMIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-coresMIUVIG],[Human-vaginalMIUVIG],[Human-skinMIUVIG],[Human-oralMIUVIG],[Human-gutMIUVIG],[Human-associatedMIUVIG],[Host-associatedMIUVIG],[BuiltEnvironmentMIUVIG],[AirMIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[QuantityValue][MIUVIG],[WastewaterSludgeMIUVIG]uses%20-.->[MIUVIG],[SoilMIUVIG]uses%20-.->[MIUVIG],[SedimentMIUVIG]uses%20-.->[MIUVIG],[Plant-associatedMIUVIG]uses%20-.->[MIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG]uses%20-.->[MIUVIG],[MicrobialMatBiofilmMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG]uses%20-.->[MIUVIG],[HydrocarbonResources-coresMIUVIG]uses%20-.->[MIUVIG],[Human-vaginalMIUVIG]uses%20-.->[MIUVIG],[Human-skinMIUVIG]uses%20-.->[MIUVIG],[Human-oralMIUVIG]uses%20-.->[MIUVIG],[Human-gutMIUVIG]uses%20-.->[MIUVIG],[Human-associatedMIUVIG]uses%20-.->[MIUVIG],[Host-associatedMIUVIG]uses%20-.->[MIUVIG],[BuiltEnvironmentMIUVIG]uses%20-.->[MIUVIG],[AirMIUVIG]uses%20-.->[MIUVIG],[WaterMIUVIG],[WastewaterSludgeMIUVIG],[SoilMIUVIG],[SedimentMIUVIG],[Plant-associatedMIUVIG],[MiscellaneousNaturalOrArtificialEnvironmentMIUVIG],[MicrobialMatBiofilmMIUVIG],[HydrocarbonResources-fluidsSwabsMIUVIG],[HydrocarbonResources-coresMIUVIG],[Human-vaginalMIUVIG],[Human-skinMIUVIG],[Human-oralMIUVIG],[Human-gutMIUVIG],[Human-associatedMIUVIG],[Host-associatedMIUVIG],[BuiltEnvironmentMIUVIG],[AirMIUVIG]) ## Mixin for @@ -54,7 +54,7 @@ URI: [mixs.vocab:MIUVIG](https://w3id.org/mixs/vocab/MIUVIG) * [MIUVIG➞biotic_relationship](MIUVIG_biotic_relationship.md) OPT * range: * [MIUVIG➞collection_date](MIUVIG_collection_date.md) REQ - * range: [String](types/String.md) + * range: [Date](types/Date.md) * [MIUVIG➞compl_appr](MIUVIG_compl_appr.md) OPT * range: * [MIUVIG➞compl_score](MIUVIG_compl_score.md) OPT @@ -123,13 +123,15 @@ URI: [mixs.vocab:MIUVIG](https://w3id.org/mixs/vocab/MIUVIG) * range: [String](types/String.md) * [MIUVIG➞ref_db](MIUVIG_ref_db.md) OPT * range: [String](types/String.md) - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT - * range: [String](types/String.md) * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT * range: [QuantityValue](QuantityValue.md) - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) * [MIUVIG➞seq_meth](MIUVIG_seq_meth.md) REQ * range: diff --git a/mixs6/OccupDocumentEnum.md b/mixs6/OccupDocumentEnum.md new file mode 100644 index 00000000..4fd15713 --- /dev/null +++ b/mixs6/OccupDocumentEnum.md @@ -0,0 +1,19 @@ + +# Enum: occup_document_enum + + + + +URI: [mixs.vocab:occup_document_enum](https://w3id.org/mixs/vocab/occup_document_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/OrganismCountEnum.md b/mixs6/OrganismCountEnum.md new file mode 100644 index 00000000..a1aedaad --- /dev/null +++ b/mixs6/OrganismCountEnum.md @@ -0,0 +1,19 @@ + +# Enum: organism_count_enum + + + + +URI: [mixs.vocab:organism_count_enum](https://w3id.org/mixs/vocab/organism_count_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/OxyStatSampEnum.md b/mixs6/OxyStatSampEnum.md new file mode 100644 index 00000000..7194db37 --- /dev/null +++ b/mixs6/OxyStatSampEnum.md @@ -0,0 +1,19 @@ + +# Enum: oxy_stat_samp_enum + + + + +URI: [mixs.vocab:oxy_stat_samp_enum](https://w3id.org/mixs/vocab/oxy_stat_samp_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Plant-associated.md b/mixs6/Plant-associated.md index b30a2b34..177f773f 100644 --- a/mixs6/Plant-associated.md +++ b/mixs6/Plant-associated.md @@ -7,7 +7,7 @@ plant-associated URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG],[Plant-associatedMISAG],[Plant-associatedMIMARKSSurvey],[Plant-associatedMIMARKSSpecimen],[Plant-associatedMIMAG],[Plant-associatedMIGSVirus],[Plant-associatedMIGSPlant],[Plant-associatedMIGSOrg],[Plant-associatedMIGSEukaryote],[Plant-associatedMIGSBacteria],[Plant-associatedME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -69,14 +69,14 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -179,6 +179,10 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -215,6 +219,10 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Description: Any other measurement performed or parameter collected, that is not listed here * range: [String](types/String.md) * Example: Bicarbonate ion concentration;2075 micromole per kilogram None + * [misc_param](misc_param.md) OPT + * Description: Any other measurement performed or parameter collected, that is not listed here + * range: [String](types/String.md) + * Example: Bicarbonate ion concentration;2075 micromole per kilogram None * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens * range: [String](types/String.md) @@ -305,7 +313,7 @@ URI: [mixs.vocab:Plant-associated](https://w3id.org/mixs/vocab/Plant-associated) * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater diff --git a/mixs6/Plant-associatedMIGSBacteria.md b/mixs6/Plant-associatedMIGSBacteria.md index 9bd2c6bf..6c048164 100644 --- a/mixs6/Plant-associatedMIGSBacteria.md +++ b/mixs6/Plant-associatedMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant-associatedMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSBacteria],[Plant-associated]^-[Plant-associatedMIGSBacteria],[Plant-associated],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSBacteria],[Plant-associated]^-[Plant-associatedMIGSBacteria],[Plant-associated],[MIGSBacteria]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -505,22 +509,27 @@ URI: [mixs.vocab:Plant-associatedMIGSBacteria](https://w3id.org/mixs/vocab/Plant ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/Plant-associatedMIGSEukaryote.md b/mixs6/Plant-associatedMIGSEukaryote.md index 3486854b..dd19f16d 100644 --- a/mixs6/Plant-associatedMIGSEukaryote.md +++ b/mixs6/Plant-associatedMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plant-associatedMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Plant-associated]^-[Plant-associatedMIGSEukaryote],[Plant-associated],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Plant-associated]^-[Plant-associatedMIGSEukaryote],[Plant-associated],[MIGSEukaryote]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -505,22 +509,27 @@ URI: [mixs.vocab:Plant-associatedMIGSEukaryote](https://w3id.org/mixs/vocab/Plan ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/Plant-associatedMIGSPlant.md b/mixs6/Plant-associatedMIGSPlant.md index aec619ea..7830fc06 100644 --- a/mixs6/Plant-associatedMIGSPlant.md +++ b/mixs6/Plant-associatedMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-associatedMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSPlant],[Plant-associated]^-[Plant-associatedMIGSPlant],[Plant-associated],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSPlant],[Plant-associated]^-[Plant-associatedMIGSPlant],[Plant-associated],[MIGSPlant]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -480,22 +484,27 @@ URI: [mixs.vocab:Plant-associatedMIGSPlant](https://w3id.org/mixs/vocab/Plant-as ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/Plant-associatedMIGSVirus.md b/mixs6/Plant-associatedMIGSVirus.md index 17400154..a7541c8d 100644 --- a/mixs6/Plant-associatedMIGSVirus.md +++ b/mixs6/Plant-associatedMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-associatedMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSVirus],[Plant-associated]^-[Plant-associatedMIGSVirus],[Plant-associated],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSVirus],[Plant-associated]^-[Plant-associatedMIGSVirus],[Plant-associated],[MIGSVirus]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -500,22 +504,27 @@ URI: [mixs.vocab:Plant-associatedMIGSVirus](https://w3id.org/mixs/vocab/Plant-as ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/Plant-associatedMIMARKSSpecimen.md b/mixs6/Plant-associatedMIMARKSSpecimen.md index 9f74e05d..6dfb4da1 100644 --- a/mixs6/Plant-associatedMIMARKSSpecimen.md +++ b/mixs6/Plant-associatedMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Plant-associated]^-[Plant-associatedMIMARKSSpecimen],[Plant-associated],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Plant-associated]^-[Plant-associatedMIMARKSSpecimen],[Plant-associated],[MIMARKSSpecimen]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -435,22 +439,27 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSpecimen](https://w3id.org/mixs/vocab/Pl ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/Plant-associatedMIMARKSSurvey.md b/mixs6/Plant-associatedMIMARKSSurvey.md index 40d16752..cae69306 100644 --- a/mixs6/Plant-associatedMIMARKSSurvey.md +++ b/mixs6/Plant-associatedMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plant-associatedMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Plant-associated]^-[Plant-associatedMIMARKSSurvey],[Plant-associated],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Plant-associated]^-[Plant-associatedMIMARKSSurvey],[Plant-associated],[MIMARKSSurvey]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -410,22 +414,27 @@ URI: [mixs.vocab:Plant-associatedMIMARKSSurvey](https://w3id.org/mixs/vocab/Plan ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/Plant-associatedMe.md b/mixs6/Plant-associatedMe.md index 46fb10ed..92025096 100644 --- a/mixs6/Plant-associatedMe.md +++ b/mixs6/Plant-associatedMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package p URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associatedME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[ME],[Plant-associated]^-[Plant-associatedME],[Plant-associated],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[ME],[Plant-associated]^-[Plant-associatedME],[Plant-associated],[ME]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -455,22 +459,27 @@ URI: [mixs.vocab:Plant-associatedME](https://w3id.org/mixs/vocab/Plant-associate ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/Plant-associatedMigsBa.md b/mixs6/Plant-associatedMigsBa.md deleted file mode 100644 index be306b51..00000000 --- a/mixs6/Plant-associatedMigsBa.md +++ /dev/null @@ -1,579 +0,0 @@ - -# Class: Plant-associatedMigsBa - - -Combinatorial checklist for plant-associated with migs_ba - -URI: [mixs.vocab:Plant-associatedMigsBa](https://w3id.org/mixs/vocab/Plant-associatedMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsBa],[Plant-associated]^-[Plant-associatedMigsBa],[Plant-associated],[MigsBa]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsEu.md b/mixs6/Plant-associatedMigsEu.md deleted file mode 100644 index c2b3e73e..00000000 --- a/mixs6/Plant-associatedMigsEu.md +++ /dev/null @@ -1,579 +0,0 @@ - -# Class: Plant-associatedMigsEu - - -Combinatorial checklist for plant-associated with migs_eu - -URI: [mixs.vocab:Plant-associatedMigsEu](https://w3id.org/mixs/vocab/Plant-associatedMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsEu],[Plant-associated]^-[Plant-associatedMigsEu],[Plant-associated],[MigsEu]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsOrg.md b/mixs6/Plant-associatedMigsOrg.md index b6b9d055..1e41adc1 100644 --- a/mixs6/Plant-associatedMigsOrg.md +++ b/mixs6/Plant-associatedMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-associatedMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIGSOrg],[Plant-associated]^-[Plant-associatedMIGSOrg],[Plant-associated],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIGSOrg],[Plant-associated]^-[Plant-associatedMIGSOrg],[Plant-associated],[MIGSOrg]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -470,22 +474,27 @@ URI: [mixs.vocab:Plant-associatedMIGSOrg](https://w3id.org/mixs/vocab/Plant-asso ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/Plant-associatedMigsPl.md b/mixs6/Plant-associatedMigsPl.md deleted file mode 100644 index 7bc1bea7..00000000 --- a/mixs6/Plant-associatedMigsPl.md +++ /dev/null @@ -1,549 +0,0 @@ - -# Class: Plant-associatedMigsPl - - -Combinatorial checklist for plant-associated with migs_pl - -URI: [mixs.vocab:Plant-associatedMigsPl](https://w3id.org/mixs/vocab/Plant-associatedMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsPl],[Plant-associated]^-[Plant-associatedMigsPl],[Plant-associated],[MigsPl]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMigsVi.md b/mixs6/Plant-associatedMigsVi.md deleted file mode 100644 index 70e3efa3..00000000 --- a/mixs6/Plant-associatedMigsVi.md +++ /dev/null @@ -1,574 +0,0 @@ - -# Class: Plant-associatedMigsVi - - -Combinatorial checklist for plant-associated with migs_vi - -URI: [mixs.vocab:Plant-associatedMigsVi](https://w3id.org/mixs/vocab/Plant-associatedMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MigsVi],[Plant-associated]^-[Plant-associatedMigsVi],[Plant-associated],[MigsVi]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/Plant-associatedMimag.md b/mixs6/Plant-associatedMimag.md index 354893e1..c524f740 100644 --- a/mixs6/Plant-associatedMimag.md +++ b/mixs6/Plant-associatedMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associatedMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIMAG],[Plant-associated]^-[Plant-associatedMIMAG],[Plant-associated],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIMAG],[Plant-associated]^-[Plant-associatedMIMAG],[Plant-associated],[MIMAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -510,22 +514,27 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -587,8 +596,3 @@ URI: [mixs.vocab:Plant-associatedMIMAG](https://w3id.org/mixs/vocab/Plant-associ * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimarksC.md b/mixs6/Plant-associatedMimarksC.md deleted file mode 100644 index 8daf889c..00000000 --- a/mixs6/Plant-associatedMimarksC.md +++ /dev/null @@ -1,479 +0,0 @@ - -# Class: Plant-associatedMimarksC - - -Combinatorial checklist for plant-associated with mimarks_c - -URI: [mixs.vocab:Plant-associatedMimarksC](https://w3id.org/mixs/vocab/Plant-associatedMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksC],[Plant-associated]^-[Plant-associatedMimarksC],[Plant-associated],[MimarksC]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMimarksS.md b/mixs6/Plant-associatedMimarksS.md deleted file mode 100644 index 8974d1fd..00000000 --- a/mixs6/Plant-associatedMimarksS.md +++ /dev/null @@ -1,499 +0,0 @@ - -# Class: Plant-associatedMimarksS - - -Combinatorial checklist for plant-associated with mimarks_s - -URI: [mixs.vocab:Plant-associatedMimarksS](https://w3id.org/mixs/vocab/Plant-associatedMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MimarksS],[Plant-associated]^-[Plant-associatedMimarksS],[Plant-associated],[MimarksS]) - -## Parents - - * is_a: [Plant-associated](Plant-associated.md) - plant-associated - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from plant-associated: - - * [air_temp_regm](air_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens - * range: [String](types/String.md) - * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [ances_data](ances_data.md) OPT - * Description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) - * range: [String](types/String.md) - * Example: A/3*B None - * [antibiotic_regm](antibiotic_regm.md) OPT - * Description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens - * range: [String](types/String.md) - * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification - * range: - * Example: natural None - * [biotic_regm](biotic_regm.md) OPT - * Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. - * range: [String](types/String.md) - * Example: sample inoculated with Rhizobium spp. Culture None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_mutagen](chem_mutagen.md) OPT - * Description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens - * range: [String](types/String.md) - * Example: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [climate_environment](climate_environment.md) OPT - * Description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates - * range: [String](types/String.md) - * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [cult_root_med](cult_root_med.md) OPT - * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fertilizer_regm](fertilizer_regm.md) OPT - * Description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens - * range: [String](types/String.md) - * Example: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [fungicide_regm](fungicide_regm.md) OPT - * Description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens - * range: [String](types/String.md) - * Example: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [gaseous_environment](gaseous_environment.md) OPT - * Description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens - * range: [String](types/String.md) - * Example: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [genetic_mod](genetic_mod.md) OPT - * Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection - * range: [String](types/String.md) - * Example: aox1A transgenic None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [gravity](gravity.md) OPT - * Description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments - * range: [String](types/String.md) - * Example: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [growth_facil](growth_facil.md) OPT - * Description: Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research - * range: [String](types/String.md) - * Example: Growth chamber [CO_715:0000189] None - * [growth_habit](growth_habit.md) OPT - * Description: Characteristic shape, appearance or growth form of a plant species - * range: - * Example: spreading None - * [growth_hormone_regm](growth_hormone_regm.md) OPT - * Description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens - * range: [String](types/String.md) - * Example: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [herbicide_regm](herbicide_regm.md) OPT - * Description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [host_age](host_age.md) OPT - * Description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees - * range: [QuantityValue](QuantityValue.md) - * Example: 10 days None - * [host_common_name](host_common_name.md) OPT - * Description: Common name of the host, e.g. Human - * range: [String](types/String.md) - * Example: mussel None - * [host_disease_stat](host_disease_stat.md) OPT - * Description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - * range: [String](types/String.md) - * Example: rabies [DOID:11260] None - * [host_dry_mass](host_dry_mass.md) OPT - * Description: Measurement of dry mass - * range: [QuantityValue](QuantityValue.md) - * Example: 500 gram None - * [host_genotype](host_genotype.md) OPT - * Description: Observed genotype - * range: [String](types/String.md) - * Example: C57BL/6 None - * [host_height](host_height.md) OPT - * Description: The height of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 meter None - * [host_infra_specific_name](host_infra_specific_name.md) OPT - * Description: Taxonomic information about the host below subspecies level - * range: [String](types/String.md) - * Example: borealis None - * [host_infra_specific_rank](host_infra_specific_rank.md) OPT - * Description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. - * range: [String](types/String.md) - * Example: subspecies None - * [host_length](host_length.md) OPT - * Description: The length of subject - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter None - * [host_life_stage](host_life_stage.md) OPT - * Description: Description of life stage of host - * range: [String](types/String.md) - * Example: adult None - * [host_phenotype](host_phenotype.md) OPT - * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - * range: [String](types/String.md) - * Example: elongated [PATO:0001154] None - * [host_taxid](host_taxid.md) OPT - * Description: NCBI taxon id of the host, e.g. 9606 - * range: [String](types/String.md) - * Example: 7955 None - * [host_tot_mass](host_tot_mass.md) OPT - * Description: Total mass of the host at collection, the unit depends on host - * range: [QuantityValue](QuantityValue.md) - * Example: 2500 gram None - * [host_wet_mass](host_wet_mass.md) OPT - * Description: Measurement of wet mass - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 gram None - * [humidity_regm](humidity_regm.md) OPT - * Description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_regm](light_regm.md) OPT - * Description: Information about treatment(s) involving exposure to light, including both light intensity and quality. - * range: [String](types/String.md) - * Example: incandescant light;10 lux;450 nanometer None - * [mechanical_damage](mechanical_damage.md) OPT - * Description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites - * range: [String](types/String.md) - * Example: pruning;bark None - * [mineral_nutr_regm](mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens - * range: [String](types/String.md) - * Example: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [non_mineral_nutr_regm](non_mineral_nutr_regm.md) OPT - * Description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens - * range: [String](types/String.md) - * Example: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [pesticide_regm](pesticide_regm.md) OPT - * Description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens - * range: [String](types/String.md) - * Example: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [ph_regm](ph_regm.md) OPT - * Description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen - * range: [String](types/String.md) - * Example: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M None - * [plant_growth_med](plant_growth_med.md) OPT - * Description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary - * range: - * Example: hydroponic plant culture media [EO:0007067] None - * [plant_product](plant_product.md) OPT - * Description: Substance produced by the plant, where the sample was obtained from - * range: [String](types/String.md) - * Example: xylem sap [PO:0025539] None - * [plant_sex](plant_sex.md) OPT - * Description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. - * range: - * Example: Hermaphroditic None - * [plant_struc](plant_struc.md) OPT - * Description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. - * range: [String](types/String.md) - * Example: epidermis [PO:0005679] None - * [radiation_regm](radiation_regm.md) OPT - * Description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens - * range: [String](types/String.md) - * Example: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [rainfall_regm](rainfall_regm.md) OPT - * Description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [root_cond](root_cond.md) OPT - * Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. - * range: [String](types/String.md) - * Example: http://himedialabs.com/TD/PT158.pdf None - * [root_med_carbon](root_med_carbon.md) OPT - * Description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - * range: [String](types/String.md) - * Example: sucrose None - * [root_med_macronutr](root_med_macronutr.md) OPT - * Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - * range: [String](types/String.md) - * Example: KH2PO4;170¬†milligram per liter None - * [root_med_micronutr](root_med_micronutr.md) OPT - * Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - * range: [String](types/String.md) - * Example: H3BO3;6.2¬†milligram per liter None - * [root_med_ph](root_med_ph.md) OPT - * Description: pH measurement of the culture rooting medium; e.g. 5.5. - * range: [Double](types/Double.md) - * Example: 7.5 None - * [root_med_regl](root_med_regl.md) OPT - * Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - * range: [String](types/String.md) - * Example: abscisic acid;0.75 milligram per liter None - * [root_med_solid](root_med_solid.md) OPT - * Description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. - * range: [String](types/String.md) - * Example: agar None - * [root_med_suppl](root_med_suppl.md) OPT - * Description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). - * range: [String](types/String.md) - * Example: nicotinic acid;0.5 milligram per liter None - * [salt_regm](salt_regm.md) OPT - * Description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens - * range: [String](types/String.md) - * Example: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [samp_capt_status](samp_capt_status.md) OPT - * Description: Reason for the sample - * range: - * Example: farm sample None - * [samp_dis_stage](samp_dis_stage.md) OPT - * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) - * Example: infection None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_environment](season_environment.md) OPT - * Description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment - * range: [String](types/String.md) - * Example: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [standing_water_regm](standing_water_regm.md) OPT - * Description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tiss_cult_growth_med](tiss_cult_growth_med.md) OPT - * Description: Description of plant tissue culture growth media used - * range: [String](types/String.md) - * Example: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf None - * [water_temp_regm](water_temp_regm.md) OPT - * Description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - * [watering_regm](watering_regm.md) OPT - * Description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens - * range: [String](types/String.md) - * Example: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMisag.md b/mixs6/Plant-associatedMisag.md index 5963f27d..351af4f4 100644 --- a/mixs6/Plant-associatedMisag.md +++ b/mixs6/Plant-associatedMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associatedMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MISAG],[Plant-associated]^-[Plant-associatedMISAG],[Plant-associated],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MISAG],[Plant-associated]^-[Plant-associatedMISAG],[Plant-associated],[MISAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -490,22 +494,27 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -592,8 +601,3 @@ URI: [mixs.vocab:Plant-associatedMISAG](https://w3id.org/mixs/vocab/Plant-associ * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/Plant-associatedMiuvig.md b/mixs6/Plant-associatedMiuvig.md index 781df78d..31caac74 100644 --- a/mixs6/Plant-associatedMiuvig.md +++ b/mixs6/Plant-associatedMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-associatedMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F]uses%20-.->[MIUVIG],[Plant-associated]^-[Plant-associatedMIUVIG],[Plant-associated],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[QuantityValue],[Plant-associatedMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;air_temp_regm(i):string%20%3F;ances_data(i):string%20%3F;antibiotic_regm(i):string%20%3F;biol_stat(i):biol_stat_enum%20%3F;biotic_regm(i):string%20%3F;chem_administration(i):string%20%3F;chem_mutagen(i):string%20%3F;climate_environment(i):string%20%3F;cult_root_med(i):string%20%3F;fertilizer_regm(i):string%20%3F;fungicide_regm(i):string%20%3F;gaseous_environment(i):string%20%3F;genetic_mod(i):string%20%3F;gravity(i):string%20%3F;growth_facil(i):string%20%3F;growth_habit(i):growth_habit_enum%20%3F;growth_hormone_regm(i):string%20%3F;herbicide_regm(i):string%20%3F;host_common_name(i):string%20%3F;host_disease_stat(i):string%20%3F;host_genotype(i):string%20%3F;host_infra_specific_name(i):string%20%3F;host_infra_specific_rank(i):string%20%3F;host_life_stage(i):string%20%3F;host_phenotype(i):string%20%3F;host_taxid(i):string%20%3F;humidity_regm(i):string%20%3F;light_regm(i):string%20%3F;mechanical_damage(i):string%20%3F;mineral_nutr_regm(i):string%20%3F;misc_param(i):string%20%3F;non_mineral_nutr_regm(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph_regm(i):string%20%3F;perturbation(i):string%20%3F;pesticide_regm(i):string%20%3F;plant_growth_med(i):plant_growth_med_enum%20%3F;plant_product(i):string%20%3F;plant_sex(i):plant_sex_enum%20%3F;plant_struc(i):string%20%3F;radiation_regm(i):string%20%3F;rainfall_regm(i):string%20%3F;root_cond(i):string%20%3F;root_med_carbon(i):string%20%3F;root_med_macronutr(i):string%20%3F;root_med_micronutr(i):string%20%3F;root_med_suppl(i):string%20%3F;root_med_ph(i):double%20%3F;root_med_regl(i):string%20%3F;root_med_solid(i):string%20%3F;salt_regm(i):string%20%3F;samp_capt_status(i):samp_capt_status_enum%20%3F;samp_dis_stage(i):samp_dis_stage_enum%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;season_environment(i):string%20%3F;standing_water_regm(i):string%20%3F;tiss_cult_growth_med(i):string%20%3F;water_temp_regm(i):string%20%3F;watering_regm(i):string%20%3F;host_symbiont(i):string%20%3F]uses%20-.->[MIUVIG],[Plant-associated]^-[Plant-associatedMIUVIG],[Plant-associated],[MIUVIG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc * range: [String](types/String.md) * Example: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [ances_data](ances_data.md) OPT @@ -39,7 +39,7 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc * range: [String](types/String.md) * Example: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [biol_stat](biol_stat.md) OPT - * Description: The level of genome modification + * Description: The level of genome modification. * range: * Example: natural None * [biotic_regm](biotic_regm.md) OPT @@ -60,14 +60,14 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc * Example: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [cult_root_med](cult_root_med.md) OPT * Description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. * range: [String](types/String.md) * Example: http://himedialabs.com/TD/PT158.pdf None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [elev](elev.md) OPT @@ -170,6 +170,10 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc * Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP * range: [String](types/String.md) * Example: elongated [PATO:0001154] None + * [host_symbiont](host_symbiont.md) OPT + * Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + * range: [String](types/String.md) + * Example: flukeworms None * [host_taxid](host_taxid.md) OPT * Description: NCBI taxon id of the host, e.g. 9606 * range: [String](types/String.md) @@ -296,7 +300,7 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc * Example: farm sample None * [samp_dis_stage](samp_dis_stage.md) OPT * Description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. - * range: [String](types/String.md) + * range: * Example: infection None * [samp_salinity](samp_salinity.md) OPT * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater @@ -530,22 +534,27 @@ URI: [mixs.vocab:Plant-associatedMIUVIG](https://w3id.org/mixs/vocab/Plant-assoc ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/PlantGrowthMedEnum.md b/mixs6/PlantGrowthMedEnum.md new file mode 100644 index 00000000..f11c5c35 --- /dev/null +++ b/mixs6/PlantGrowthMedEnum.md @@ -0,0 +1,19 @@ + +# Enum: plant_growth_med_enum + + + + +URI: [mixs.vocab:plant_growth_med_enum](https://w3id.org/mixs/vocab/plant_growth_med_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PlantSexEnum.md b/mixs6/PlantSexEnum.md new file mode 100644 index 00000000..95d2940a --- /dev/null +++ b/mixs6/PlantSexEnum.md @@ -0,0 +1,19 @@ + +# Enum: plant_sex_enum + + + + +URI: [mixs.vocab:plant_sex_enum](https://w3id.org/mixs/vocab/plant_sex_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PredGenomeStrucEnum.md b/mixs6/PredGenomeStrucEnum.md new file mode 100644 index 00000000..0fb044dc --- /dev/null +++ b/mixs6/PredGenomeStrucEnum.md @@ -0,0 +1,19 @@ + +# Enum: pred_genome_struc_enum + + + + +URI: [mixs.vocab:pred_genome_struc_enum](https://w3id.org/mixs/vocab/pred_genome_struc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PredGenomeTypeEnum.md b/mixs6/PredGenomeTypeEnum.md new file mode 100644 index 00000000..c47cf479 --- /dev/null +++ b/mixs6/PredGenomeTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: pred_genome_type_enum + + + + +URI: [mixs.vocab:pred_genome_type_enum](https://w3id.org/mixs/vocab/pred_genome_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/PresAnimalEnum.md b/mixs6/PresAnimalEnum.md new file mode 100644 index 00000000..7529f727 --- /dev/null +++ b/mixs6/PresAnimalEnum.md @@ -0,0 +1,19 @@ + +# Enum: pres_animal_enum + + + + +URI: [mixs.vocab:pres_animal_enum](https://w3id.org/mixs/vocab/pres_animal_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ProfilePositionEnum.md b/mixs6/ProfilePositionEnum.md new file mode 100644 index 00000000..763d9908 --- /dev/null +++ b/mixs6/ProfilePositionEnum.md @@ -0,0 +1,19 @@ + +# Enum: profile_position_enum + + + + +URI: [mixs.vocab:profile_position_enum](https://w3id.org/mixs/vocab/profile_position_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/QuadPosEnum.md b/mixs6/QuadPosEnum.md new file mode 100644 index 00000000..0e2fb6a5 --- /dev/null +++ b/mixs6/QuadPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: quad_pos_enum + + + + +URI: [mixs.vocab:quad_pos_enum](https://w3id.org/mixs/vocab/quad_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RelSampLocEnum.md b/mixs6/RelSampLocEnum.md new file mode 100644 index 00000000..7a40bb43 --- /dev/null +++ b/mixs6/RelSampLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: rel_samp_loc_enum + + + + +URI: [mixs.vocab:rel_samp_loc_enum](https://w3id.org/mixs/vocab/rel_samp_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RelToOxygenEnum.md b/mixs6/RelToOxygenEnum.md new file mode 100644 index 00000000..25d2e92d --- /dev/null +++ b/mixs6/RelToOxygenEnum.md @@ -0,0 +1,19 @@ + +# Enum: rel_to_oxygen_enum + + + + +URI: [mixs.vocab:rel_to_oxygen_enum](https://w3id.org/mixs/vocab/rel_to_oxygen_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomCondtEnum.md b/mixs6/RoomCondtEnum.md new file mode 100644 index 00000000..56e0d3c7 --- /dev/null +++ b/mixs6/RoomCondtEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_condt_enum + + + + +URI: [mixs.vocab:room_condt_enum](https://w3id.org/mixs/vocab/room_condt_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomConnectedEnum.md b/mixs6/RoomConnectedEnum.md new file mode 100644 index 00000000..87895180 --- /dev/null +++ b/mixs6/RoomConnectedEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_connected_enum + + + + +URI: [mixs.vocab:room_connected_enum](https://w3id.org/mixs/vocab/room_connected_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomLocEnum.md b/mixs6/RoomLocEnum.md new file mode 100644 index 00000000..73672520 --- /dev/null +++ b/mixs6/RoomLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_loc_enum + + + + +URI: [mixs.vocab:room_loc_enum](https://w3id.org/mixs/vocab/room_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomSampPosEnum.md b/mixs6/RoomSampPosEnum.md new file mode 100644 index 00000000..f486e3c1 --- /dev/null +++ b/mixs6/RoomSampPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_samp_pos_enum + + + + +URI: [mixs.vocab:room_samp_pos_enum](https://w3id.org/mixs/vocab/room_samp_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/RoomTypeEnum.md b/mixs6/RoomTypeEnum.md new file mode 100644 index 00000000..71b1cd10 --- /dev/null +++ b/mixs6/RoomTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: room_type_enum + + + + +URI: [mixs.vocab:room_type_enum](https://w3id.org/mixs/vocab/room_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampCaptStatusEnum.md b/mixs6/SampCaptStatusEnum.md new file mode 100644 index 00000000..7dc54050 --- /dev/null +++ b/mixs6/SampCaptStatusEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_capt_status_enum + + + + +URI: [mixs.vocab:samp_capt_status_enum](https://w3id.org/mixs/vocab/samp_capt_status_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampCollectionPointEnum.md b/mixs6/SampCollectionPointEnum.md new file mode 100644 index 00000000..51f7de7b --- /dev/null +++ b/mixs6/SampCollectionPointEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_collection_point_enum + + + + +URI: [mixs.vocab:samp_collection_point_enum](https://w3id.org/mixs/vocab/samp_collection_point_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampDisStageEnum.md b/mixs6/SampDisStageEnum.md new file mode 100644 index 00000000..62c596f5 --- /dev/null +++ b/mixs6/SampDisStageEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_dis_stage_enum + + + + +URI: [mixs.vocab:samp_dis_stage_enum](https://w3id.org/mixs/vocab/samp_dis_stage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampFloorEnum.md b/mixs6/SampFloorEnum.md new file mode 100644 index 00000000..bc05f407 --- /dev/null +++ b/mixs6/SampFloorEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_floor_enum + + + + +URI: [mixs.vocab:samp_floor_enum](https://w3id.org/mixs/vocab/samp_floor_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampMdEnum.md b/mixs6/SampMdEnum.md new file mode 100644 index 00000000..19366ebf --- /dev/null +++ b/mixs6/SampMdEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_md_enum + + + + +URI: [mixs.vocab:samp_md_enum](https://w3id.org/mixs/vocab/samp_md_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampSubtypeEnum.md b/mixs6/SampSubtypeEnum.md new file mode 100644 index 00000000..59bd72fa --- /dev/null +++ b/mixs6/SampSubtypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_subtype_enum + + + + +URI: [mixs.vocab:samp_subtype_enum](https://w3id.org/mixs/vocab/samp_subtype_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampTypeEnum.md b/mixs6/SampTypeEnum.md new file mode 100644 index 00000000..9a475694 --- /dev/null +++ b/mixs6/SampTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_type_enum + + + + +URI: [mixs.vocab:samp_type_enum](https://w3id.org/mixs/vocab/samp_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SampWeatherEnum.md b/mixs6/SampWeatherEnum.md new file mode 100644 index 00000000..eb0dc515 --- /dev/null +++ b/mixs6/SampWeatherEnum.md @@ -0,0 +1,19 @@ + +# Enum: samp_weather_enum + + + + +URI: [mixs.vocab:samp_weather_enum](https://w3id.org/mixs/vocab/samp_weather_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SeasonUseEnum.md b/mixs6/SeasonUseEnum.md new file mode 100644 index 00000000..db48c17e --- /dev/null +++ b/mixs6/SeasonUseEnum.md @@ -0,0 +1,19 @@ + +# Enum: season_use_enum + + + + +URI: [mixs.vocab:season_use_enum](https://w3id.org/mixs/vocab/season_use_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Sediment.md b/mixs6/Sediment.md index 3ce7b16d..1f1461b7 100644 --- a/mixs6/Sediment.md +++ b/mixs6/Sediment.md @@ -7,7 +7,7 @@ sediment URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG],[SedimentMISAG],[SedimentMIMARKSSurvey],[SedimentMIMARKSSpecimen],[SedimentMIMAG],[SedimentMIGSVirus],[SedimentMIGSPlant],[SedimentMIGSOrg],[SedimentMIGSEukaryote],[SedimentMIGSBacteria],[SedimentME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -89,14 +89,14 @@ URI: [mixs.vocab:Sediment](https://w3id.org/mixs/vocab/Sediment) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT diff --git a/mixs6/SedimentMIGSBacteria.md b/mixs6/SedimentMIGSBacteria.md index 1a2245ef..ffc2078d 100644 --- a/mixs6/SedimentMIGSBacteria.md +++ b/mixs6/SedimentMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:SedimentMIGSBacteria](https://w3id.org/mixs/vocab/SedimentMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Sediment]^-[SedimentMIGSBacteria],[Sediment],[QuantityValue],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Sediment]^-[SedimentMIGSBacteria],[Sediment],[QuantityValue],[MIGSBacteria]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIGSBacteria](https://w3id.org/mixs/vocab/SedimentMIGSB * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIGSBacteria](https://w3id.org/mixs/vocab/SedimentMIGSB * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -485,22 +485,27 @@ URI: [mixs.vocab:SedimentMIGSBacteria](https://w3id.org/mixs/vocab/SedimentMIGSB ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/SedimentMIGSEukaryote.md b/mixs6/SedimentMIGSEukaryote.md index 98b47fc9..8c4115f2 100644 --- a/mixs6/SedimentMIGSEukaryote.md +++ b/mixs6/SedimentMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Sediment]^-[SedimentMIGSEukaryote],[Sediment],[QuantityValue],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Sediment]^-[SedimentMIGSEukaryote],[Sediment],[QuantityValue],[MIGSEukaryote]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGS * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGS * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -485,22 +485,27 @@ URI: [mixs.vocab:SedimentMIGSEukaryote](https://w3id.org/mixs/vocab/SedimentMIGS ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/SedimentMIGSPlant.md b/mixs6/SedimentMIGSPlant.md index a372cb36..6798ae18 100644 --- a/mixs6/SedimentMIGSPlant.md +++ b/mixs6/SedimentMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Sediment]^-[SedimentMIGSPlant],[Sediment],[QuantityValue],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Sediment]^-[SedimentMIGSPlant],[Sediment],[QuantityValue],[MIGSPlant]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlan * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlan * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -460,22 +460,27 @@ URI: [mixs.vocab:SedimentMIGSPlant](https://w3id.org/mixs/vocab/SedimentMIGSPlan ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/SedimentMIGSVirus.md b/mixs6/SedimentMIGSVirus.md index a6f2352f..bbeeb795 100644 --- a/mixs6/SedimentMIGSVirus.md +++ b/mixs6/SedimentMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Sediment]^-[SedimentMIGSVirus],[Sediment],[QuantityValue],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Sediment]^-[SedimentMIGSVirus],[Sediment],[QuantityValue],[MIGSVirus]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSViru * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSViru * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -480,22 +480,27 @@ URI: [mixs.vocab:SedimentMIGSVirus](https://w3id.org/mixs/vocab/SedimentMIGSViru ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/SedimentMIMARKSSpecimen.md b/mixs6/SedimentMIMARKSSpecimen.md index 84368dae..0567f241 100644 --- a/mixs6/SedimentMIMARKSSpecimen.md +++ b/mixs6/SedimentMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Sediment]^-[SedimentMIMARKSSpecimen],[Sediment],[QuantityValue],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Sediment]^-[SedimentMIMARKSSpecimen],[Sediment],[QuantityValue],[MIMARKSSpecimen]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMI * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMI * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -415,22 +415,27 @@ URI: [mixs.vocab:SedimentMIMARKSSpecimen](https://w3id.org/mixs/vocab/SedimentMI ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/SedimentMIMARKSSurvey.md b/mixs6/SedimentMIMARKSSurvey.md index 23b8e9f5..6175819c 100644 --- a/mixs6/SedimentMIMARKSSurvey.md +++ b/mixs6/SedimentMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Sediment]^-[SedimentMIMARKSSurvey],[Sediment],[QuantityValue],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Sediment]^-[SedimentMIMARKSSurvey],[Sediment],[QuantityValue],[MIMARKSSurvey]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMA * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMA * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -390,22 +390,27 @@ URI: [mixs.vocab:SedimentMIMARKSSurvey](https://w3id.org/mixs/vocab/SedimentMIMA ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/SedimentMe.md b/mixs6/SedimentMe.md index e80089a8..6079b26a 100644 --- a/mixs6/SedimentMe.md +++ b/mixs6/SedimentMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package s URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Sediment]^-[SedimentME],[Sediment],[QuantityValue],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Sediment]^-[SedimentME],[Sediment],[QuantityValue],[ME]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -435,22 +435,27 @@ URI: [mixs.vocab:SedimentME](https://w3id.org/mixs/vocab/SedimentME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/SedimentMigsBa.md b/mixs6/SedimentMigsBa.md deleted file mode 100644 index e6501b5c..00000000 --- a/mixs6/SedimentMigsBa.md +++ /dev/null @@ -1,559 +0,0 @@ - -# Class: SedimentMigsBa - - -Combinatorial checklist for sediment with migs_ba - -URI: [mixs.vocab:SedimentMigsBa](https://w3id.org/mixs/vocab/SedimentMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsBa],[Sediment]^-[SedimentMigsBa],[Sediment],[QuantityValue],[MigsBa]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsEu.md b/mixs6/SedimentMigsEu.md deleted file mode 100644 index 3d272fc7..00000000 --- a/mixs6/SedimentMigsEu.md +++ /dev/null @@ -1,559 +0,0 @@ - -# Class: SedimentMigsEu - - -Combinatorial checklist for sediment with migs_eu - -URI: [mixs.vocab:SedimentMigsEu](https://w3id.org/mixs/vocab/SedimentMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsEu],[Sediment]^-[SedimentMigsEu],[Sediment],[QuantityValue],[MigsEu]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsOrg.md b/mixs6/SedimentMigsOrg.md index 20109f52..983e6a4d 100644 --- a/mixs6/SedimentMigsOrg.md +++ b/mixs6/SedimentMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Sediment]^-[SedimentMIGSOrg],[Sediment],[QuantityValue],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Sediment]^-[SedimentMIGSOrg],[Sediment],[QuantityValue],[MIGSOrg]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -450,22 +450,27 @@ URI: [mixs.vocab:SedimentMIGSOrg](https://w3id.org/mixs/vocab/SedimentMIGSOrg) ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/SedimentMigsPl.md b/mixs6/SedimentMigsPl.md deleted file mode 100644 index 175a953f..00000000 --- a/mixs6/SedimentMigsPl.md +++ /dev/null @@ -1,529 +0,0 @@ - -# Class: SedimentMigsPl - - -Combinatorial checklist for sediment with migs_pl - -URI: [mixs.vocab:SedimentMigsPl](https://w3id.org/mixs/vocab/SedimentMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsPl],[Sediment]^-[SedimentMigsPl],[Sediment],[QuantityValue],[MigsPl]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMigsVi.md b/mixs6/SedimentMigsVi.md deleted file mode 100644 index e0ed85ab..00000000 --- a/mixs6/SedimentMigsVi.md +++ /dev/null @@ -1,554 +0,0 @@ - -# Class: SedimentMigsVi - - -Combinatorial checklist for sediment with migs_vi - -URI: [mixs.vocab:SedimentMigsVi](https://w3id.org/mixs/vocab/SedimentMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsVi],[Sediment]^-[SedimentMigsVi],[Sediment],[QuantityValue],[MigsVi]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/SedimentMimag.md b/mixs6/SedimentMimag.md index a97b940f..458a33ae 100644 --- a/mixs6/SedimentMimag.md +++ b/mixs6/SedimentMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Sediment]^-[SedimentMIMAG],[Sediment],[QuantityValue],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Sediment]^-[SedimentMIMAG],[Sediment],[QuantityValue],[MIMAG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -490,22 +490,27 @@ URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -567,8 +572,3 @@ URI: [mixs.vocab:SedimentMIMAG](https://w3id.org/mixs/vocab/SedimentMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMimarksC.md b/mixs6/SedimentMimarksC.md deleted file mode 100644 index 5da00c06..00000000 --- a/mixs6/SedimentMimarksC.md +++ /dev/null @@ -1,459 +0,0 @@ - -# Class: SedimentMimarksC - - -Combinatorial checklist for sediment with mimarks_c - -URI: [mixs.vocab:SedimentMimarksC](https://w3id.org/mixs/vocab/SedimentMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksC],[Sediment]^-[SedimentMimarksC],[Sediment],[QuantityValue],[MimarksC]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMimarksS.md b/mixs6/SedimentMimarksS.md deleted file mode 100644 index 85575182..00000000 --- a/mixs6/SedimentMimarksS.md +++ /dev/null @@ -1,479 +0,0 @@ - -# Class: SedimentMimarksS - - -Combinatorial checklist for sediment with mimarks_s - -URI: [mixs.vocab:SedimentMimarksS](https://w3id.org/mixs/vocab/SedimentMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksS],[Sediment]^-[SedimentMimarksS],[Sediment],[QuantityValue],[MimarksS]) - -## Parents - - * is_a: [Sediment](Sediment.md) - sediment - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from sediment: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [methane](methane.md) OPT - * Description: Methane (gas) amount or concentration at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 1800 parts per billion None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [particle_class](particle_class.md) OPT - * Description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values - * range: [String](types/String.md) - * Example: None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [porosity](porosity.md) OPT - * Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample - * range: [String](types/String.md) - * Example: None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [sediment_type](sediment_type.md) OPT - * Description: Information about the sediment type based on major constituents - * range: - * Example: biogenous None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_carb](tot_carb.md) OPT - * Description: Total carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMisag.md b/mixs6/SedimentMisag.md index 40a1b0f2..e6f79eb2 100644 --- a/mixs6/SedimentMisag.md +++ b/mixs6/SedimentMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Sediment]^-[SedimentMISAG],[Sediment],[QuantityValue],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Sediment]^-[SedimentMISAG],[Sediment],[QuantityValue],[MISAG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -470,22 +470,27 @@ URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -572,8 +577,3 @@ URI: [mixs.vocab:SedimentMISAG](https://w3id.org/mixs/vocab/SedimentMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SedimentMiuvig.md b/mixs6/SedimentMiuvig.md index e1137cff..3cb6ddab 100644 --- a/mixs6/SedimentMiuvig.md +++ b/mixs6/SedimentMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Sediment]^-[SedimentMIUVIG],[Sediment],[QuantityValue],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SedimentMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;particle_class(i):string%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;porosity(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;sediment_type(i):sediment_type_enum%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Sediment]^-[SedimentMIUVIG],[Sediment],[QuantityValue],[MIUVIG]) ## Parents @@ -31,7 +31,7 @@ URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -80,14 +80,14 @@ URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [density](density.md) OPT * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -510,22 +510,27 @@ URI: [mixs.vocab:SedimentMIUVIG](https://w3id.org/mixs/vocab/SedimentMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/SedimentTypeEnum.md b/mixs6/SedimentTypeEnum.md new file mode 100644 index 00000000..02433ebd --- /dev/null +++ b/mixs6/SedimentTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sediment_type_enum + + + + +URI: [mixs.vocab:sediment_type_enum](https://w3id.org/mixs/vocab/sediment_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SeqMethEnum.md b/mixs6/SeqMethEnum.md new file mode 100644 index 00000000..c21edb54 --- /dev/null +++ b/mixs6/SeqMethEnum.md @@ -0,0 +1,19 @@ + +# Enum: seq_meth_enum + + + + +URI: [mixs.vocab:seq_meth_enum](https://w3id.org/mixs/vocab/seq_meth_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ShadingDeviceCondEnum.md b/mixs6/ShadingDeviceCondEnum.md new file mode 100644 index 00000000..6f9708f3 --- /dev/null +++ b/mixs6/ShadingDeviceCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: shading_device_cond_enum + + + + +URI: [mixs.vocab:shading_device_cond_enum](https://w3id.org/mixs/vocab/shading_device_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/ShadingDeviceTypeEnum.md b/mixs6/ShadingDeviceTypeEnum.md new file mode 100644 index 00000000..5a805ada --- /dev/null +++ b/mixs6/ShadingDeviceTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: shading_device_type_enum + + + + +URI: [mixs.vocab:shading_device_type_enum](https://w3id.org/mixs/vocab/shading_device_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SingleCellLysisApprEnum.md b/mixs6/SingleCellLysisApprEnum.md new file mode 100644 index 00000000..b76f64f4 --- /dev/null +++ b/mixs6/SingleCellLysisApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: single_cell_lysis_appr_enum + + + + +URI: [mixs.vocab:single_cell_lysis_appr_enum](https://w3id.org/mixs/vocab/single_cell_lysis_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/Soil.md b/mixs6/Soil.md index a793f98e..bd35c6f5 100644 --- a/mixs6/Soil.md +++ b/mixs6/Soil.md @@ -7,7 +7,7 @@ soil URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG],[SoilMISAG],[SoilMIMARKSSurvey],[SoilMIMARKSSpecimen],[SoilMIMAG],[SoilMIGSVirus],[SoilMIGSPlant],[SoilMIGSOrg],[SoilMIGSEukaryote],[SoilMIGSBacteria],[SoilME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -57,7 +57,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -76,7 +76,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -101,7 +101,7 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -113,11 +113,11 @@ URI: [mixs.vocab:Soil](https://w3id.org/mixs/vocab/Soil) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) diff --git a/mixs6/SoilMIGSBacteria.md b/mixs6/SoilMIGSBacteria.md index 2c9c7556..2a262e74 100644 --- a/mixs6/SoilMIGSBacteria.md +++ b/mixs6/SoilMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Soil]^-[SoilMIGSBacteria],[Soil],[QuantityValue],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSBacteria],[Soil]^-[SoilMIGSBacteria],[Soil],[QuantityValue],[MIGSBacteria]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -429,22 +429,27 @@ URI: [mixs.vocab:SoilMIGSBacteria](https://w3id.org/mixs/vocab/SoilMIGSBacteria) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/SoilMIGSEukaryote.md b/mixs6/SoilMIGSEukaryote.md index 9625d385..ba9736cf 100644 --- a/mixs6/SoilMIGSEukaryote.md +++ b/mixs6/SoilMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Soil]^-[SoilMIGSEukaryote],[Soil],[QuantityValue],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSEukaryote],[Soil]^-[SoilMIGSEukaryote],[Soil],[QuantityValue],[MIGSEukaryote]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -429,22 +429,27 @@ URI: [mixs.vocab:SoilMIGSEukaryote](https://w3id.org/mixs/vocab/SoilMIGSEukaryot ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/SoilMIGSPlant.md b/mixs6/SoilMIGSPlant.md index 2b70935f..1da40d48 100644 --- a/mixs6/SoilMIGSPlant.md +++ b/mixs6/SoilMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Soil]^-[SoilMIGSPlant],[Soil],[QuantityValue],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSPlant],[Soil]^-[SoilMIGSPlant],[Soil],[QuantityValue],[MIGSPlant]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -404,22 +404,27 @@ URI: [mixs.vocab:SoilMIGSPlant](https://w3id.org/mixs/vocab/SoilMIGSPlant) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/SoilMIGSVirus.md b/mixs6/SoilMIGSVirus.md index 5b98bb31..75bb3b12 100644 --- a/mixs6/SoilMIGSVirus.md +++ b/mixs6/SoilMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Soil]^-[SoilMIGSVirus],[Soil],[QuantityValue],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSVirus],[Soil]^-[SoilMIGSVirus],[Soil],[QuantityValue],[MIGSVirus]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -424,22 +424,27 @@ URI: [mixs.vocab:SoilMIGSVirus](https://w3id.org/mixs/vocab/SoilMIGSVirus) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/SoilMIMARKSSpecimen.md b/mixs6/SoilMIMARKSSpecimen.md index e8fb6847..18d7b82a 100644 --- a/mixs6/SoilMIMARKSSpecimen.md +++ b/mixs6/SoilMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Soil]^-[SoilMIMARKSSpecimen],[Soil],[QuantityValue],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[Soil]^-[SoilMIMARKSSpecimen],[Soil],[QuantityValue],[MIMARKSSpecimen]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -359,22 +359,27 @@ URI: [mixs.vocab:SoilMIMARKSSpecimen](https://w3id.org/mixs/vocab/SoilMIMARKSSpe ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/SoilMIMARKSSurvey.md b/mixs6/SoilMIMARKSSurvey.md index f7628dd5..7da6c55e 100644 --- a/mixs6/SoilMIMARKSSurvey.md +++ b/mixs6/SoilMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Soil]^-[SoilMIMARKSSurvey],[Soil],[QuantityValue],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[Soil]^-[SoilMIMARKSSurvey],[Soil],[QuantityValue],[MIMARKSSurvey]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -334,22 +334,27 @@ URI: [mixs.vocab:SoilMIMARKSSurvey](https://w3id.org/mixs/vocab/SoilMIMARKSSurve ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/SoilMe.md b/mixs6/SoilMe.md index c48b99d7..b2568dd7 100644 --- a/mixs6/SoilMe.md +++ b/mixs6/SoilMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package s URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Soil]^-[SoilME],[Soil],[QuantityValue],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[ME],[Soil]^-[SoilME],[Soil],[QuantityValue],[ME]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -379,22 +379,27 @@ URI: [mixs.vocab:SoilME](https://w3id.org/mixs/vocab/SoilME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/SoilMigsBa.md b/mixs6/SoilMigsBa.md deleted file mode 100644 index 46f2ef02..00000000 --- a/mixs6/SoilMigsBa.md +++ /dev/null @@ -1,503 +0,0 @@ - -# Class: SoilMigsBa - - -Combinatorial checklist for soil with migs_ba - -URI: [mixs.vocab:SoilMigsBa](https://w3id.org/mixs/vocab/SoilMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsBa],[Soil]^-[SoilMigsBa],[Soil],[QuantityValue],[MigsBa]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMigsEu.md b/mixs6/SoilMigsEu.md deleted file mode 100644 index b93a9199..00000000 --- a/mixs6/SoilMigsEu.md +++ /dev/null @@ -1,503 +0,0 @@ - -# Class: SoilMigsEu - - -Combinatorial checklist for soil with migs_eu - -URI: [mixs.vocab:SoilMigsEu](https://w3id.org/mixs/vocab/SoilMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsEu],[Soil]^-[SoilMigsEu],[Soil],[QuantityValue],[MigsEu]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMigsOrg.md b/mixs6/SoilMigsOrg.md index ea63bc82..a393f06c 100644 --- a/mixs6/SoilMigsOrg.md +++ b/mixs6/SoilMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Soil]^-[SoilMIGSOrg],[Soil],[QuantityValue],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIGSOrg],[Soil]^-[SoilMIGSOrg],[Soil],[QuantityValue],[MIGSOrg]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -394,22 +394,27 @@ URI: [mixs.vocab:SoilMIGSOrg](https://w3id.org/mixs/vocab/SoilMIGSOrg) ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/SoilMigsPl.md b/mixs6/SoilMigsPl.md deleted file mode 100644 index 75035ccf..00000000 --- a/mixs6/SoilMigsPl.md +++ /dev/null @@ -1,473 +0,0 @@ - -# Class: SoilMigsPl - - -Combinatorial checklist for soil with migs_pl - -URI: [mixs.vocab:SoilMigsPl](https://w3id.org/mixs/vocab/SoilMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsPl],[Soil]^-[SoilMigsPl],[Soil],[QuantityValue],[MigsPl]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMigsVi.md b/mixs6/SoilMigsVi.md deleted file mode 100644 index ff60ef30..00000000 --- a/mixs6/SoilMigsVi.md +++ /dev/null @@ -1,498 +0,0 @@ - -# Class: SoilMigsVi - - -Combinatorial checklist for soil with migs_vi - -URI: [mixs.vocab:SoilMigsVi](https://w3id.org/mixs/vocab/SoilMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MigsVi],[Soil]^-[SoilMigsVi],[Soil],[QuantityValue],[MigsVi]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/SoilMimag.md b/mixs6/SoilMimag.md index f4cda22c..9d27e573 100644 --- a/mixs6/SoilMimag.md +++ b/mixs6/SoilMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Soil]^-[SoilMIMAG],[Soil],[QuantityValue],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIMAG],[Soil]^-[SoilMIMAG],[Soil],[QuantityValue],[MIMAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -434,22 +434,27 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -511,8 +516,3 @@ URI: [mixs.vocab:SoilMIMAG](https://w3id.org/mixs/vocab/SoilMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMimarksC.md b/mixs6/SoilMimarksC.md deleted file mode 100644 index a9dcb3b2..00000000 --- a/mixs6/SoilMimarksC.md +++ /dev/null @@ -1,403 +0,0 @@ - -# Class: SoilMimarksC - - -Combinatorial checklist for soil with mimarks_c - -URI: [mixs.vocab:SoilMimarksC](https://w3id.org/mixs/vocab/SoilMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksC],[Soil]^-[SoilMimarksC],[Soil],[QuantityValue],[MimarksC]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMimarksS.md b/mixs6/SoilMimarksS.md deleted file mode 100644 index a32e8f72..00000000 --- a/mixs6/SoilMimarksS.md +++ /dev/null @@ -1,423 +0,0 @@ - -# Class: SoilMimarksS - - -Combinatorial checklist for soil with mimarks_s - -URI: [mixs.vocab:SoilMimarksS](https://w3id.org/mixs/vocab/SoilMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MimarksS],[Soil]^-[SoilMimarksS],[Soil],[QuantityValue],[MimarksS]) - -## Parents - - * is_a: [Soil](Soil.md) - soil - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from soil: - - * [agrochem_addition](agrochem_addition.md) OPT - * Description: Addition of fertilizers, pesticides, etc. - amount and time of applications - * range: [String](types/String.md) - * Example: roundup;5 milligram per liter;2018-06-21 None - * [al_sat](al_sat.md) OPT - * Description: Aluminum saturation (esp. For tropical soils) - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [al_sat_meth](al_sat_meth.md) OPT - * Description: Reference or method used in determining Al saturation - * range: [String](types/String.md) - * Example: None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [annual_precpt](annual_precpt.md) OPT - * Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [annual_temp](annual_temp.md) OPT - * Description: Mean annual temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 12.5 degree Celsius None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [crop_rotation](crop_rotation.md) OPT - * Description: Whether or not crop is rotated, and if yes, rotation schedule - * range: [String](types/String.md) - * Example: yes;R2/2017-01-01/2018-12-31/P6M None - * [cur_land_use](cur_land_use.md) OPT - * Description: Present state of sample site - * range: - * Example: conifers None - * [cur_vegetation](cur_vegetation.md) OPT - * Description: Vegetation classification from one or more standard classification systems, or agricultural crop - * range: [String](types/String.md) - * Example: None - * [cur_vegetation_meth](cur_vegetation_meth.md) OPT - * Description: Reference or method used in vegetation classification - * range: [String](types/String.md) - * Example: None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [drainage_class](drainage_class.md) OPT - * Description: Drainage classification from a standard system such as the USDA system - * range: - * Example: well None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [extreme_event](extreme_event.md) OPT - * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) - * Example: None - * [extreme_salinity](extreme_salinity.md) OPT - * Description: Measured salinity - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [fao_class](fao_class.md) OPT - * Description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - * range: - * Example: Luvisols None - * [fire](fire.md) OPT - * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) - * Example: None - * [flooding](flooding.md) OPT - * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [heavy_metals](heavy_metals.md) OPT - * Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations - * range: [String](types/String.md) - * Example: None - * [heavy_metals_meth](heavy_metals_meth.md) OPT - * Description: Reference or method used in determining heavy metals - * range: [String](types/String.md) - * Example: None - * [horizon](horizon.md) OPT - * Description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath - * range: - * Example: A horizon None - * [horizon_meth](horizon_meth.md) OPT - * Description: Reference or method used in determining the horizon - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [link_addit_analys](link_addit_analys.md) OPT - * Description: Link to additional analysis results performed on the sample - * range: [String](types/String.md) - * Example: None - * [link_class_info](link_class_info.md) OPT - * Description: Link to digitized soil maps or other soil classification information - * range: [String](types/String.md) - * Example: None - * [link_climate_info](link_climate_info.md) OPT - * Description: Link to climate resource - * range: [String](types/String.md) - * Example: None - * [local_class](local_class.md) OPT - * Description: Soil classification based on local soil classification system - * range: [String](types/String.md) - * Example: None - * [local_class_meth](local_class_meth.md) OPT - * Description: Reference or method used in determining the local soil classification - * range: [String](types/String.md) - * Example: None - * [microbial_biomass](microbial_biomass.md) OPT - * Description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [microbial_biomass_meth](microbial_biomass_meth.md) OPT - * Description: Reference or method used in determining microbial biomass - * range: [String](types/String.md) - * Example: None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [ph_meth](ph_meth.md) OPT - * Description: Reference or method used in determining ph - * range: [String](types/String.md) - * Example: None - * [pool_dna_extracts](pool_dna_extracts.md) OPT - * Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given - * range: [String](types/String.md) - * Example: yes;5 None - * [previous_land_use](previous_land_use.md) OPT - * Description: Previous land use and dates - * range: [String](types/String.md) - * Example: None - * [previous_land_use_meth](previous_land_use_meth.md) OPT - * Description: Reference or method used in determining previous land use and dates - * range: [String](types/String.md) - * Example: None - * [profile_position](profile_position.md) OPT - * Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas - * range: - * Example: summit None - * [salinity_meth](salinity_meth.md) OPT - * Description: Reference or method used in determining salinity - * range: [String](types/String.md) - * Example: None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [season_precpt](season_precpt.md) OPT - * Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [season_temp](season_temp.md) OPT - * Description: Mean seasonal temperature - * range: [QuantityValue](QuantityValue.md) - * Example: 18 degree Celsius None - * [sieving](sieving.md) OPT - * Description: Collection design of pooled samples and/or sieve size and amount of sample sieved - * range: [String](types/String.md) - * Example: None - * [slope_aspect](slope_aspect.md) OPT - * Description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [slope_gradient](slope_gradient.md) OPT - * Description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [soil_type](soil_type.md) OPT - * Description: Soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [soil_type_meth](soil_type_meth.md) OPT - * Description: Reference or method used in determining soil series name or other lower-level classification - * range: [String](types/String.md) - * Example: None - * [store_cond](store_cond.md) OPT - * Description: Explain how and for how long the soil sample was stored before DNA extraction - * range: [String](types/String.md) - * Example: -20 degree Celsius freezer;P2Y10D None - * [texture](texture.md) OPT - * Description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [texture_meth](texture_meth.md) OPT - * Description: Reference or method used in determining soil texture - * range: [String](types/String.md) - * Example: None - * [tillage](tillage.md) OPT - * Description: Note method(s) used for tilling - * range: - * Example: chisel None - * [tot_nitro_content](tot_nitro_content.md) OPT - * Description: Total nitrogen content of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [tot_nitro_content_meth](tot_nitro_content_meth.md) OPT - * Description: Reference or method used in determining the total nitrogen - * range: [String](types/String.md) - * Example: None - * [tot_org_c_meth](tot_org_c_meth.md) OPT - * Description: Reference or method used in determining total organic carbon - * range: [String](types/String.md) - * Example: None - * [tot_org_carb](tot_org_carb.md) OPT - * Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content](water_content.md) OPT - * Description: Water content measurement - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [water_content_soil_meth](water_content_soil_meth.md) OPT - * Description: Reference or method used in determining the water content of soil - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMisag.md b/mixs6/SoilMisag.md index 03788bf3..489e5e81 100644 --- a/mixs6/SoilMisag.md +++ b/mixs6/SoilMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Soil]^-[SoilMISAG],[Soil],[QuantityValue],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MISAG],[Soil]^-[SoilMISAG],[Soil],[QuantityValue],[MISAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -414,22 +414,27 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -516,8 +521,3 @@ URI: [mixs.vocab:SoilMISAG](https://w3id.org/mixs/vocab/SoilMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/SoilMiuvig.md b/mixs6/SoilMiuvig.md index 8941ac26..76fa154d 100644 --- a/mixs6/SoilMiuvig.md +++ b/mixs6/SoilMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):string%20%3F;flooding(i):string%20%3F;extreme_event(i):string%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Soil]^-[SoilMIUVIG],[Soil],[QuantityValue],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SoilMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;cur_land_use(i):cur_land_use_enum%20%3F;cur_vegetation(i):string%20%3F;cur_vegetation_meth(i):string%20%3F;previous_land_use(i):string%20%3F;previous_land_use_meth(i):string%20%3F;crop_rotation(i):string%20%3F;agrochem_addition(i):string%20%3F;tillage(i):tillage_enum%20%3F;fire(i):date%20%3F;flooding(i):date%20%3F;extreme_event(i):date%20%3F;horizon(i):horizon_enum%20%3F;horizon_meth(i):string%20%3F;sieving(i):string%20%3F;water_content_soil_meth(i):string%20%3F;pool_dna_extracts(i):string%20%3F;store_cond(i):string%20%3F;link_climate_info(i):string%20%3F;link_class_info(i):string%20%3F;fao_class(i):fao_class_enum%20%3F;local_class(i):string%20%3F;local_class_meth(i):string%20%3F;soil_type(i):string%20%3F;soil_type_meth(i):string%20%3F;profile_position(i):profile_position_enum%20%3F;drainage_class(i):drainage_class_enum%20%3F;texture_meth(i):string%20%3F;ph(i):double%20%3F;ph_meth(i):string%20%3F;tot_org_c_meth(i):string%20%3F;tot_nitro_content_meth(i):string%20%3F;microbial_biomass_meth(i):string%20%3F;link_addit_analys(i):string%20%3F;salinity_meth(i):string%20%3F;heavy_metals(i):string%20%3F;heavy_metals_meth(i):string%20%3F;al_sat_meth(i):string%20%3F;misc_param(i):string%20%3F]uses%20-.->[MIUVIG],[Soil]^-[SoilMIUVIG],[Soil],[QuantityValue],[MIUVIG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) * range: [String](types/String.md) * Example: None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [annual_precpt](annual_precpt.md) OPT @@ -48,7 +48,7 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) * Example: 12.5 degree Celsius None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [crop_rotation](crop_rotation.md) OPT * Description: Whether or not crop is rotated, and if yes, rotation schedule @@ -67,7 +67,7 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) * range: [String](types/String.md) * Example: None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [drainage_class](drainage_class.md) OPT @@ -92,7 +92,7 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) * Example: soil [ENVO:00001998] None * [extreme_event](extreme_event.md) OPT * Description: Unusual physical events that may have affected microbial populations - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [extreme_salinity](extreme_salinity.md) OPT * Description: Measured salinity @@ -104,11 +104,11 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) * Example: Luvisols None * [fire](fire.md) OPT * Description: Historical and/or physical evidence of fire - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [flooding](flooding.md) OPT * Description: Historical and/or physical evidence of flooding - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: None * [geo_loc_name](geo_loc_name.md) OPT * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) @@ -454,22 +454,27 @@ URI: [mixs.vocab:SoilMIUVIG](https://w3id.org/mixs/vocab/SoilMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/SortTechEnum.md b/mixs6/SortTechEnum.md new file mode 100644 index 00000000..e2c68a73 --- /dev/null +++ b/mixs6/SortTechEnum.md @@ -0,0 +1,19 @@ + +# Enum: sort_tech_enum + + + + +URI: [mixs.vocab:sort_tech_enum](https://w3id.org/mixs/vocab/sort_tech_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SourceUvigEnum.md b/mixs6/SourceUvigEnum.md new file mode 100644 index 00000000..ded313b3 --- /dev/null +++ b/mixs6/SourceUvigEnum.md @@ -0,0 +1,19 @@ + +# Enum: source_uvig_enum + + + + +URI: [mixs.vocab:source_uvig_enum](https://w3id.org/mixs/vocab/source_uvig_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SpecialDietEnum.md b/mixs6/SpecialDietEnum.md new file mode 100644 index 00000000..9dba3a66 --- /dev/null +++ b/mixs6/SpecialDietEnum.md @@ -0,0 +1,19 @@ + +# Enum: special_diet_enum + + + + +URI: [mixs.vocab:special_diet_enum](https://w3id.org/mixs/vocab/special_diet_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SpecificEnum.md b/mixs6/SpecificEnum.md new file mode 100644 index 00000000..00553595 --- /dev/null +++ b/mixs6/SpecificEnum.md @@ -0,0 +1,19 @@ + +# Enum: specific_enum + + + + +URI: [mixs.vocab:specific_enum](https://w3id.org/mixs/vocab/specific_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrDepEnvEnum.md b/mixs6/SrDepEnvEnum.md new file mode 100644 index 00000000..49ea3e6e --- /dev/null +++ b/mixs6/SrDepEnvEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_dep_env_enum + + + + +URI: [mixs.vocab:sr_dep_env_enum](https://w3id.org/mixs/vocab/sr_dep_env_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrGeolAgeEnum.md b/mixs6/SrGeolAgeEnum.md new file mode 100644 index 00000000..db971dee --- /dev/null +++ b/mixs6/SrGeolAgeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_geol_age_enum + + + + +URI: [mixs.vocab:sr_geol_age_enum](https://w3id.org/mixs/vocab/sr_geol_age_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrKerogTypeEnum.md b/mixs6/SrKerogTypeEnum.md new file mode 100644 index 00000000..4b537dc6 --- /dev/null +++ b/mixs6/SrKerogTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_kerog_type_enum + + + + +URI: [mixs.vocab:sr_kerog_type_enum](https://w3id.org/mixs/vocab/sr_kerog_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SrLithologyEnum.md b/mixs6/SrLithologyEnum.md new file mode 100644 index 00000000..74791f8c --- /dev/null +++ b/mixs6/SrLithologyEnum.md @@ -0,0 +1,19 @@ + +# Enum: sr_lithology_enum + + + + +URI: [mixs.vocab:sr_lithology_enum](https://w3id.org/mixs/vocab/sr_lithology_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/StudyCompltStatEnum.md b/mixs6/StudyCompltStatEnum.md new file mode 100644 index 00000000..8c25de2c --- /dev/null +++ b/mixs6/StudyCompltStatEnum.md @@ -0,0 +1,19 @@ + +# Enum: study_complt_stat_enum + + + + +URI: [mixs.vocab:study_complt_stat_enum](https://w3id.org/mixs/vocab/study_complt_stat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SubstructureTypeEnum.md b/mixs6/SubstructureTypeEnum.md new file mode 100644 index 00000000..be4a1a03 --- /dev/null +++ b/mixs6/SubstructureTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: substructure_type_enum + + + + +URI: [mixs.vocab:substructure_type_enum](https://w3id.org/mixs/vocab/substructure_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SurfAirContEnum.md b/mixs6/SurfAirContEnum.md new file mode 100644 index 00000000..d305ad79 --- /dev/null +++ b/mixs6/SurfAirContEnum.md @@ -0,0 +1,19 @@ + +# Enum: surf_air_cont_enum + + + + +URI: [mixs.vocab:surf_air_cont_enum](https://w3id.org/mixs/vocab/surf_air_cont_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/SurfMaterialEnum.md b/mixs6/SurfMaterialEnum.md new file mode 100644 index 00000000..08d405cd --- /dev/null +++ b/mixs6/SurfMaterialEnum.md @@ -0,0 +1,19 @@ + +# Enum: surf_material_enum + + + + +URI: [mixs.vocab:surf_material_enum](https://w3id.org/mixs/vocab/surf_material_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TaxIdentEnum.md b/mixs6/TaxIdentEnum.md new file mode 100644 index 00000000..199885e6 --- /dev/null +++ b/mixs6/TaxIdentEnum.md @@ -0,0 +1,19 @@ + +# Enum: tax_ident_enum + + + + +URI: [mixs.vocab:tax_ident_enum](https://w3id.org/mixs/vocab/tax_ident_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TidalStageEnum.md b/mixs6/TidalStageEnum.md new file mode 100644 index 00000000..1e58cb2f --- /dev/null +++ b/mixs6/TidalStageEnum.md @@ -0,0 +1,19 @@ + +# Enum: tidal_stage_enum + + + + +URI: [mixs.vocab:tidal_stage_enum](https://w3id.org/mixs/vocab/tidal_stage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TillageEnum.md b/mixs6/TillageEnum.md new file mode 100644 index 00000000..0779cd90 --- /dev/null +++ b/mixs6/TillageEnum.md @@ -0,0 +1,19 @@ + +# Enum: tillage_enum + + + + +URI: [mixs.vocab:tillage_enum](https://w3id.org/mixs/vocab/tillage_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainLineEnum.md b/mixs6/TrainLineEnum.md new file mode 100644 index 00000000..3a7801bd --- /dev/null +++ b/mixs6/TrainLineEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_line_enum + + + + +URI: [mixs.vocab:train_line_enum](https://w3id.org/mixs/vocab/train_line_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainStatLocEnum.md b/mixs6/TrainStatLocEnum.md new file mode 100644 index 00000000..96b361ce --- /dev/null +++ b/mixs6/TrainStatLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_stat_loc_enum + + + + +URI: [mixs.vocab:train_stat_loc_enum](https://w3id.org/mixs/vocab/train_stat_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrainStopLocEnum.md b/mixs6/TrainStopLocEnum.md new file mode 100644 index 00000000..bffbb402 --- /dev/null +++ b/mixs6/TrainStopLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: train_stop_loc_enum + + + + +URI: [mixs.vocab:train_stop_loc_enum](https://w3id.org/mixs/vocab/train_stop_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/TrophicLevelEnum.md b/mixs6/TrophicLevelEnum.md new file mode 100644 index 00000000..a433f913 --- /dev/null +++ b/mixs6/TrophicLevelEnum.md @@ -0,0 +1,19 @@ + +# Enum: trophic_level_enum + + + + +URI: [mixs.vocab:trophic_level_enum](https://w3id.org/mixs/vocab/trophic_level_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/VirusEnrichApprEnum.md b/mixs6/VirusEnrichApprEnum.md new file mode 100644 index 00000000..0be83d9a --- /dev/null +++ b/mixs6/VirusEnrichApprEnum.md @@ -0,0 +1,19 @@ + +# Enum: virus_enrich_appr_enum + + + + +URI: [mixs.vocab:virus_enrich_appr_enum](https://w3id.org/mixs/vocab/virus_enrich_appr_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/VisMediaEnum.md b/mixs6/VisMediaEnum.md new file mode 100644 index 00000000..736292bb --- /dev/null +++ b/mixs6/VisMediaEnum.md @@ -0,0 +1,19 @@ + +# Enum: vis_media_enum + + + + +URI: [mixs.vocab:vis_media_enum](https://w3id.org/mixs/vocab/vis_media_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallConstTypeEnum.md b/mixs6/WallConstTypeEnum.md new file mode 100644 index 00000000..526c7222 --- /dev/null +++ b/mixs6/WallConstTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_const_type_enum + + + + +URI: [mixs.vocab:wall_const_type_enum](https://w3id.org/mixs/vocab/wall_const_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallFinishMatEnum.md b/mixs6/WallFinishMatEnum.md new file mode 100644 index 00000000..02bfe0bb --- /dev/null +++ b/mixs6/WallFinishMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_finish_mat_enum + + + + +URI: [mixs.vocab:wall_finish_mat_enum](https://w3id.org/mixs/vocab/wall_finish_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallLocEnum.md b/mixs6/WallLocEnum.md new file mode 100644 index 00000000..cd3fa234 --- /dev/null +++ b/mixs6/WallLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_loc_enum + + + + +URI: [mixs.vocab:wall_loc_enum](https://w3id.org/mixs/vocab/wall_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallSurfTreatmentEnum.md b/mixs6/WallSurfTreatmentEnum.md new file mode 100644 index 00000000..a33e5e15 --- /dev/null +++ b/mixs6/WallSurfTreatmentEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_surf_treatment_enum + + + + +URI: [mixs.vocab:wall_surf_treatment_enum](https://w3id.org/mixs/vocab/wall_surf_treatment_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WallTextureEnum.md b/mixs6/WallTextureEnum.md new file mode 100644 index 00000000..2f970b73 --- /dev/null +++ b/mixs6/WallTextureEnum.md @@ -0,0 +1,19 @@ + +# Enum: wall_texture_enum + + + + +URI: [mixs.vocab:wall_texture_enum](https://w3id.org/mixs/vocab/wall_texture_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WastewaterSludge.md b/mixs6/WastewaterSludge.md index e79f569a..3e6e6e08 100644 --- a/mixs6/WastewaterSludge.md +++ b/mixs6/WastewaterSludge.md @@ -7,7 +7,7 @@ wastewater/sludge URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG],[WastewaterSludgeMISAG],[WastewaterSludgeMIMARKSSurvey],[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludgeMIMAG],[WastewaterSludgeMIGSVirus],[WastewaterSludgeMIGSPlant],[WastewaterSludgeMIGSOrg],[WastewaterSludgeMIGSEukaryote],[WastewaterSludgeMIGSBacteria],[WastewaterSludgeME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -53,10 +53,10 @@ URI: [mixs.vocab:WastewaterSludge](https://w3id.org/mixs/vocab/WastewaterSludge) * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT diff --git a/mixs6/WastewaterSludgeMIGSBacteria.md b/mixs6/WastewaterSludgeMIGSBacteria.md index 9e480133..0ebf375e 100644 --- a/mixs6/WastewaterSludgeMIGSBacteria.md +++ b/mixs6/WastewaterSludgeMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:WastewaterSludgeMIGSBacteria](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSBacteria],[WastewaterSludge]^-[WastewaterSludgeMIGSBacteria],[WastewaterSludge],[QuantityValue],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSBacteria],[WastewaterSludge]^-[WastewaterSludgeMIGSBacteria],[WastewaterSludge],[QuantityValue],[MIGSBacteria]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIGSBacteria](https://w3id.org/mixs/vocab/Waste * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIGSBacteria](https://w3id.org/mixs/vocab/Waste * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -369,22 +369,27 @@ URI: [mixs.vocab:WastewaterSludgeMIGSBacteria](https://w3id.org/mixs/vocab/Waste ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/WastewaterSludgeMIGSEukaryote.md b/mixs6/WastewaterSludgeMIGSEukaryote.md index 689b2143..95ef1235 100644 --- a/mixs6/WastewaterSludgeMIGSEukaryote.md +++ b/mixs6/WastewaterSludgeMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSEukaryote],[WastewaterSludge]^-[WastewaterSludgeMIGSEukaryote],[WastewaterSludge],[QuantityValue],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSEukaryote],[WastewaterSludge]^-[WastewaterSludgeMIGSEukaryote],[WastewaterSludge],[QuantityValue],[MIGSEukaryote]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/Wast * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/Wast * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -369,22 +369,27 @@ URI: [mixs.vocab:WastewaterSludgeMIGSEukaryote](https://w3id.org/mixs/vocab/Wast ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/WastewaterSludgeMIGSPlant.md b/mixs6/WastewaterSludgeMIGSPlant.md index b1101bab..35088ae6 100644 --- a/mixs6/WastewaterSludgeMIGSPlant.md +++ b/mixs6/WastewaterSludgeMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSPlant],[WastewaterSludge]^-[WastewaterSludgeMIGSPlant],[WastewaterSludge],[QuantityValue],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSPlant],[WastewaterSludge]^-[WastewaterSludgeMIGSPlant],[WastewaterSludge],[QuantityValue],[MIGSPlant]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/Wastewat * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/Wastewat * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -344,22 +344,27 @@ URI: [mixs.vocab:WastewaterSludgeMIGSPlant](https://w3id.org/mixs/vocab/Wastewat ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/WastewaterSludgeMIGSVirus.md b/mixs6/WastewaterSludgeMIGSVirus.md index a011b650..79c26233 100644 --- a/mixs6/WastewaterSludgeMIGSVirus.md +++ b/mixs6/WastewaterSludgeMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSVirus],[WastewaterSludge]^-[WastewaterSludgeMIGSVirus],[WastewaterSludge],[QuantityValue],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSVirus],[WastewaterSludge]^-[WastewaterSludgeMIGSVirus],[WastewaterSludge],[QuantityValue],[MIGSVirus]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/Wastewat * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/Wastewat * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -364,22 +364,27 @@ URI: [mixs.vocab:WastewaterSludgeMIGSVirus](https://w3id.org/mixs/vocab/Wastewat ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/WastewaterSludgeMIMARKSSpecimen.md b/mixs6/WastewaterSludgeMIMARKSSpecimen.md index d05256a9..ca926300 100644 --- a/mixs6/WastewaterSludgeMIMARKSSpecimen.md +++ b/mixs6/WastewaterSludgeMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludge],[QuantityValue],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSpecimen],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSpecimen],[WastewaterSludge],[QuantityValue],[MIMARKSSpecimen]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/Wa * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/Wa * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -299,22 +299,27 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSpecimen](https://w3id.org/mixs/vocab/Wa ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/WastewaterSludgeMIMARKSSurvey.md b/mixs6/WastewaterSludgeMIMARKSSurvey.md index d7ff24dd..95c96308 100644 --- a/mixs6/WastewaterSludgeMIMARKSSurvey.md +++ b/mixs6/WastewaterSludgeMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/WastewaterSludgeMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSurvey],[WastewaterSludge],[QuantityValue],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMARKSSurvey],[WastewaterSludge]^-[WastewaterSludgeMIMARKSSurvey],[WastewaterSludge],[QuantityValue],[MIMARKSSurvey]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/Wast * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/Wast * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -274,22 +274,27 @@ URI: [mixs.vocab:WastewaterSludgeMIMARKSSurvey](https://w3id.org/mixs/vocab/Wast ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/WastewaterSludgeMe.md b/mixs6/WastewaterSludgeMe.md index 105f9315..60f42f51 100644 --- a/mixs6/WastewaterSludgeMe.md +++ b/mixs6/WastewaterSludgeMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package w URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludgeME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[ME],[WastewaterSludge]^-[WastewaterSludgeME],[WastewaterSludge],[QuantityValue],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[ME],[WastewaterSludge]^-[WastewaterSludgeME],[WastewaterSludge],[QuantityValue],[ME]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludg * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludg * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -319,22 +319,27 @@ URI: [mixs.vocab:WastewaterSludgeME](https://w3id.org/mixs/vocab/WastewaterSludg ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/WastewaterSludgeMigsBa.md b/mixs6/WastewaterSludgeMigsBa.md deleted file mode 100644 index b3a10a64..00000000 --- a/mixs6/WastewaterSludgeMigsBa.md +++ /dev/null @@ -1,443 +0,0 @@ - -# Class: WastewaterSludgeMigsBa - - -Combinatorial checklist for wastewater_sludge with migs_ba - -URI: [mixs.vocab:WastewaterSludgeMigsBa](https://w3id.org/mixs/vocab/WastewaterSludgeMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsBa],[WastewaterSludge]^-[WastewaterSludgeMigsBa],[WastewaterSludge],[QuantityValue],[MigsBa]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsEu.md b/mixs6/WastewaterSludgeMigsEu.md deleted file mode 100644 index b2a7097d..00000000 --- a/mixs6/WastewaterSludgeMigsEu.md +++ /dev/null @@ -1,443 +0,0 @@ - -# Class: WastewaterSludgeMigsEu - - -Combinatorial checklist for wastewater_sludge with migs_eu - -URI: [mixs.vocab:WastewaterSludgeMigsEu](https://w3id.org/mixs/vocab/WastewaterSludgeMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsEu],[WastewaterSludge]^-[WastewaterSludgeMigsEu],[WastewaterSludge],[QuantityValue],[MigsEu]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsOrg.md b/mixs6/WastewaterSludgeMigsOrg.md index 391e1d6c..0c9d239f 100644 --- a/mixs6/WastewaterSludgeMigsOrg.md +++ b/mixs6/WastewaterSludgeMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/WastewaterSludgeMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSOrg],[WastewaterSludge]^-[WastewaterSludgeMIGSOrg],[WastewaterSludge],[QuantityValue],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIGSOrg],[WastewaterSludge]^-[WastewaterSludgeMIGSOrg],[WastewaterSludge],[QuantityValue],[MIGSOrg]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/Wastewater * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/Wastewater * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -334,22 +334,27 @@ URI: [mixs.vocab:WastewaterSludgeMIGSOrg](https://w3id.org/mixs/vocab/Wastewater ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/WastewaterSludgeMigsPl.md b/mixs6/WastewaterSludgeMigsPl.md deleted file mode 100644 index 816023f0..00000000 --- a/mixs6/WastewaterSludgeMigsPl.md +++ /dev/null @@ -1,413 +0,0 @@ - -# Class: WastewaterSludgeMigsPl - - -Combinatorial checklist for wastewater_sludge with migs_pl - -URI: [mixs.vocab:WastewaterSludgeMigsPl](https://w3id.org/mixs/vocab/WastewaterSludgeMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsPl],[WastewaterSludge]^-[WastewaterSludgeMigsPl],[WastewaterSludge],[QuantityValue],[MigsPl]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMigsVi.md b/mixs6/WastewaterSludgeMigsVi.md deleted file mode 100644 index ecafa006..00000000 --- a/mixs6/WastewaterSludgeMigsVi.md +++ /dev/null @@ -1,438 +0,0 @@ - -# Class: WastewaterSludgeMigsVi - - -Combinatorial checklist for wastewater_sludge with migs_vi - -URI: [mixs.vocab:WastewaterSludgeMigsVi](https://w3id.org/mixs/vocab/WastewaterSludgeMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MigsVi],[WastewaterSludge]^-[WastewaterSludgeMigsVi],[WastewaterSludge],[QuantityValue],[MigsVi]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/WastewaterSludgeMimag.md b/mixs6/WastewaterSludgeMimag.md index 26c6dc62..9d636a17 100644 --- a/mixs6/WastewaterSludgeMimag.md +++ b/mixs6/WastewaterSludgeMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSludgeMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMAG],[WastewaterSludge]^-[WastewaterSludgeMIMAG],[WastewaterSludge],[QuantityValue],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIMAG],[WastewaterSludge]^-[WastewaterSludgeMIMAG],[WastewaterSludge],[QuantityValue],[MIMAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSl * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -374,22 +374,27 @@ URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSl ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -451,8 +456,3 @@ URI: [mixs.vocab:WastewaterSludgeMIMAG](https://w3id.org/mixs/vocab/WastewaterSl * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimarksC.md b/mixs6/WastewaterSludgeMimarksC.md deleted file mode 100644 index 8d90d637..00000000 --- a/mixs6/WastewaterSludgeMimarksC.md +++ /dev/null @@ -1,343 +0,0 @@ - -# Class: WastewaterSludgeMimarksC - - -Combinatorial checklist for wastewater_sludge with mimarks_c - -URI: [mixs.vocab:WastewaterSludgeMimarksC](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksC],[WastewaterSludge]^-[WastewaterSludgeMimarksC],[WastewaterSludge],[QuantityValue],[MimarksC]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMimarksS.md b/mixs6/WastewaterSludgeMimarksS.md deleted file mode 100644 index d32da042..00000000 --- a/mixs6/WastewaterSludgeMimarksS.md +++ /dev/null @@ -1,363 +0,0 @@ - -# Class: WastewaterSludgeMimarksS - - -Combinatorial checklist for wastewater_sludge with mimarks_s - -URI: [mixs.vocab:WastewaterSludgeMimarksS](https://w3id.org/mixs/vocab/WastewaterSludgeMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MimarksS],[WastewaterSludge]^-[WastewaterSludgeMimarksS],[WastewaterSludge],[QuantityValue],[MimarksS]) - -## Parents - - * is_a: [WastewaterSludge](WastewaterSludge.md) - wastewater/sludge - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from wastewater_sludge: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT - * Description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chem_oxygen_dem](chem_oxygen_dem.md) OPT - * Description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [efficiency_percent](efficiency_percent.md) OPT - * Description: Percentage of volatile solids removed from the anaerobic digestor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [emulsions](emulsions.md) OPT - * Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types - * range: [String](types/String.md) - * Example: None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [gaseous_substances](gaseous_substances.md) OPT - * Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [indust_eff_percent](indust_eff_percent.md) OPT - * Description: Percentage of industrial effluents received by wastewater treatment plant - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [inorg_particles](inorg_particles.md) OPT - * Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles - * range: [String](types/String.md) - * Example: None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [org_particles](org_particles.md) OPT - * Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. - * range: [String](types/String.md) - * Example: None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [pre_treatment](pre_treatment.md) OPT - * Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater - * range: [String](types/String.md) - * Example: None - * [primary_treatment](primary_treatment.md) OPT - * Description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed - * range: [String](types/String.md) - * Example: None - * [reactor_type](reactor_type.md) OPT - * Description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage - * range: [String](types/String.md) - * Example: None - * [samp_salinity](samp_salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 1 milligram per liter None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [secondary_treatment](secondary_treatment.md) OPT - * Description: The process for substantially degrading the biological content of the sewage - * range: [String](types/String.md) - * Example: None - * [sewage_type](sewage_type.md) OPT - * Description: Type of wastewater treatment plant as municipial or industrial - * range: [String](types/String.md) - * Example: None - * [sludge_retent_time](sludge_retent_time.md) OPT - * Description: The time activated sludge remains in reactor - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_inorg_mat](soluble_inorg_mat.md) OPT - * Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - * range: [String](types/String.md) - * Example: None - * [soluble_org_mat](soluble_org_mat.md) OPT - * Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. - * range: [String](types/String.md) - * Example: None - * [suspend_solids](suspend_solids.md) OPT - * Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances - * range: [String](types/String.md) - * Example: None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tertiary_treatment](tertiary_treatment.md) OPT - * Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment - * range: [String](types/String.md) - * Example: None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_phosphate](tot_phosphate.md) OPT - * Description: Total amount or concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: None - * [wastewater_type](wastewater_type.md) OPT - * Description: The origin of wastewater such as human waste, rainfall, storm drains, etc. - * range: [String](types/String.md) - * Example: None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMisag.md b/mixs6/WastewaterSludgeMisag.md index 53d84cc7..6ca39949 100644 --- a/mixs6/WastewaterSludgeMisag.md +++ b/mixs6/WastewaterSludgeMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSludgeMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MISAG],[WastewaterSludge]^-[WastewaterSludgeMISAG],[WastewaterSludge],[QuantityValue],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MISAG],[WastewaterSludge]^-[WastewaterSludgeMISAG],[WastewaterSludge],[QuantityValue],[MISAG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSl * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSl * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -354,22 +354,27 @@ URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSl ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -456,8 +461,3 @@ URI: [mixs.vocab:WastewaterSludgeMISAG](https://w3id.org/mixs/vocab/WastewaterSl * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WastewaterSludgeMiuvig.md b/mixs6/WastewaterSludgeMiuvig.md index 9c418938..0d955ed0 100644 --- a/mixs6/WastewaterSludgeMiuvig.md +++ b/mixs6/WastewaterSludgeMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterSludgeMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIUVIG],[WastewaterSludge]^-[WastewaterSludgeMIUVIG],[WastewaterSludge],[QuantityValue],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WastewaterSludgeMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;chem_administration(i):string%20%3F;emulsions(i):string%20%3F;gaseous_substances(i):string%20%3F;inorg_particles(i):string%20%3F;misc_param(i):string%20%3F;org_particles(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;pre_treatment(i):string%20%3F;primary_treatment(i):string%20%3F;reactor_type(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;secondary_treatment(i):string%20%3F;sewage_type(i):string%20%3F;soluble_inorg_mat(i):string%20%3F;soluble_org_mat(i):string%20%3F;suspend_solids(i):string%20%3F;tertiary_treatment(i):string%20%3F;wastewater_type(i):string%20%3F]uses%20-.->[MIUVIG],[WastewaterSludge]^-[WastewaterSludgeMIUVIG],[WastewaterSludge],[QuantityValue],[MIUVIG]) ## Parents @@ -27,7 +27,7 @@ URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterS * range: [QuantityValue](QuantityValue.md) * Example: 50 milligram per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [biochem_oxygen_dem](biochem_oxygen_dem.md) OPT @@ -44,10 +44,10 @@ URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterS * Example: None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [efficiency_percent](efficiency_percent.md) OPT @@ -394,22 +394,27 @@ URI: [mixs.vocab:WastewaterSludgeMIUVIG](https://w3id.org/mixs/vocab/WastewaterS ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/Water.md b/mixs6/Water.md index 9a69b7dc..28c7f802 100644 --- a/mixs6/Water.md +++ b/mixs6/Water.md @@ -7,7 +7,7 @@ water URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG],[WaterMISAG],[WaterMIMARKSSurvey],[WaterMIMARKSSpecimen],[WaterMIMAG],[WaterMIGSVirus],[WaterMIGSPlant],[WaterMIGSOrg],[WaterMIGSEukaryote],[WaterMIGSBacteria],[WaterME],[QuantityValue]OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -105,7 +105,7 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -116,7 +116,7 @@ URI: [mixs.vocab:Water](https://w3id.org/mixs/vocab/Water) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT diff --git a/mixs6/WaterFeatTypeEnum.md b/mixs6/WaterFeatTypeEnum.md new file mode 100644 index 00000000..6de4e273 --- /dev/null +++ b/mixs6/WaterFeatTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: water_feat_type_enum + + + + +URI: [mixs.vocab:water_feat_type_enum](https://w3id.org/mixs/vocab/water_feat_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WaterMIGSBacteria.md b/mixs6/WaterMIGSBacteria.md index 5980bbe0..271f653a 100644 --- a/mixs6/WaterMIGSBacteria.md +++ b/mixs6/WaterMIGSBacteria.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteria) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Water]^-[WaterMIGSBacteria],[Water],[QuantityValue],[MIGSBacteria]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSBacteria|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSBacteria],[Water]^-[WaterMIGSBacteria],[Water],[QuantityValue],[MIGSBacteria]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteri * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteri * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteri * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -545,22 +545,27 @@ URI: [mixs.vocab:WaterMIGSBacteria](https://w3id.org/mixs/vocab/WaterMIGSBacteri ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) OPT + * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) OPT + * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS bacteria: + + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞samp_size](MIGS_bacteria_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS bacteria: - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) OPT + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS bacteria: diff --git a/mixs6/WaterMIGSEukaryote.md b/mixs6/WaterMIGSEukaryote.md index b3c47be3..52868af6 100644 --- a/mixs6/WaterMIGSEukaryote.md +++ b/mixs6/WaterMIGSEukaryote.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote w URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukaryote) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Water]^-[WaterMIGSEukaryote],[Water],[QuantityValue],[MIGSEukaryote]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSEukaryote|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSEukaryote],[Water]^-[WaterMIGSEukaryote],[Water],[QuantityValue],[MIGSEukaryote]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukary * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukary * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukary * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -545,22 +545,27 @@ URI: [mixs.vocab:WaterMIGSEukaryote](https://w3id.org/mixs/vocab/WaterMIGSEukary ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) OPT + * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) OPT + * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS eukaryote: + + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞samp_size](MIGS_eukaryote_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) OPT + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS eukaryote: diff --git a/mixs6/WaterMIGSPlant.md b/mixs6/WaterMIGSPlant.md index ce6ec339..54858469 100644 --- a/mixs6/WaterMIGSPlant.md +++ b/mixs6/WaterMIGSPlant.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: plant with URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Water]^-[WaterMIGSPlant],[Water],[QuantityValue],[MIGSPlant]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSPlant|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSPlant],[Water]^-[WaterMIGSPlant],[Water],[QuantityValue],[MIGSPlant]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -520,22 +520,27 @@ URI: [mixs.vocab:WaterMIGSPlant](https://w3id.org/mixs/vocab/WaterMIGSPlant) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) OPT + * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_mat_process](MIGS_plant_samp_mat_process.md) OPT + * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS plant: + + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞samp_size](MIGS_plant_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS plant: - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) OPT + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS plant: diff --git a/mixs6/WaterMIGSVirus.md b/mixs6/WaterMIGSVirus.md index aaead86a..1439c0ab 100644 --- a/mixs6/WaterMIGSVirus.md +++ b/mixs6/WaterMIGSVirus.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: cultured ba URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Water]^-[WaterMIGSVirus],[Water],[QuantityValue],[MIGSVirus]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSVirus|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSVirus],[Water]^-[WaterMIGSVirus],[Water],[QuantityValue],[MIGSVirus]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -540,22 +540,27 @@ URI: [mixs.vocab:WaterMIGSVirus](https://w3id.org/mixs/vocab/WaterMIGSVirus) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) OPT + * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_mat_process](MIGS_virus_samp_mat_process.md) OPT + * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS virus: + + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞samp_size](MIGS_virus_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS virus: - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) OPT + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS virus: diff --git a/mixs6/WaterMIMARKSSpecimen.md b/mixs6/WaterMIMARKSSpecimen.md index 90772ab7..9299fcc4 100644 --- a/mixs6/WaterMIMARKSSpecimen.md +++ b/mixs6/WaterMIMARKSSpecimen.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: specimen wi URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSSpecimen) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Water]^-[WaterMIMARKSSpecimen],[Water],[QuantityValue],[MIMARKSSpecimen]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSpecimen|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSpecimen],[Water]^-[WaterMIMARKSSpecimen],[Water],[QuantityValue],[MIMARKSSpecimen]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSS * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSS * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSS * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -475,22 +475,27 @@ URI: [mixs.vocab:WaterMIMARKSSpecimen](https://w3id.org/mixs/vocab/WaterMIMARKSS ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) OPT + * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_mat_process](MIMARKS_specimen_samp_mat_process.md) OPT + * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS specimen: + + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞samp_size](MIMARKS_specimen_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) OPT + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS specimen: diff --git a/mixs6/WaterMIMARKSSurvey.md b/mixs6/WaterMIMARKSSurvey.md index 150f3d46..c4e515e3 100644 --- a/mixs6/WaterMIMARKSSurvey.md +++ b/mixs6/WaterMIMARKSSurvey.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Marker Specimen: survey with URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSurvey) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Water]^-[WaterMIMARKSSurvey],[Water],[QuantityValue],[MIMARKSSurvey]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMARKSSurvey|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMARKSSurvey],[Water]^-[WaterMIMARKSSurvey],[Water],[QuantityValue],[MIMARKSSurvey]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSur * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSur * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSur * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -450,22 +450,27 @@ URI: [mixs.vocab:WaterMIMARKSSurvey](https://w3id.org/mixs/vocab/WaterMIMARKSSur ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) OPT + * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_mat_process](MIMARKS_survey_samp_mat_process.md) OPT + * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMARKS survey: + + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMARKS survey: - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) OPT + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMARKS survey: diff --git a/mixs6/WaterMe.md b/mixs6/WaterMe.md index 7223710b..5dc05831 100644 --- a/mixs6/WaterMe.md +++ b/mixs6/WaterMe.md @@ -7,7 +7,7 @@ Combinatorial checklist Metagenome or Environmental with environmental package w URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Water]^-[WaterME],[Water],[QuantityValue],[ME]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterME|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string%20%3F;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[ME],[Water]^-[WaterME],[Water],[QuantityValue],[ME]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -495,22 +495,27 @@ URI: [mixs.vocab:WaterME](https://w3id.org/mixs/vocab/WaterME) ### Mixed in from ME: - * [ME➞samp_collect_device](ME_samp_collect_device.md) OPT + * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_mat_process](ME_samp_mat_process.md) OPT + * [ME➞samp_size](ME_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from ME: + + * [ME➞sample_collect_device](ME_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞samp_size](ME_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [ME➞sample_collect_method](ME_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from ME: - * [ME➞sample_name](ME_sample_name.md) OPT + * [ME➞sample_name](ME_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from ME: diff --git a/mixs6/WaterMigsBa.md b/mixs6/WaterMigsBa.md deleted file mode 100644 index 024811eb..00000000 --- a/mixs6/WaterMigsBa.md +++ /dev/null @@ -1,619 +0,0 @@ - -# Class: WaterMigsBa - - -Combinatorial checklist for water with migs_ba - -URI: [mixs.vocab:WaterMigsBa](https://w3id.org/mixs/vocab/WaterMigsBa) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsBa|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;encoded_traits:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsBa],[Water]^-[WaterMigsBa],[Water],[QuantityValue],[MigsBa]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MigsBa](MigsBa.md) - migs_ba Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_ba: - - * [migs_ba➞adapters](migs_ba_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞annot](migs_ba_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_name](migs_ba_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_qual](migs_ba_assembly_qual.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞assembly_software](migs_ba_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞biotic_relationship](migs_ba_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_score](migs_ba_compl_score.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞compl_software](migs_ba_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞encoded_traits](migs_ba_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞env_package](migs_ba_env_package.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞estimated_size](migs_ba_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞experimental_factor](migs_ba_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞extrachrom_elements](migs_ba_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞feat_pred](migs_ba_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞health_disease_stat](migs_ba_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞host_spec_range](migs_ba_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞investigation_type](migs_ba_investigation_type.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞isol_growth_condt](migs_ba_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_layout](migs_ba_lib_layout.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞lib_reads_seqd](migs_ba_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_screen](migs_ba_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_size](migs_ba_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞lib_vector](migs_ba_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_amp](migs_ba_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞nucl_acid_ext](migs_ba_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞num_replicons](migs_ba_num_replicons.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞number_contig](migs_ba_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞pathogenicity](migs_ba_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞project_name](migs_ba_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_biomaterial](migs_ba_ref_biomaterial.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞ref_db](migs_ba_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞rel_to_oxygen](migs_ba_rel_to_oxygen.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞samp_collect_device](migs_ba_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_mat_process](migs_ba_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞samp_size](migs_ba_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sample_name](migs_ba_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞seq_meth](migs_ba_seq_meth.md) REQ - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞sim_search_meth](migs_ba_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞sop](migs_ba_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞source_mat_id](migs_ba_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞specific_host](migs_ba_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞submitted_to_insdc](migs_ba_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞subspecf_gen_lin](migs_ba_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_class](migs_ba_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_ba: - - * [migs_ba➞tax_ident](migs_ba_tax_ident.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞trophic_level](migs_ba_trophic_level.md) OPT - * range: - -### Mixed in from migs_ba: - - * [migs_ba➞url](migs_ba_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMigsEu.md b/mixs6/WaterMigsEu.md deleted file mode 100644 index b7a697a4..00000000 --- a/mixs6/WaterMigsEu.md +++ /dev/null @@ -1,619 +0,0 @@ - -# Class: WaterMigsEu - - -Combinatorial checklist for water with migs_eu - -URI: [mixs.vocab:WaterMigsEu](https://w3id.org/mixs/vocab/WaterMigsEu) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsEu|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;ploidy:string%20%3F;num_replicons:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;trophic_level:trophic_level_enum%20%3F;propagation:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsEu],[Water]^-[WaterMigsEu],[Water],[QuantityValue],[MigsEu]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MigsEu](MigsEu.md) - migs_eu Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_eu: - - * [migs_eu➞adapters](migs_eu_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞annot](migs_eu_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_name](migs_eu_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_qual](migs_eu_assembly_qual.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞assembly_software](migs_eu_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞biotic_relationship](migs_eu_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_score](migs_eu_compl_score.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞compl_software](migs_eu_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞env_package](migs_eu_env_package.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞estimated_size](migs_eu_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞experimental_factor](migs_eu_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞extrachrom_elements](migs_eu_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞feat_pred](migs_eu_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞health_disease_stat](migs_eu_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞host_spec_range](migs_eu_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞investigation_type](migs_eu_investigation_type.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞isol_growth_condt](migs_eu_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_layout](migs_eu_lib_layout.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞lib_reads_seqd](migs_eu_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_screen](migs_eu_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_size](migs_eu_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞lib_vector](migs_eu_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_amp](migs_eu_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞nucl_acid_ext](migs_eu_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞num_replicons](migs_eu_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞number_contig](migs_eu_number_contig.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞pathogenicity](migs_eu_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ploidy](migs_eu_ploidy.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞project_name](migs_eu_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞propagation](migs_eu_propagation.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_biomaterial](migs_eu_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞ref_db](migs_eu_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_collect_device](migs_eu_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_mat_process](migs_eu_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞samp_size](migs_eu_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sample_name](migs_eu_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞seq_meth](migs_eu_seq_meth.md) REQ - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞sim_search_meth](migs_eu_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞sop](migs_eu_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞source_mat_id](migs_eu_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞specific_host](migs_eu_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞submitted_to_insdc](migs_eu_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞subspecf_gen_lin](migs_eu_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_class](migs_eu_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_eu: - - * [migs_eu➞tax_ident](migs_eu_tax_ident.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞trophic_level](migs_eu_trophic_level.md) OPT - * range: - -### Mixed in from migs_eu: - - * [migs_eu➞url](migs_eu_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMigsOrg.md b/mixs6/WaterMigsOrg.md index 00716a11..73f6a989 100644 --- a/mixs6/WaterMigsOrg.md +++ b/mixs6/WaterMigsOrg.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimal Information about a Genome Sequence: org with en URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Water]^-[WaterMIGSOrg],[Water],[QuantityValue],[MIGSOrg]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIGSOrg|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;isol_growth_condt:string;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIGSOrg],[Water]^-[WaterMIGSOrg],[Water],[QuantityValue],[MIGSOrg]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -510,22 +510,27 @@ URI: [mixs.vocab:WaterMIGSOrg](https://w3id.org/mixs/vocab/WaterMIGSOrg) ### Mixed in from MIGS org: - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) OPT + * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_mat_process](MIGS_org_samp_mat_process.md) OPT + * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIGS org: + + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞samp_size](MIGS_org_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIGS org: - * [MIGS org➞sample_name](MIGS_org_sample_name.md) OPT + * [MIGS org➞sample_name](MIGS_org_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIGS org: diff --git a/mixs6/WaterMigsPl.md b/mixs6/WaterMigsPl.md deleted file mode 100644 index 9e2f8f3d..00000000 --- a/mixs6/WaterMigsPl.md +++ /dev/null @@ -1,589 +0,0 @@ - -# Class: WaterMigsPl - - -Combinatorial checklist for water with migs_pl - -URI: [mixs.vocab:WaterMigsPl](https://w3id.org/mixs/vocab/WaterMigsPl) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsPl|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsPl],[Water]^-[WaterMigsPl],[Water],[QuantityValue],[MigsPl]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MigsPl](MigsPl.md) - migs_pl Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_pl: - - * [migs_pl➞adapters](migs_pl_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞annot](migs_pl_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_name](migs_pl_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_qual](migs_pl_assembly_qual.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞assembly_software](migs_pl_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞compl_score](migs_pl_compl_score.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞compl_software](migs_pl_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞encoded_traits](migs_pl_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞env_package](migs_pl_env_package.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞estimated_size](migs_pl_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞experimental_factor](migs_pl_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞feat_pred](migs_pl_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞host_spec_range](migs_pl_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞investigation_type](migs_pl_investigation_type.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞isol_growth_condt](migs_pl_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_layout](migs_pl_lib_layout.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞lib_reads_seqd](migs_pl_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_screen](migs_pl_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_size](migs_pl_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞lib_vector](migs_pl_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_amp](migs_pl_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞nucl_acid_ext](migs_pl_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞number_contig](migs_pl_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞project_name](migs_pl_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞propagation](migs_pl_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_biomaterial](migs_pl_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞ref_db](migs_pl_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_collect_device](migs_pl_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_mat_process](migs_pl_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞samp_size](migs_pl_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sample_name](migs_pl_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞seq_meth](migs_pl_seq_meth.md) REQ - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞sim_search_meth](migs_pl_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞sop](migs_pl_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞source_mat_id](migs_pl_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞specific_host](migs_pl_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞submitted_to_insdc](migs_pl_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞subspecf_gen_lin](migs_pl_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_class](migs_pl_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_pl: - - * [migs_pl➞tax_ident](migs_pl_tax_ident.md) OPT - * range: - -### Mixed in from migs_pl: - - * [migs_pl➞url](migs_pl_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMigsVi.md b/mixs6/WaterMigsVi.md deleted file mode 100644 index 69a67fc7..00000000 --- a/mixs6/WaterMigsVi.md +++ /dev/null @@ -1,614 +0,0 @@ - -# Class: WaterMigsVi - - -Combinatorial checklist for water with migs_vi - -URI: [mixs.vocab:WaterMigsVi](https://w3id.org/mixs/vocab/WaterMigsVi) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMigsVi|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;num_replicons:string%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;health_disease_stat:health_disease_stat_enum%20%3F;propagation:string;encoded_traits:string%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;virus_enrich_appr:virus_enrich_appr_enum%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum%20%3F;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MigsVi],[Water]^-[WaterMigsVi],[Water],[QuantityValue],[MigsVi]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MigsVi](MigsVi.md) - migs_vi Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from migs_vi: - - * [migs_vi➞adapters](migs_vi_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞annot](migs_vi_annot.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_name](migs_vi_assembly_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_qual](migs_vi_assembly_qual.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞assembly_software](migs_vi_assembly_software.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞biotic_relationship](migs_vi_biotic_relationship.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_score](migs_vi_compl_score.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞compl_software](migs_vi_compl_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞encoded_traits](migs_vi_encoded_traits.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞env_package](migs_vi_env_package.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞estimated_size](migs_vi_estimated_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞experimental_factor](migs_vi_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞feat_pred](migs_vi_feat_pred.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞health_disease_stat](migs_vi_health_disease_stat.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞host_spec_range](migs_vi_host_spec_range.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞investigation_type](migs_vi_investigation_type.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞isol_growth_condt](migs_vi_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_layout](migs_vi_lib_layout.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞lib_reads_seqd](migs_vi_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_screen](migs_vi_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_size](migs_vi_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞lib_vector](migs_vi_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_amp](migs_vi_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞nucl_acid_ext](migs_vi_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞num_replicons](migs_vi_num_replicons.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞number_contig](migs_vi_number_contig.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞pathogenicity](migs_vi_pathogenicity.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞project_name](migs_vi_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞propagation](migs_vi_propagation.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_biomaterial](migs_vi_ref_biomaterial.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞ref_db](migs_vi_ref_db.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_collect_device](migs_vi_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_mat_process](migs_vi_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞samp_size](migs_vi_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sample_name](migs_vi_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞seq_meth](migs_vi_seq_meth.md) REQ - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞sim_search_meth](migs_vi_sim_search_meth.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞sop](migs_vi_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞source_mat_id](migs_vi_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞specific_host](migs_vi_specific_host.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞submitted_to_insdc](migs_vi_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞subspecf_gen_lin](migs_vi_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_class](migs_vi_tax_class.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞tax_ident](migs_vi_tax_ident.md) OPT - * range: - -### Mixed in from migs_vi: - - * [migs_vi➞url](migs_vi_url.md) OPT - * range: [String](types/String.md) - -### Mixed in from migs_vi: - - * [migs_vi➞virus_enrich_appr](migs_vi_virus_enrich_appr.md) OPT - * range: diff --git a/mixs6/WaterMimag.md b/mixs6/WaterMimag.md index d1e8bcb4..69803349 100644 --- a/mixs6/WaterMimag.md +++ b/mixs6/WaterMimag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Water]^-[WaterMIMAG],[Water],[QuantityValue],[MIMAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIMAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;bin_param:bin_param_enum;bin_software:bin_software_enum;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIMAG],[Water]^-[WaterMIMAG],[Water],[QuantityValue],[MIMAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -550,22 +550,27 @@ URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) ### Mixed in from MIMAG: - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) OPT + * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_mat_process](MIMAG_samp_mat_process.md) OPT + * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIMAG: + + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞samp_size](MIMAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIMAG: - * [MIMAG➞sample_name](MIMAG_sample_name.md) OPT + * [MIMAG➞sample_name](MIMAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIMAG: @@ -627,8 +632,3 @@ URI: [mixs.vocab:WaterMIMAG](https://w3id.org/mixs/vocab/WaterMIMAG) * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MIMAG: - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMimarksC.md b/mixs6/WaterMimarksC.md deleted file mode 100644 index 780713da..00000000 --- a/mixs6/WaterMimarksC.md +++ /dev/null @@ -1,519 +0,0 @@ - -# Class: WaterMimarksC - - -Combinatorial checklist for water with mimarks_c - -URI: [mixs.vocab:WaterMimarksC](https://w3id.org/mixs/vocab/WaterMimarksC) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksC|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;subspecf_gen_lin:string%20%3F;extrachrom_elements:string%20%3F;source_mat_id:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;trophic_level:trophic_level_enum%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;isol_growth_condt:string;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksC],[Water]^-[WaterMimarksC],[Water],[QuantityValue],[MimarksC]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MimarksC](MimarksC.md) - mimarks_c Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from mimarks_c: - - * [mimarks_c➞biotic_relationship](mimarks_c_biotic_relationship.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞chimera_check](mimarks_c_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞env_package](mimarks_c_env_package.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞experimental_factor](mimarks_c_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞extrachrom_elements](mimarks_c_extrachrom_elements.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞investigation_type](mimarks_c_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞isol_growth_condt](mimarks_c_isol_growth_condt.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_amp](mimarks_c_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞nucl_acid_ext](mimarks_c_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_cond](mimarks_c_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞pcr_primers](mimarks_c_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞project_name](mimarks_c_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞rel_to_oxygen](mimarks_c_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_collect_device](mimarks_c_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_mat_process](mimarks_c_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞samp_size](mimarks_c_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sample_name](mimarks_c_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_meth](mimarks_c_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞seq_quality_check](mimarks_c_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞sop](mimarks_c_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞source_mat_id](mimarks_c_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞submitted_to_insdc](mimarks_c_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞subspecf_gen_lin](mimarks_c_subspecf_gen_lin.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_gene](mimarks_c_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞target_subfragment](mimarks_c_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_c: - - * [mimarks_c➞trophic_level](mimarks_c_trophic_level.md) OPT - * range: - -### Mixed in from mimarks_c: - - * [mimarks_c➞url](mimarks_c_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMimarksS.md b/mixs6/WaterMimarksS.md deleted file mode 100644 index 0d32b1bc..00000000 --- a/mixs6/WaterMimarksS.md +++ /dev/null @@ -1,539 +0,0 @@ - -# Class: WaterMimarksS - - -Combinatorial checklist for water with mimarks_s - -URI: [mixs.vocab:WaterMimarksS](https://w3id.org/mixs/vocab/WaterMimarksS) - - -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMimarksS|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;target_gene:string;target_subfragment:string%20%3F;pcr_primers:string%20%3F;mid:string%20%3F;adapters:string%20%3F;pcr_cond:string%20%3F;seq_meth:seq_meth_enum;seq_quality_check:string%20%3F;chimera_check:string%20%3F;assembly_software:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MimarksS],[Water]^-[WaterMimarksS],[Water],[QuantityValue],[MimarksS]) - -## Parents - - * is_a: [Water](Water.md) - water - -## Uses Mixins - - * mixin: [MimarksS](MimarksS.md) - mimarks_s Checklist - -## Attributes - - -### Inherited from water: - - * [alkalinity](alkalinity.md) OPT - * Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate - * range: [QuantityValue](QuantityValue.md) - * Example: 50 milligram per liter None - * [alkalinity_method](alkalinity_method.md) OPT - * Description: Method used for alkalinity measurement - * range: [String](types/String.md) - * Example: titration None - * [alkyl_diethers](alkyl_diethers.md) OPT - * Description: Concentration of alkyl diethers - * range: [QuantityValue](QuantityValue.md) - * Example: 0.005 mole per liter None - * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [aminopept_act](aminopept_act.md) OPT - * Description: Measurement of aminopeptidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.269 mole per liter per hour None - * [ammonium](ammonium.md) OPT - * Description: Concentration of ammonium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 milligram per liter None - * [atmospheric_data](atmospheric_data.md) OPT - * Description: Measurement of atmospheric data; can include multiple data - * range: [String](types/String.md) - * Example: wind speed;9 knots None - * [bac_prod](bac_prod.md) OPT - * Description: Bacterial production in the water column measured by isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter per day None - * [bac_resp](bac_resp.md) OPT - * Description: Measurement of bacterial respiration in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 300 micromole oxygen per liter per hour None - * [bacteria_carb_prod](bacteria_carb_prod.md) OPT - * Description: Measurement of bacterial carbon production - * range: [QuantityValue](QuantityValue.md) - * Example: 2.53 microgram per liter per hour None - * [biomass](biomass.md) OPT - * Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements - * range: [String](types/String.md) - * Example: total;20 gram None - * [bishomohopanol](bishomohopanol.md) OPT - * Description: Concentration of bishomohopanol - * range: [QuantityValue](QuantityValue.md) - * Example: 14 microgram per liter None - * [bromide](bromide.md) OPT - * Description: Concentration of bromide - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 parts per million None - * [calcium](calcium.md) OPT - * Description: Concentration of calcium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micromole per liter None - * [carb_nitro_ratio](carb_nitro_ratio.md) OPT - * Description: Ratio of amount or concentrations of carbon to nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.417361111 None - * [chem_administration](chem_administration.md) OPT - * Description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - * range: [String](types/String.md) - * Example: agar [CHEBI:2509];2018-05-11T20:00Z None - * [chloride](chloride.md) OPT - * Description: Concentration of chloride in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5000 milligram per liter None - * [chlorophyll](chlorophyll.md) OPT - * Description: Concentration of chlorophyll - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per cubic meter None - * [collection_date](collection_date.md) OPT - * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) - * Example: 2018-05-11T10:00:00+01:00 None - * [conduc](conduc.md) OPT - * Description: Electrical conductivity of water - * range: [QuantityValue](QuantityValue.md) - * Example: 10 milliSiemens per centimeter None - * [density](density.md) OPT - * Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) - * range: [QuantityValue](QuantityValue.md) - * Example: 1000 kilogram per cubic meter None - * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages - * range: [String](types/String.md) - * Example: None - * [diether_lipids](diether_lipids.md) OPT - * Description: Concentration of diether lipids; can include multiple types of diether lipids - * range: [String](types/String.md) - * Example: 0.2 nanogram per liter None - * [diss_carb_dioxide](diss_carb_dioxide.md) OPT - * Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 milligram per liter None - * [diss_hydrogen](diss_hydrogen.md) OPT - * Description: Concentration of dissolved hydrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [diss_inorg_carb](diss_inorg_carb.md) OPT - * Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter - * range: [QuantityValue](QuantityValue.md) - * Example: 2059 micromole per kilogram None - * [diss_inorg_nitro](diss_inorg_nitro.md) OPT - * Description: Concentration of dissolved inorganic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 761 micromole per liter None - * [diss_inorg_phosp](diss_inorg_phosp.md) OPT - * Description: Concentration of dissolved inorganic phosphorus in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 56.5 micromole per liter None - * [diss_org_carb](diss_org_carb.md) OPT - * Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 197 micromole per liter None - * [diss_org_nitro](diss_org_nitro.md) OPT - * Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [diss_oxygen](diss_oxygen.md) OPT - * Description: Concentration of dissolved oxygen - * range: [QuantityValue](QuantityValue.md) - * Example: 175 micromole per kilogram None - * [down_par](down_par.md) OPT - * Description: Visible waveband radiance and irradiance measurements in the water column - * range: [QuantityValue](QuantityValue.md) - * Example: 28.71 microEinstein per square meter per second None - * [elev](elev.md) OPT - * Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit - * range: [QuantityValue](QuantityValue.md) - * Example: 100 meter None - * [env_broad_scale](env_broad_scale.md) OPT - * Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: forest biome [ENVO:01000174] None - * [env_local_scale](env_local_scale.md) OPT - * Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: litter layer [ENVO:01000338] None - * [env_medium](env_medium.md) OPT - * Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html - * range: [String](types/String.md) - * Example: soil [ENVO:00001998] None - * [fluor](fluor.md) OPT - * Description: Raw or converted fluorescence of water - * range: [QuantityValue](QuantityValue.md) - * Example: 2.5 volts None - * [geo_loc_name](geo_loc_name.md) OPT - * Description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - * range: [String](types/String.md) - * Example: Germany;North Rhine-Westphalia;Eifel National Park None - * [glucosidase_act](glucosidase_act.md) OPT - * Description: Measurement of glucosidase activity - * range: [QuantityValue](QuantityValue.md) - * Example: 5 mol per liter per hour None - * [lat_lon](lat_lon.md) OPT - * Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system - * range: [String](types/String.md) - * Example: 50.586825 6.408977 None - * [light_intensity](light_intensity.md) OPT - * Description: Measurement of light intensity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 lux None - * [magnesium](magnesium.md) OPT - * Description: Concentration of magnesium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 52.8 micromole per kilogram None - * [mean_frict_vel](mean_frict_vel.md) OPT - * Description: Measurement of mean friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 meter per second None - * [mean_peak_frict_vel](mean_peak_frict_vel.md) OPT - * Description: Measurement of mean peak friction velocity - * range: [QuantityValue](QuantityValue.md) - * Example: 1 meter per second None - * [misc_param](misc_param.md) OPT - * Description: Any other measurement performed or parameter collected, that is not listed here - * range: [String](types/String.md) - * Example: Bicarbonate ion concentration;2075 micromole per kilogram None - * [n_alkanes](n_alkanes.md) OPT - * Description: Concentration of n-alkanes; can include multiple n-alkanes - * range: [String](types/String.md) - * Example: n-hexadecane;100 milligram per liter None - * [nitrate](nitrate.md) OPT - * Description: Concentration of nitrate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 65 micromole per liter None - * [nitrite](nitrite.md) OPT - * Description: Concentration of nitrite in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 micromole per liter None - * [nitro](nitro.md) OPT - * Description: Concentration of nitrogen (total) - * range: [QuantityValue](QuantityValue.md) - * Example: 4.2 micromole per liter None - * [org_carb](org_carb.md) OPT - * Description: Concentration of organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.5 microgram per liter None - * [org_matter](org_matter.md) OPT - * Description: Concentration of organic matter - * range: [QuantityValue](QuantityValue.md) - * Example: 1.75 milligram per cubic meter None - * [org_nitro](org_nitro.md) OPT - * Description: Concentration of organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 4 micromole per liter None - * [organism_count](organism_count.md) OPT - * Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) - * range: - * Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None - * [oxy_stat_samp](oxy_stat_samp.md) OPT - * Description: Oxygenation status of sample - * range: - * Example: aerobic None - * [part_org_carb](part_org_carb.md) OPT - * Description: Concentration of particulate organic carbon - * range: [QuantityValue](QuantityValue.md) - * Example: 1.92 micromole per liter None - * [part_org_nitro](part_org_nitro.md) OPT - * Description: Concentration of particulate organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 micromole per liter None - * [perturbation](perturbation.md) OPT - * Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types - * range: [String](types/String.md) - * Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None - * [petroleum_hydrocarb](petroleum_hydrocarb.md) OPT - * Description: Concentration of petroleum hydrocarbon - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [ph](ph.md) OPT - * Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid - * range: [Double](types/Double.md) - * Example: 7.2 None - * [phaeopigments](phaeopigments.md) OPT - * Description: Concentration of phaeopigments; can include multiple phaeopigments - * range: [String](types/String.md) - * Example: 2.5 milligram per cubic meter None - * [phosphate](phosphate.md) OPT - * Description: Concentration of phosphate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.7 micromole per liter None - * [phosplipid_fatt_acid](phosplipid_fatt_acid.md) OPT - * Description: Concentration of phospholipid fatty acids; can include multiple values - * range: [String](types/String.md) - * Example: 2.98 milligram per liter None - * [photon_flux](photon_flux.md) OPT - * Description: Measurement of photon flux - * range: [QuantityValue](QuantityValue.md) - * Example: 3.926 micromole photons per second per square meter None - * [potassium](potassium.md) OPT - * Description: Concentration of potassium in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 463 milligram per liter None - * [pressure](pressure.md) OPT - * Description: Pressure to which the sample is subject to, in atmospheres - * range: [QuantityValue](QuantityValue.md) - * Example: 50 atmosphere None - * [primary_prod](primary_prod.md) OPT - * Description: Measurement of primary production, generally measured as isotope uptake - * range: [QuantityValue](QuantityValue.md) - * Example: 100 milligram per cubic meter per day None - * [redox_potential](redox_potential.md) OPT - * Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - * range: [QuantityValue](QuantityValue.md) - * Example: 300 millivolt None - * [salinity](salinity.md) OPT - * Description: Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater - * range: [QuantityValue](QuantityValue.md) - * Example: 25 practical salinity unit None - * [samp_store_dur](samp_store_dur.md) OPT - * Description: Duration for which the sample was stored - * range: [String](types/String.md) - * Example: P1Y6M None - * [samp_store_loc](samp_store_loc.md) OPT - * Description: Location at which sample was stored, usually name of a specific freezer/room - * range: [String](types/String.md) - * Example: Freezer no:5 None - * [samp_store_temp](samp_store_temp.md) OPT - * Description: Temperature at which sample was stored, e.g. -80 degree Celsius - * range: [QuantityValue](QuantityValue.md) - * Example: -80 degree Celsius None - * [samp_vol_we_dna_ext](samp_vol_we_dna_ext.md) OPT - * Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction - * range: [QuantityValue](QuantityValue.md) - * Example: 1500 milliliter None - * [silicate](silicate.md) OPT - * Description: Concentration of silicate - * range: [QuantityValue](QuantityValue.md) - * Example: 0.05 micromole per liter None - * [size_frac_low](size_frac_low.md) OPT - * Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 0.2 micrometer None - * [size_frac_up](size_frac_up.md) OPT - * Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 20 micrometer None - * [sodium](sodium.md) OPT - * Description: Sodium concentration in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 10.5 milligram per liter None - * [soluble_react_phosp](soluble_react_phosp.md) OPT - * Description: Concentration of soluble reactive phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.1 milligram per liter None - * [sulfate](sulfate.md) OPT - * Description: Concentration of sulfate in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 5 micromole per liter None - * [sulfide](sulfide.md) OPT - * Description: Concentration of sulfide in the sample - * range: [QuantityValue](QuantityValue.md) - * Example: 2 micromole per liter None - * [suspend_part_matter](suspend_part_matter.md) OPT - * Description: Concentration of suspended particulate matter - * range: [QuantityValue](QuantityValue.md) - * Example: 0.5 milligram per liter None - * [temp](temp.md) OPT - * Description: Temperature of the sample at the time of sampling - * range: [QuantityValue](QuantityValue.md) - * Example: 25 degree Celsius None - * [tidal_stage](tidal_stage.md) OPT - * Description: Stage of tide - * range: - * Example: high tide None - * [tot_depth_water_col](tot_depth_water_col.md) OPT - * Description: Measurement of total depth of water column - * range: [QuantityValue](QuantityValue.md) - * Example: 500 meter None - * [tot_diss_nitro](tot_diss_nitro.md) OPT - * Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_inorg_nitro](tot_inorg_nitro.md) OPT - * Description: Total inorganic nitrogen content - * range: [QuantityValue](QuantityValue.md) - * Example: 40 microgram per liter None - * [tot_nitro](tot_nitro.md) OPT - * Description: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen - * range: [QuantityValue](QuantityValue.md) - * Example: 50 micromole per liter None - * [tot_part_carb](tot_part_carb.md) OPT - * Description: Total particulate carbon content - * range: [QuantityValue](QuantityValue.md) - * Example: 35 micromole per liter None - * [tot_phosp](tot_phosp.md) OPT - * Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus - * range: [QuantityValue](QuantityValue.md) - * Example: 0.03 milligram per liter None - * [turbidity](turbidity.md) OPT - * Description: Measure of the amount of cloudiness or haziness in water caused by individual particles - * range: [QuantityValue](QuantityValue.md) - * Example: 0.3 nephelometric turbidity units None - * [water_current](water_current.md) OPT - * Description: Measurement of magnitude and direction of flow within a fluid - * range: [QuantityValue](QuantityValue.md) - * Example: 10 cubic meter per second None - -### Mixed in from mimarks_s: - - * [mimarks_s➞adapters](mimarks_s_adapters.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞assembly_software](mimarks_s_assembly_software.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞chimera_check](mimarks_s_chimera_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞env_package](mimarks_s_env_package.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞experimental_factor](mimarks_s_experimental_factor.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞investigation_type](mimarks_s_investigation_type.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_layout](mimarks_s_lib_layout.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_reads_seqd](mimarks_s_lib_reads_seqd.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_screen](mimarks_s_lib_screen.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_size](mimarks_s_lib_size.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞lib_vector](mimarks_s_lib_vector.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞mid](mimarks_s_mid.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_amp](mimarks_s_nucl_acid_amp.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞nucl_acid_ext](mimarks_s_nucl_acid_ext.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_cond](mimarks_s_pcr_cond.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞pcr_primers](mimarks_s_pcr_primers.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞project_name](mimarks_s_project_name.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞rel_to_oxygen](mimarks_s_rel_to_oxygen.md) OPT - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_collect_device](mimarks_s_samp_collect_device.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_mat_process](mimarks_s_samp_mat_process.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞samp_size](mimarks_s_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sample_name](mimarks_s_sample_name.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_meth](mimarks_s_seq_meth.md) REQ - * range: - -### Mixed in from mimarks_s: - - * [mimarks_s➞seq_quality_check](mimarks_s_seq_quality_check.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞size_frac](mimarks_s_size_frac.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞sop](mimarks_s_sop.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞source_mat_id](mimarks_s_source_mat_id.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞submitted_to_insdc](mimarks_s_submitted_to_insdc.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_gene](mimarks_s_target_gene.md) REQ - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞target_subfragment](mimarks_s_target_subfragment.md) OPT - * range: [String](types/String.md) - -### Mixed in from mimarks_s: - - * [mimarks_s➞url](mimarks_s_url.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMisag.md b/mixs6/WaterMisag.md index 725e677a..169665f2 100644 --- a/mixs6/WaterMisag.md +++ b/mixs6/WaterMisag.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About a Single Amplified Genome with URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;x_16s_recover_software:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Water]^-[WaterMISAG],[Water],[QuantityValue],[MISAG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMISAG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;rel_to_oxygen:rel_to_oxygen_enum%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string%20%3F;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;x_16s_recover:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum;compl_software:string;compl_appr:compl_appr_enum%20%3F;contam_score:string;contam_screen_input:string%20%3F;contam_screen_param:contam_screen_param_enum%20%3F;decontam_software:decontam_software_enum%20%3F;sort_tech:sort_tech_enum;single_cell_lysis_appr:single_cell_lysis_appr_enum;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string;wga_amp_kit:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MISAG],[Water]^-[WaterMISAG],[Water],[QuantityValue],[MISAG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -530,22 +530,27 @@ URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) ### Mixed in from MISAG: - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) OPT + * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_mat_process](MISAG_samp_mat_process.md) OPT + * [MISAG➞samp_size](MISAG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MISAG: + + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞samp_size](MISAG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MISAG: - * [MISAG➞sample_name](MISAG_sample_name.md) OPT + * [MISAG➞sample_name](MISAG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MISAG: @@ -632,8 +637,3 @@ URI: [mixs.vocab:WaterMISAG](https://w3id.org/mixs/vocab/WaterMISAG) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) OPT * range: [String](types/String.md) - -### Mixed in from MISAG: - - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) OPT - * range: [String](types/String.md) diff --git a/mixs6/WaterMiuvig.md b/mixs6/WaterMiuvig.md index f7bb7fcb..cbe1713c 100644 --- a/mixs6/WaterMiuvig.md +++ b/mixs6/WaterMiuvig.md @@ -7,7 +7,7 @@ Combinatorial checklist Minimum Information About an Uncultivated Virus Genome w URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) -![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string%20%3F;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;samp_collect_device:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):string%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Water]^-[WaterMIUVIG],[Water],[QuantityValue],[MIUVIG]) +![img](http://yuml.me/diagram/nofunky;dir:TB/class/[WaterMIUVIG|submitted_to_insdc:string;investigation_type:investigation_type_enum;sample_name:string;project_name:string;experimental_factor:string%20%3F;env_package:env_package_enum%20%3F;estimated_size:string%20%3F;ref_biomaterial:string%20%3F;source_mat_id:string%20%3F;pathogenicity:string%20%3F;biotic_relationship:biotic_relationship_enum%20%3F;specific_host:string%20%3F;host_spec_range:string%20%3F;sample_collect_device:string%20%3F;sample_collect_method:string%20%3F;samp_mat_process:string%20%3F;size_frac:string%20%3F;source_uvig:source_uvig_enum;virus_enrich_appr:virus_enrich_appr_enum;nucl_acid_ext:string%20%3F;nucl_acid_amp:string%20%3F;lib_size:string%20%3F;lib_reads_seqd:string%20%3F;lib_layout:lib_layout_enum%20%3F;lib_vector:string%20%3F;lib_screen:string%20%3F;mid:string%20%3F;adapters:string%20%3F;seq_meth:seq_meth_enum;tax_ident:tax_ident_enum%20%3F;assembly_qual:assembly_qual_enum;assembly_name:string%20%3F;assembly_software:string;annot:string%20%3F;number_contig:string;feat_pred:string%20%3F;ref_db:string%20%3F;sim_search_meth:string%20%3F;tax_class:string%20%3F;trnas:string%20%3F;trna_ext_software:string%20%3F;compl_score:compl_score_enum%20%3F;compl_software:string%20%3F;compl_appr:compl_appr_enum%20%3F;sort_tech:sort_tech_enum%20%3F;single_cell_lysis_appr:single_cell_lysis_appr_enum%20%3F;single_cell_lysis_prot:string%20%3F;wga_amp_appr:string%20%3F;wga_amp_kit:string%20%3F;bin_param:bin_param_enum%20%3F;bin_software:bin_software_enum%20%3F;reassembly_bin:string%20%3F;mag_cov_software:mag_cov_software_enum%20%3F;vir_ident_software:string;pred_genome_type:pred_genome_type_enum;pred_genome_struc:pred_genome_struc_enum;detec_type:string;votu_class_appr:string%20%3F;votu_seq_comp_appr:string%20%3F;votu_db:string%20%3F;host_pred_appr:host_pred_appr_enum%20%3F;host_pred_est_acc:string%20%3F;url:string%20%3F;sop:string%20%3F;lat_lon(i):string%20%3F;depth(i):string%20%3F;geo_loc_name(i):string%20%3F;collection_date(i):date%20%3F;env_broad_scale(i):string%20%3F;env_local_scale(i):string%20%3F;env_medium(i):string%20%3F;alkalinity_method(i):string%20%3F;atmospheric_data(i):string%20%3F;biomass(i):string%20%3F;chem_administration(i):string%20%3F;diether_lipids(i):string%20%3F;misc_param(i):string%20%3F;n_alkanes(i):string%20%3F;organism_count(i):organism_count_enum%20%3F;oxy_stat_samp(i):oxy_stat_samp_enum%20%3F;ph(i):double%20%3F;perturbation(i):string%20%3F;phaeopigments(i):string%20%3F;phosplipid_fatt_acid(i):string%20%3F;samp_store_dur(i):string%20%3F;samp_store_loc(i):string%20%3F;tidal_stage(i):tidal_stage_enum%20%3F]uses%20-.->[MIUVIG],[Water]^-[WaterMIUVIG],[Water],[QuantityValue],[MIUVIG]) ## Parents @@ -35,7 +35,7 @@ URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) * range: [QuantityValue](QuantityValue.md) * Example: 0.005 mole per liter None * [alt](alt.md) OPT - * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * range: [QuantityValue](QuantityValue.md) * Example: 100 meter None * [aminopept_act](aminopept_act.md) OPT @@ -96,7 +96,7 @@ URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) * Example: 5 milligram per cubic meter None * [collection_date](collection_date.md) OPT * Description: The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant - * range: [String](types/String.md) + * range: [Date](types/Date.md) * Example: 2018-05-11T10:00:00+01:00 None * [conduc](conduc.md) OPT * Description: Electrical conductivity of water @@ -107,7 +107,7 @@ URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) * range: [QuantityValue](QuantityValue.md) * Example: 1000 kilogram per cubic meter None * [depth](depth.md) OPT - * Description: Please refer to the definitions of depth in the environmental packages + * Description: The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * range: [String](types/String.md) * Example: None * [diether_lipids](diether_lipids.md) OPT @@ -570,22 +570,27 @@ URI: [mixs.vocab:WaterMIUVIG](https://w3id.org/mixs/vocab/WaterMIUVIG) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) OPT + * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_mat_process](MIUVIG_samp_mat_process.md) OPT + * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT + * range: [QuantityValue](QuantityValue.md) + +### Mixed in from MIUVIG: + + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) OPT * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞samp_size](MIUVIG_samp_size.md) OPT - * range: [QuantityValue](QuantityValue.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) OPT + * range: [String](types/String.md) ### Mixed in from MIUVIG: - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) OPT + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) REQ * range: [String](types/String.md) ### Mixed in from MIUVIG: diff --git a/mixs6/WeekdayEnum.md b/mixs6/WeekdayEnum.md new file mode 100644 index 00000000..4607b41b --- /dev/null +++ b/mixs6/WeekdayEnum.md @@ -0,0 +1,19 @@ + +# Enum: weekday_enum + + + + +URI: [mixs.vocab:weekday_enum](https://w3id.org/mixs/vocab/weekday_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowCondEnum.md b/mixs6/WindowCondEnum.md new file mode 100644 index 00000000..0e047652 --- /dev/null +++ b/mixs6/WindowCondEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_cond_enum + + + + +URI: [mixs.vocab:window_cond_enum](https://w3id.org/mixs/vocab/window_cond_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowCoverEnum.md b/mixs6/WindowCoverEnum.md new file mode 100644 index 00000000..5a1d6074 --- /dev/null +++ b/mixs6/WindowCoverEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_cover_enum + + + + +URI: [mixs.vocab:window_cover_enum](https://w3id.org/mixs/vocab/window_cover_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowHorizPosEnum.md b/mixs6/WindowHorizPosEnum.md new file mode 100644 index 00000000..2f1701ed --- /dev/null +++ b/mixs6/WindowHorizPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_horiz_pos_enum + + + + +URI: [mixs.vocab:window_horiz_pos_enum](https://w3id.org/mixs/vocab/window_horiz_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowLocEnum.md b/mixs6/WindowLocEnum.md new file mode 100644 index 00000000..1a976f3a --- /dev/null +++ b/mixs6/WindowLocEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_loc_enum + + + + +URI: [mixs.vocab:window_loc_enum](https://w3id.org/mixs/vocab/window_loc_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowMatEnum.md b/mixs6/WindowMatEnum.md new file mode 100644 index 00000000..0a65204c --- /dev/null +++ b/mixs6/WindowMatEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_mat_enum + + + + +URI: [mixs.vocab:window_mat_enum](https://w3id.org/mixs/vocab/window_mat_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowTypeEnum.md b/mixs6/WindowTypeEnum.md new file mode 100644 index 00000000..333a57b8 --- /dev/null +++ b/mixs6/WindowTypeEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_type_enum + + + + +URI: [mixs.vocab:window_type_enum](https://w3id.org/mixs/vocab/window_type_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/WindowVertPosEnum.md b/mixs6/WindowVertPosEnum.md new file mode 100644 index 00000000..137b1ec9 --- /dev/null +++ b/mixs6/WindowVertPosEnum.md @@ -0,0 +1,19 @@ + +# Enum: window_vert_pos_enum + + + + +URI: [mixs.vocab:window_vert_pos_enum](https://w3id.org/mixs/vocab/window_vert_pos_enum) + + +## Other properties + +| | | | +| --- | --- | --- | + +## Permissible Values + +| Text | Meaning | +| :--- | --------: | + diff --git a/mixs6/abs_air_humidity.md b/mixs6/abs_air_humidity.md index 52486c9e..883bf48a 100644 --- a/mixs6/abs_air_humidity.md +++ b/mixs6/abs_air_humidity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram per gram, kilogram per kilogram, kilogram, pound | | | | Occurrence: 1 | -| | | Position: 4 | +| | | Position: 4.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='9 gram per gram', description=None) | diff --git a/mixs6/adapters.md b/mixs6/adapters.md index 35017538..8a40140b 100644 --- a/mixs6/adapters.md +++ b/mixs6/adapters.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | adapters | | **Comments:** | | Expected value: adapter A and B sequence | -| | | Preferred unit: | | | | Position: 48.0 | | **Examples:** | | Example(value='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT', description=None) | diff --git a/mixs6/add_recov_method.md b/mixs6/add_recov_method.md index 8b9f14d7..fa820018 100644 --- a/mixs6/add_recov_method.md +++ b/mixs6/add_recov_method.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | secondary and tertiary recovery methods and start date | | **Mappings:** | | MIXS:0001009 | | **Comments:** | | Expected value: enumeration;timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 28 | +| | | Position: 28.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Polymer Addition;2018-06-21T14:30Z', description=None) | diff --git a/mixs6/additional_info.md b/mixs6/additional_info.md index 4f35a316..1098387f 100644 --- a/mixs6/additional_info.md +++ b/mixs6/additional_info.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | additional info | | **Mappings:** | | MIXS:0000300 | | **Comments:** | | Expected value: text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 94 | +| | | Position: 94.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/address.md b/mixs6/address.md index 9331d40d..19d2dac4 100644 --- a/mixs6/address.md +++ b/mixs6/address.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | address | | **Mappings:** | | MIXS:0000218 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 27 | +| | | Position: 27.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/adj_room.md b/mixs6/adj_room.md index 1e4e6da6..7a3dc91b 100644 --- a/mixs6/adj_room.md +++ b/mixs6/adj_room.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | adjacent rooms | | **Mappings:** | | MIXS:0000219 | | **Comments:** | | Expected value: room name;room number | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 28 | +| | | Position: 28.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/aero_struc.md b/mixs6/aero_struc.md index 08cd9b01..0c5b5f71 100644 --- a/mixs6/aero_struc.md +++ b/mixs6/aero_struc.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | aerospace structure | | **Mappings:** | | MIXS:0000773 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 29 | +| | | Position: 29.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='plane', description=None) | diff --git a/mixs6/agrochem_addition.md b/mixs6/agrochem_addition.md index 7a611b8a..52e451ea 100644 --- a/mixs6/agrochem_addition.md +++ b/mixs6/agrochem_addition.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: agrochemical name;agrochemical amount;timestamp | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 7 | +| | | Position: 7.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='roundup;5 milligram per liter;2018-06-21', description=None) | diff --git a/mixs6/air_temp.md b/mixs6/air_temp.md index 03e92a96..32fe90e7 100644 --- a/mixs6/air_temp.md +++ b/mixs6/air_temp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 6 | +| | | Position: 6.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='20 degree Celsius', description=None) | diff --git a/mixs6/air_temp_regm.md b/mixs6/air_temp_regm.md index a1b41176..1821389c 100644 --- a/mixs6/air_temp_regm.md +++ b/mixs6/air_temp_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: temperature value;treatment interval and duration | | | | Preferred unit: degree Celsius | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/al_sat.md b/mixs6/al_sat.md index a7b1fed3..711f0197 100644 --- a/mixs6/al_sat.md +++ b/mixs6/al_sat.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 50 | +| | | Position: 50.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/al_sat_meth.md b/mixs6/al_sat_meth.md index 34aaed58..53a1459e 100644 --- a/mixs6/al_sat_meth.md +++ b/mixs6/al_sat_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | extreme_unusual_properties/Al saturation method | | **Mappings:** | | MIXS:0000324 | | **Comments:** | | Expected value: PMID,DOI or URL | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 51 | +| | | Position: 51.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/alkalinity.md b/mixs6/alkalinity.md index b40c67e7..5f538b1a 100644 --- a/mixs6/alkalinity.md +++ b/mixs6/alkalinity.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milliequivalent per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 56 | +| | | Position: 56.0 | | | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='50 milligram per liter', description=None) | diff --git a/mixs6/alkalinity_method.md b/mixs6/alkalinity_method.md index cd94bfa5..5b506d6d 100644 --- a/mixs6/alkalinity_method.md +++ b/mixs6/alkalinity_method.md @@ -64,9 +64,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | alkalinity method | | **Mappings:** | | MIXS:0000298 | | **Comments:** | | Expected value: description of method | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 57 | +| | | Position: 57.0 | | | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | | **Examples:** | | Example(value='titration', description=None) | diff --git a/mixs6/alkyl_diethers.md b/mixs6/alkyl_diethers.md index 81358d6d..d4ff39e8 100644 --- a/mixs6/alkyl_diethers.md +++ b/mixs6/alkyl_diethers.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: mole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.005 mole per liter', description=None) | diff --git a/mixs6/alt.md b/mixs6/alt.md index 8feed6ad..ef22d9dc 100644 --- a/mixs6/alt.md +++ b/mixs6/alt.md @@ -2,7 +2,7 @@ # Slot: alt -Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air +Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air URI: [mixs.vocab:alt](https://w3id.org/mixs/vocab/alt) @@ -232,8 +232,6 @@ None -> OPT [QuantityValue](QuantityValue.md) | --- | --- | --- | | **Aliases:** | | altitude | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | -| | | Position: | | | | This field is used in: 3 packages: air, host-associated, miscellaneous natural or artificial environment | | **Examples:** | | Example(value='100 meter', description=None) | diff --git a/mixs6/aminopept_act.md b/mixs6/aminopept_act.md index c9fdfca1..3d18d6b2 100644 --- a/mixs6/aminopept_act.md +++ b/mixs6/aminopept_act.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: mole per liter per hour | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.269 mole per liter per hour', description=None) | diff --git a/mixs6/ammonium.md b/mixs6/ammonium.md index 2d1c6e91..370e5033 100644 --- a/mixs6/ammonium.md +++ b/mixs6/ammonium.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 63 | +| | | Position: 63.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='1.5 milligram per liter', description=None) | diff --git a/mixs6/amniotic_fluid_color.md b/mixs6/amniotic_fluid_color.md index 2de32e94..dd4303fb 100644 --- a/mixs6/amniotic_fluid_color.md +++ b/mixs6/amniotic_fluid_color.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | amniotic fluid/color | | **Mappings:** | | MIXS:0000276 | | **Comments:** | | Expected value: color | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 39 | +| | | Position: 39.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/amount_light.md b/mixs6/amount_light.md index 4b6adda1..3bffc550 100644 --- a/mixs6/amount_light.md +++ b/mixs6/amount_light.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: lux, lumens per square meter | | | | Occurrence: 1 | -| | | Position: 30 | +| | | Position: 30.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/ances_data.md b/mixs6/ances_data.md index 287183ce..bcc38dcf 100644 --- a/mixs6/ances_data.md +++ b/mixs6/ances_data.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | ancestral data | | **Mappings:** | | MIXS:0000247 | | **Comments:** | | Expected value: free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='A/3*B', description=None) | diff --git a/mixs6/annot.md b/mixs6/annot.md index bbfc7741..0c989460 100644 --- a/mixs6/annot.md +++ b/mixs6/annot.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | annotation | | **Comments:** | | Expected value: name of tool or pipeline used, or annotation source description | -| | | Preferred unit: | | | | Position: 57.0 | | **Examples:** | | Example(value='prokka', description=None) | diff --git a/mixs6/annual_precpt.md b/mixs6/annual_precpt.md index b08b6538..b77827ef 100644 --- a/mixs6/annual_precpt.md +++ b/mixs6/annual_precpt.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millimeter | | | | Occurrence: 1 | -| | | Position: 23 | +| | | Position: 23.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/annual_temp.md b/mixs6/annual_temp.md index d5c13234..9875d42e 100644 --- a/mixs6/annual_temp.md +++ b/mixs6/annual_temp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 21 | +| | | Position: 21.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='12.5 degree Celsius', description=None) | diff --git a/mixs6/antibiotic_regm.md b/mixs6/antibiotic_regm.md index 4f1beafb..8df08c68 100644 --- a/mixs6/antibiotic_regm.md +++ b/mixs6/antibiotic_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: antibiotic name;antibiotic amount;treatment interval and duration | | | | Preferred unit: milligram | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/api.md b/mixs6/api.md index 752d1c42..dddf3fb4 100644 --- a/mixs6/api.md +++ b/mixs6/api.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degrees API | | | | Occurrence: 1 | -| | | Position: 85 | +| | | Position: 85.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/arch_struc.md b/mixs6/arch_struc.md index 83de3d0f..48e8f837 100644 --- a/mixs6/arch_struc.md +++ b/mixs6/arch_struc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | architectural structure | | **Mappings:** | | MIXS:0000774 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 31 | +| | | Position: 31.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='shed', description=None) | diff --git a/mixs6/aromatics_pc.md b/mixs6/aromatics_pc.md index ec591f0b..a0705e1b 100644 --- a/mixs6/aromatics_pc.md +++ b/mixs6/aromatics_pc.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name;measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 90 | +| | | Position: 90.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/asphaltenes_pc.md b/mixs6/asphaltenes_pc.md index a565766a..5b23e2ac 100644 --- a/mixs6/asphaltenes_pc.md +++ b/mixs6/asphaltenes_pc.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name;measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 92 | +| | | Position: 92.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/assembly_name.md b/mixs6/assembly_name.md index 35e9b919..7581f31e 100644 --- a/mixs6/assembly_name.md +++ b/mixs6/assembly_name.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | assembly name | | **Comments:** | | Expected value: name and version of assembly | -| | | Preferred unit: | | | | Position: 55.0 | | **Examples:** | | Example(value='HuRef, JCVI_ISG_i3_1.0', description=None) | diff --git a/mixs6/assembly_qual.md b/mixs6/assembly_qual.md index bc33715d..564db584 100644 --- a/mixs6/assembly_qual.md +++ b/mixs6/assembly_qual.md @@ -37,7 +37,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | assembly quality | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 54.0 | | **Examples:** | | Example(value='High-quality draft genome', description=None) | diff --git a/mixs6/assembly_software.md b/mixs6/assembly_software.md index d1febe3b..adeb6672 100644 --- a/mixs6/assembly_software.md +++ b/mixs6/assembly_software.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | assembly software | | **Comments:** | | Expected value: name and version of software, parameters used | -| | | Preferred unit: | | | | Position: 56.0 | | **Examples:** | | Example(value='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise', description=None) | diff --git a/mixs6/atmospheric_data.md b/mixs6/atmospheric_data.md index c6fcc0ea..a1b96df5 100644 --- a/mixs6/atmospheric_data.md +++ b/mixs6/atmospheric_data.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | atmospheric data | | **Mappings:** | | MIXS:0001097 | | **Comments:** | | Expected value: atmospheric data name;measurement value | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='wind speed;9 knots', description=None) | diff --git a/mixs6/avg_dew_point.md b/mixs6/avg_dew_point.md index 5eeef9fd..4c259061 100644 --- a/mixs6/avg_dew_point.md +++ b/mixs6/avg_dew_point.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 33 | +| | | Position: 33.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='25.5 degree Celsius', description=None) | diff --git a/mixs6/avg_occup.md b/mixs6/avg_occup.md index c8264297..33442fba 100644 --- a/mixs6/avg_occup.md +++ b/mixs6/avg_occup.md @@ -40,9 +40,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | average daily occupancy | | **Mappings:** | | MIXS:0000775 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 32 | +| | | Position: 32.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2', description=None) | diff --git a/mixs6/avg_temp.md b/mixs6/avg_temp.md index f9a2bcbb..2cf2906d 100644 --- a/mixs6/avg_temp.md +++ b/mixs6/avg_temp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 34 | +| | | Position: 34.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='12.5 degree Celsius', description=None) | diff --git a/mixs6/bac_prod.md b/mixs6/bac_prod.md index 0bf8ba45..42f01de5 100644 --- a/mixs6/bac_prod.md +++ b/mixs6/bac_prod.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per cubic meter per day | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='5 milligram per cubic meter per day', description=None) | diff --git a/mixs6/bac_resp.md b/mixs6/bac_resp.md index 86bfb147..c1731627 100644 --- a/mixs6/bac_resp.md +++ b/mixs6/bac_resp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per cubic meter per day, micromole oxygen per liter per hour | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='300 micromole oxygen per liter per hour', description=None) | diff --git a/mixs6/bacteria_carb_prod.md b/mixs6/bacteria_carb_prod.md index 2eb8662c..f5181c9d 100644 --- a/mixs6/bacteria_carb_prod.md +++ b/mixs6/bacteria_carb_prod.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: nanogram per hour | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='2.53 microgram per liter per hour', description=None) | diff --git a/mixs6/barometric_press.md b/mixs6/barometric_press.md index e49fb0a2..ce02cd17 100644 --- a/mixs6/barometric_press.md +++ b/mixs6/barometric_press.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millibar | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='5 millibar', description=None) | diff --git a/mixs6/basin.md b/mixs6/basin.md index 1230a7f8..03f012aa 100644 --- a/mixs6/basin.md +++ b/mixs6/basin.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | basin name | | **Mappings:** | | MIXS:0000290 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/bathroom_count.md b/mixs6/bathroom_count.md index 4e4fc5de..05be8611 100644 --- a/mixs6/bathroom_count.md +++ b/mixs6/bathroom_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | bathroom count | | **Mappings:** | | MIXS:0000776 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 35 | +| | | Position: 35.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='1', description=None) | diff --git a/mixs6/bedroom_count.md b/mixs6/bedroom_count.md index 7d582a91..5c375d78 100644 --- a/mixs6/bedroom_count.md +++ b/mixs6/bedroom_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | bedroom count | | **Mappings:** | | MIXS:0000777 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 36 | +| | | Position: 36.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2', description=None) | diff --git a/mixs6/benzene.md b/mixs6/benzene.md index 4a7ff31d..587b4884 100644 --- a/mixs6/benzene.md +++ b/mixs6/benzene.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 81 | +| | | Position: 81.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/bin_param.md b/mixs6/bin_param.md index 7d4875c0..df2f6c85 100644 --- a/mixs6/bin_param.md +++ b/mixs6/bin_param.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | binning parameters | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 79.0 | | **Examples:** | | Example(value='coverage and kmer', description=None) | diff --git a/mixs6/bin_software.md b/mixs6/bin_software.md index caad1712..ecf4de12 100644 --- a/mixs6/bin_software.md +++ b/mixs6/bin_software.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | binning software | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 80.0 | | **Examples:** | | Example(value='concoct and maxbin', description=None) | diff --git a/mixs6/biochem_oxygen_dem.md b/mixs6/biochem_oxygen_dem.md index e317baa5..2109a9fd 100644 --- a/mixs6/biochem_oxygen_dem.md +++ b/mixs6/biochem_oxygen_dem.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/biocide.md b/mixs6/biocide.md index 0bf76430..a1814000 100644 --- a/mixs6/biocide.md +++ b/mixs6/biocide.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | biocide administration | | **Mappings:** | | MIXS:0001011 | | **Comments:** | | Expected value: name;name;timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 30 | +| | | Position: 30.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='ALPHA 1427;Baker Hughes;2008-01-23', description=None) | diff --git a/mixs6/biocide_admin_method.md b/mixs6/biocide_admin_method.md index c7abc3e9..8d7fc6bb 100644 --- a/mixs6/biocide_admin_method.md +++ b/mixs6/biocide_admin_method.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;frequency;duration;duration | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 31 | +| | | Position: 31.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/biol_stat.md b/mixs6/biol_stat.md index a968623e..cfb19634 100644 --- a/mixs6/biol_stat.md +++ b/mixs6/biol_stat.md @@ -2,7 +2,7 @@ # Slot: biol_stat -The level of genome modification +The level of genome modification. URI: [mixs.vocab:biol_stat](https://w3id.org/mixs/vocab/biol_stat) @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | biological status | | **Mappings:** | | MIXS:0000858 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='natural', description=None) | diff --git a/mixs6/biomass.md b/mixs6/biomass.md index ff37aeee..2dda0f85 100644 --- a/mixs6/biomass.md +++ b/mixs6/biomass.md @@ -78,7 +78,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: biomass type;measurement value | | | | Preferred unit: ton, kilogram, gram | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='total;20 gram', description=None) | diff --git a/mixs6/biotic_regm.md b/mixs6/biotic_regm.md index 784834a4..52edd831 100644 --- a/mixs6/biotic_regm.md +++ b/mixs6/biotic_regm.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | biotic regimen | | **Mappings:** | | MIXS:0001038 | | **Comments:** | | Expected value: free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='sample inoculated with Rhizobium spp. Culture', description=None) | diff --git a/mixs6/biotic_relationship.md b/mixs6/biotic_relationship.md index ae0b19b9..28d6e304 100644 --- a/mixs6/biotic_relationship.md +++ b/mixs6/biotic_relationship.md @@ -33,7 +33,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | observed biotic relationship | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 22.0 | | **Examples:** | | Example(value='free living', description=None) | diff --git a/mixs6/birth_control.md b/mixs6/birth_control.md index 047812ff..11ce7227 100644 --- a/mixs6/birth_control.md +++ b/mixs6/birth_control.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | birth control | | **Mappings:** | | MIXS:0000286 | | **Comments:** | | Expected value: medication name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/bishomohopanol.md b/mixs6/bishomohopanol.md index 66b5b3c9..bd42f065 100644 --- a/mixs6/bishomohopanol.md +++ b/mixs6/bishomohopanol.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, microgram per gram | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='14 microgram per liter', description=None) | diff --git a/mixs6/blood_blood_disord.md b/mixs6/blood_blood_disord.md index eaf58810..fc8d90f9 100644 --- a/mixs6/blood_blood_disord.md +++ b/mixs6/blood_blood_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | blood/blood disorder | | **Mappings:** | | MIXS:0000271 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 32 | +| | | Position: 32.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/bromide.md b/mixs6/bromide.md index 5f24579c..9f5c8174 100644 --- a/mixs6/bromide.md +++ b/mixs6/bromide.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.05 parts per million', description=None) | diff --git a/mixs6/build_docs.md b/mixs6/build_docs.md index f66e7f31..b136634e 100644 --- a/mixs6/build_docs.md +++ b/mixs6/build_docs.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | design, construction, and operation documents | | **Mappings:** | | MIXS:0000787 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 50 | +| | | Position: 50.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='maintenance plans', description=None) | diff --git a/mixs6/build_occup_type.md b/mixs6/build_occup_type.md index bf41605a..373b2783 100644 --- a/mixs6/build_occup_type.md +++ b/mixs6/build_occup_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | building occupancy type | | **Mappings:** | | MIXS:0000761 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 9 | +| | | Position: 9.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='market', description=None) | diff --git a/mixs6/building_setting.md b/mixs6/building_setting.md index 80eaeb9c..824f939d 100644 --- a/mixs6/building_setting.md +++ b/mixs6/building_setting.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | building setting | | **Mappings:** | | MIXS:0000768 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 20 | +| | | Position: 20.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='rural', description=None) | diff --git a/mixs6/built_struc_age.md b/mixs6/built_struc_age.md index 0d3d55a1..4741bec2 100644 --- a/mixs6/built_struc_age.md +++ b/mixs6/built_struc_age.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: year | | | | Occurrence: 1 | -| | | Position: 37 | +| | | Position: 37.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='15', description=None) | diff --git a/mixs6/built_struc_set.md b/mixs6/built_struc_set.md index fcacbd5b..9f211918 100644 --- a/mixs6/built_struc_set.md +++ b/mixs6/built_struc_set.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | built structure setting | | **Mappings:** | | MIXS:0000778 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 38 | +| | | Position: 38.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='rural', description=None) | diff --git a/mixs6/built_struc_type.md b/mixs6/built_struc_type.md index 3a74ad3a..bbe2df5d 100644 --- a/mixs6/built_struc_type.md +++ b/mixs6/built_struc_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | built structure type | | **Mappings:** | | MIXS:0000721 | | **Comments:** | | Expected value: free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 39 | +| | | Position: 39.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/calcium.md b/mixs6/calcium.md index 7e4a5246..05962436 100644 --- a/mixs6/calcium.md +++ b/mixs6/calcium.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, micromole per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 70 | +| | | Position: 70.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.2 micromole per liter', description=None) | diff --git a/mixs6/carb_dioxide.md b/mixs6/carb_dioxide.md index 9afc31b7..8214f96e 100644 --- a/mixs6/carb_dioxide.md +++ b/mixs6/carb_dioxide.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: air, built environment | | **Examples:** | | Example(value='410 parts per million', description=None) | diff --git a/mixs6/carb_monoxide.md b/mixs6/carb_monoxide.md index f2844b44..b24c845a 100644 --- a/mixs6/carb_monoxide.md +++ b/mixs6/carb_monoxide.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='0.1 parts per million', description=None) | diff --git a/mixs6/carb_nitro_ratio.md b/mixs6/carb_nitro_ratio.md index c9933b2a..be2dbb92 100644 --- a/mixs6/carb_nitro_ratio.md +++ b/mixs6/carb_nitro_ratio.md @@ -64,9 +64,8 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Aliases:** | | carbon/nitrogen ratio | | **Mappings:** | | MIXS:0000310 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.417361111', description=None) | diff --git a/mixs6/ceil_area.md b/mixs6/ceil_area.md index 1e7ba20b..e4442ee3 100644 --- a/mixs6/ceil_area.md +++ b/mixs6/ceil_area.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 40 | +| | | Position: 40.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='25 square meter', description=None) | diff --git a/mixs6/ceil_cond.md b/mixs6/ceil_cond.md index 649cecd0..d9235b0c 100644 --- a/mixs6/ceil_cond.md +++ b/mixs6/ceil_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | ceiling condition | | **Mappings:** | | MIXS:0000779 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 41 | +| | | Position: 41.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='damaged', description=None) | diff --git a/mixs6/ceil_finish_mat.md b/mixs6/ceil_finish_mat.md index 6243ac32..2fcb4efe 100644 --- a/mixs6/ceil_finish_mat.md +++ b/mixs6/ceil_finish_mat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | ceiling finish material | | **Mappings:** | | MIXS:0000780 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 42 | +| | | Position: 42.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='stucco', description=None) | diff --git a/mixs6/ceil_struc.md b/mixs6/ceil_struc.md index fa4e149e..50a00204 100644 --- a/mixs6/ceil_struc.md +++ b/mixs6/ceil_struc.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | ceiling structure | | **Mappings:** | | MIXS:0000782 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 44 | +| | | Position: 44.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='concrete', description=None) | diff --git a/mixs6/ceil_texture.md b/mixs6/ceil_texture.md index 41364d8d..2a3b318e 100644 --- a/mixs6/ceil_texture.md +++ b/mixs6/ceil_texture.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | ceiling texture | | **Mappings:** | | MIXS:0000783 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 45 | +| | | Position: 45.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='popcorn', description=None) | diff --git a/mixs6/ceil_thermal_mass.md b/mixs6/ceil_thermal_mass.md index f8cc24e5..b864db5e 100644 --- a/mixs6/ceil_thermal_mass.md +++ b/mixs6/ceil_thermal_mass.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: joule per degree Celsius | | | | Occurrence: 1 | -| | | Position: 46 | +| | | Position: 46.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/ceil_type.md b/mixs6/ceil_type.md index 08ae6bdc..3604f2c1 100644 --- a/mixs6/ceil_type.md +++ b/mixs6/ceil_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | ceiling type | | **Mappings:** | | MIXS:0000784 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 47 | +| | | Position: 47.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='coffered', description=None) | diff --git a/mixs6/ceil_water_mold.md b/mixs6/ceil_water_mold.md index 5703c98a..be453c7a 100644 --- a/mixs6/ceil_water_mold.md +++ b/mixs6/ceil_water_mold.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | ceiling signs of water/mold | | **Mappings:** | | MIXS:0000781 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 43 | +| | | Position: 43.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='presence of mold visible', description=None) | diff --git a/mixs6/chem_administration.md b/mixs6/chem_administration.md index 29d42a47..68007280 100644 --- a/mixs6/chem_administration.md +++ b/mixs6/chem_administration.md @@ -184,9 +184,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | chemical administration | | **Mappings:** | | MIXS:0000751 | | **Comments:** | | Expected value: CHEBI;timestamp | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='agar [CHEBI:2509];2018-05-11T20:00Z', description=None) | diff --git a/mixs6/chem_mutagen.md b/mixs6/chem_mutagen.md index 9ff2e8ae..ef23a9d2 100644 --- a/mixs6/chem_mutagen.md +++ b/mixs6/chem_mutagen.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: mutagen name;mutagen amount;treatment interval and duration | | | | Preferred unit: milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/chem_oxygen_dem.md b/mixs6/chem_oxygen_dem.md index 284e26df..f070d4b2 100644 --- a/mixs6/chem_oxygen_dem.md +++ b/mixs6/chem_oxygen_dem.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/chem_treatment.md b/mixs6/chem_treatment.md index d35f644d..f01e54ec 100644 --- a/mixs6/chem_treatment.md +++ b/mixs6/chem_treatment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | chemical treatment | | **Mappings:** | | MIXS:0001012 | | **Comments:** | | Expected value: name;name;timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 32 | +| | | Position: 32.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='ACCENT 1125;DOW;2010-11-17', description=None) | diff --git a/mixs6/chem_treatment_method.md b/mixs6/chem_treatment_method.md index ac48e98a..3c207a7b 100644 --- a/mixs6/chem_treatment_method.md +++ b/mixs6/chem_treatment_method.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;frequency;duration;duration | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 33 | +| | | Position: 33.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/chimera_check.md b/mixs6/chimera_check.md index db70e55b..10ead016 100644 --- a/mixs6/chimera_check.md +++ b/mixs6/chimera_check.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | chimera check | | **Comments:** | | Expected value: name and version of software, parameters used | -| | | Preferred unit: | | | | Position: 52.0 | | **Examples:** | | Example(value='uchime;v4.1;default parameters', description=None) | diff --git a/mixs6/chloride.md b/mixs6/chloride.md index 784b812d..10657fad 100644 --- a/mixs6/chloride.md +++ b/mixs6/chloride.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 67 | +| | | Position: 67.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='5000 milligram per liter', description=None) | diff --git a/mixs6/chlorophyll.md b/mixs6/chlorophyll.md index 5daab2a2..3e0c1100 100644 --- a/mixs6/chlorophyll.md +++ b/mixs6/chlorophyll.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per cubic meter, microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='5 milligram per cubic meter', description=None) | diff --git a/mixs6/climate_environment.md b/mixs6/climate_environment.md index c4977a1a..44bd69d8 100644 --- a/mixs6/climate_environment.md +++ b/mixs6/climate_environment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | climate environment | | **Mappings:** | | MIXS:0001040 | | **Comments:** | | Expected value: climate name;treatment interval and duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/collection_date.md b/mixs6/collection_date.md index 06ce45aa..c91d5e8c 100644 --- a/mixs6/collection_date.md +++ b/mixs6/collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:collection_date](https://w3id.org/mixs/vocab/collection_date) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | collection date | | **Comments:** | | Expected value: date and time | -| | | Preferred unit: | | | | Position: 9.0 | | **Examples:** | | Example(value='2018-05-11T10:00:00+01:00', description=None) | diff --git a/mixs6/compl_appr.md b/mixs6/compl_appr.md index fdd9e31d..ed7fed50 100644 --- a/mixs6/compl_appr.md +++ b/mixs6/compl_appr.md @@ -31,7 +31,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | completeness approach | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 69.0 | | **Examples:** | | Example(value='other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)', description=None) | diff --git a/mixs6/compl_score.md b/mixs6/compl_score.md index 95932536..3ed0b69d 100644 --- a/mixs6/compl_score.md +++ b/mixs6/compl_score.md @@ -36,7 +36,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | completeness score | | **Comments:** | | Expected value: quality;percent completeness | -| | | Preferred unit: | | | | Position: 67.0 | | **Examples:** | | Example(value='med;60%', description=None) | diff --git a/mixs6/compl_software.md b/mixs6/compl_software.md index 87bfdb6b..ecff4e69 100644 --- a/mixs6/compl_software.md +++ b/mixs6/compl_software.md @@ -36,7 +36,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | completeness software | | **Comments:** | | Expected value: names and versions of software(s) used | -| | | Preferred unit: | | | | Position: 68.0 | | **Examples:** | | Example(value='checkm', description=None) | diff --git a/mixs6/conduc.md b/mixs6/conduc.md index 0d335b24..90a031e4 100644 --- a/mixs6/conduc.md +++ b/mixs6/conduc.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milliSiemens per centimeter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='10 milliSiemens per centimeter', description=None) | diff --git a/mixs6/contam_score.md b/mixs6/contam_score.md index 16367a49..e7b0db8e 100644 --- a/mixs6/contam_score.md +++ b/mixs6/contam_score.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | contamination score | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Position: 70.0 | | **Examples:** | | Example(value='1%', description=None) | diff --git a/mixs6/contam_screen_input.md b/mixs6/contam_screen_input.md index 2f7bdfd1..8ceeff54 100644 --- a/mixs6/contam_screen_input.md +++ b/mixs6/contam_screen_input.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | contamination screening input | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 71.0 | | **Examples:** | | Example(value='contigs', description=None) | diff --git a/mixs6/contam_screen_param.md b/mixs6/contam_screen_param.md index 580099ea..e8910596 100644 --- a/mixs6/contam_screen_param.md +++ b/mixs6/contam_screen_param.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | contamination screening parameters | | **Comments:** | | Expected value: enumeration;value or name | -| | | Preferred unit: | | | | Position: 72.0 | | **Examples:** | | Example(value='kmer', description=None) | diff --git a/mixs6/cool_syst_id.md b/mixs6/cool_syst_id.md index 04fb27b2..be9b932f 100644 --- a/mixs6/cool_syst_id.md +++ b/mixs6/cool_syst_id.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | cooling system identifier | | **Mappings:** | | MIXS:0000785 | | **Comments:** | | Expected value: unique identifier | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 48 | +| | | Position: 48.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='12345', description=None) | diff --git a/mixs6/core_field.md b/mixs6/core_field.md index 14932e0c..9e460f92 100644 --- a/mixs6/core_field.md +++ b/mixs6/core_field.md @@ -16,7 +16,6 @@ None -> OPT [String](types/String.md) ## Children - * [sample_name](sample_name.md) ## Used by diff --git a/mixs6/crop_rotation.md b/mixs6/crop_rotation.md index b38cd615..c99fd296 100644 --- a/mixs6/crop_rotation.md +++ b/mixs6/crop_rotation.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/crop rotation | | **Mappings:** | | MIXS:0000318 | | **Comments:** | | Expected value: crop rotation status;schedule | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 6 | +| | | Position: 6.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='yes;R2/2017-01-01/2018-12-31/P6M', description=None) | diff --git a/mixs6/cult_root_med.md b/mixs6/cult_root_med.md index ee62b67d..9b4a61af 100644 --- a/mixs6/cult_root_med.md +++ b/mixs6/cult_root_med.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | culture rooting medium | | **Mappings:** | | MIXS:0001041 | | **Comments:** | | Expected value: name, PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | diff --git a/mixs6/cur_land_use.md b/mixs6/cur_land_use.md index 59cbb5b3..18cb07b6 100644 --- a/mixs6/cur_land_use.md +++ b/mixs6/cur_land_use.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | current land use | | **Mappings:** | | MIXS:0001080 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='conifers', description=None) | diff --git a/mixs6/cur_vegetation.md b/mixs6/cur_vegetation.md index 02b777e8..8b64c72f 100644 --- a/mixs6/cur_vegetation.md +++ b/mixs6/cur_vegetation.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | current vegetation | | **Mappings:** | | MIXS:0000312 | | **Comments:** | | Expected value: current vegetation type | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/cur_vegetation_meth.md b/mixs6/cur_vegetation_meth.md index f2e34850..d11c034a 100644 --- a/mixs6/cur_vegetation_meth.md +++ b/mixs6/cur_vegetation_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | current vegetation method | | **Mappings:** | | MIXS:0000314 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/date_last_rain.md b/mixs6/date_last_rain.md index b8f6730d..6ea78be7 100644 --- a/mixs6/date_last_rain.md +++ b/mixs6/date_last_rain.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:date_last_rain](https://w3id.org/mixs/vocab/date_last_rain) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | date last rain | | **Mappings:** | | MIXS:0000786 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 49 | +| | | Position: 49.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | diff --git a/mixs6/decontam_software.md b/mixs6/decontam_software.md index e22ac5c7..ccbc9c0c 100644 --- a/mixs6/decontam_software.md +++ b/mixs6/decontam_software.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | decontamination software | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 73.0 | | **Examples:** | | Example(value="anvi'o", description=None) | diff --git a/mixs6/density.md b/mixs6/density.md index 536177a0..86c203db 100644 --- a/mixs6/density.md +++ b/mixs6/density.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram per cubic meter, gram per cubic centimeter | | | | Occurrence: 1 | -| | | Position: 77 | +| | | Position: 77.0 | | | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='1000 kilogram per cubic meter', description=None) | diff --git a/mixs6/depos_env.md b/mixs6/depos_env.md index d5eb3d7b..b7114ecc 100644 --- a/mixs6/depos_env.md +++ b/mixs6/depos_env.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | depositional environment | | **Mappings:** | | MIXS:0000992 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 13 | +| | | Position: 13.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Continental - Alluvial', description=None) | diff --git a/mixs6/depth.md b/mixs6/depth.md index 38719f8c..5d491db8 100644 --- a/mixs6/depth.md +++ b/mixs6/depth.md @@ -2,7 +2,7 @@ # Slot: depth -Please refer to the definitions of depth in the environmental packages +The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. URI: [mixs.vocab:depth](https://w3id.org/mixs/vocab/depth) @@ -232,7 +232,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | geographic location (depth) | | **Comments:** | | Expected value: - | -| | | Preferred unit: | | | | Position: 6.0 | | | | This field is used in: 8 packages: host-associated, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/dermatology_disord.md b/mixs6/dermatology_disord.md index 84e28700..e6df0d9c 100644 --- a/mixs6/dermatology_disord.md +++ b/mixs6/dermatology_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | dermatology disorder | | **Mappings:** | | MIXS:0000284 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: human-skin | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/detec_type.md b/mixs6/detec_type.md index 0486ac30..ee2ab90c 100644 --- a/mixs6/detec_type.md +++ b/mixs6/detec_type.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | detection type | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 86.0 | | **Examples:** | | Example(value='independent sequence (UViG)', description=None) | diff --git a/mixs6/dew_point.md b/mixs6/dew_point.md index a87af384..9a5f0ba4 100644 --- a/mixs6/dew_point.md +++ b/mixs6/dew_point.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 11 | +| | | Position: 11.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='22 degree Celsius', description=None) | diff --git a/mixs6/diet_last_six_month.md b/mixs6/diet_last_six_month.md index b2556907..54b13d3b 100644 --- a/mixs6/diet_last_six_month.md +++ b/mixs6/diet_last_six_month.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | major diet change in last six months | | **Mappings:** | | MIXS:0000266 | | **Comments:** | | Expected value: diet change;current diet | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 21 | +| | | Position: 21.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes;vegetarian diet', description=None) | diff --git a/mixs6/diether_lipids.md b/mixs6/diether_lipids.md index 7bb3e9d2..e0f0b537 100644 --- a/mixs6/diether_lipids.md +++ b/mixs6/diether_lipids.md @@ -78,7 +78,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: diether lipid name;measurement value | | | | Preferred unit: nanogram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.2 nanogram per liter', description=None) | diff --git a/mixs6/diss_carb_dioxide.md b/mixs6/diss_carb_dioxide.md index b59f53b9..5a9262b8 100644 --- a/mixs6/diss_carb_dioxide.md +++ b/mixs6/diss_carb_dioxide.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 78 | +| | | Position: 78.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='5 milligram per liter', description=None) | diff --git a/mixs6/diss_hydrogen.md b/mixs6/diss_hydrogen.md index b6c21d0b..34bd6e41 100644 --- a/mixs6/diss_hydrogen.md +++ b/mixs6/diss_hydrogen.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.3 micromole per liter', description=None) | diff --git a/mixs6/diss_inorg_carb.md b/mixs6/diss_inorg_carb.md index 6a98db1d..9da0bd53 100644 --- a/mixs6/diss_inorg_carb.md +++ b/mixs6/diss_inorg_carb.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 73 | +| | | Position: 73.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='2059 micromole per kilogram', description=None) | diff --git a/mixs6/diss_inorg_nitro.md b/mixs6/diss_inorg_nitro.md index 7298a917..a796a8dd 100644 --- a/mixs6/diss_inorg_nitro.md +++ b/mixs6/diss_inorg_nitro.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='761 micromole per liter', description=None) | diff --git a/mixs6/diss_inorg_phosp.md b/mixs6/diss_inorg_phosp.md index b3b8e71e..b240d1f0 100644 --- a/mixs6/diss_inorg_phosp.md +++ b/mixs6/diss_inorg_phosp.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 74 | +| | | Position: 74.0 | | | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | | **Examples:** | | Example(value='56.5 micromole per liter', description=None) | diff --git a/mixs6/diss_iron.md b/mixs6/diss_iron.md index 67c3eb46..a455f06d 100644 --- a/mixs6/diss_iron.md +++ b/mixs6/diss_iron.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 65 | +| | | Position: 65.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/diss_org_carb.md b/mixs6/diss_org_carb.md index eb592270..96f74502 100644 --- a/mixs6/diss_org_carb.md +++ b/mixs6/diss_org_carb.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 72 | +| | | Position: 72.0 | | | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='197 micromole per liter', description=None) | diff --git a/mixs6/diss_org_nitro.md b/mixs6/diss_org_nitro.md index 90fa24c2..a11e8452 100644 --- a/mixs6/diss_org_nitro.md +++ b/mixs6/diss_org_nitro.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.05 micromole per liter', description=None) | diff --git a/mixs6/diss_oxygen.md b/mixs6/diss_oxygen.md index 3928c304..8907fe52 100644 --- a/mixs6/diss_oxygen.md +++ b/mixs6/diss_oxygen.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per kilogram, milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='175 micromole per kilogram', description=None) | diff --git a/mixs6/diss_oxygen_fluid.md b/mixs6/diss_oxygen_fluid.md index a0cb4d8d..d95cf666 100644 --- a/mixs6/diss_oxygen_fluid.md +++ b/mixs6/diss_oxygen_fluid.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per kilogram, milligram per liter | | | | Occurrence: 1 | -| | | Position: 79 | +| | | Position: 79.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/dominant_hand.md b/mixs6/dominant_hand.md index 2f19bf50..ee4c839c 100644 --- a/mixs6/dominant_hand.md +++ b/mixs6/dominant_hand.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | dominant hand | | **Mappings:** | | MIXS:0000944 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used uniquely in: human-skin | | **Examples:** | | Example(value='right', description=None) | diff --git a/mixs6/door_comp_type.md b/mixs6/door_comp_type.md index 61c00fa8..89c04ff9 100644 --- a/mixs6/door_comp_type.md +++ b/mixs6/door_comp_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door type, composite | | **Mappings:** | | MIXS:0000795 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 59 | +| | | Position: 59.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='revolving', description=None) | diff --git a/mixs6/door_cond.md b/mixs6/door_cond.md index a8e64b86..ae161f20 100644 --- a/mixs6/door_cond.md +++ b/mixs6/door_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door condition | | **Mappings:** | | MIXS:0000788 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 52 | +| | | Position: 52.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='new', description=None) | diff --git a/mixs6/door_direct.md b/mixs6/door_direct.md index c04cdecb..96996585 100644 --- a/mixs6/door_direct.md +++ b/mixs6/door_direct.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door direction of opening | | **Mappings:** | | MIXS:0000789 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 53 | +| | | Position: 53.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='inward', description=None) | diff --git a/mixs6/door_loc.md b/mixs6/door_loc.md index df9bad24..29c3a1c7 100644 --- a/mixs6/door_loc.md +++ b/mixs6/door_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door location | | **Mappings:** | | MIXS:0000790 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 54 | +| | | Position: 54.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='north', description=None) | diff --git a/mixs6/door_mat.md b/mixs6/door_mat.md index 30b61ae7..41db1463 100644 --- a/mixs6/door_mat.md +++ b/mixs6/door_mat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door material | | **Mappings:** | | MIXS:0000791 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 55 | +| | | Position: 55.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wood', description=None) | diff --git a/mixs6/door_move.md b/mixs6/door_move.md index b8a78d81..c00ae483 100644 --- a/mixs6/door_move.md +++ b/mixs6/door_move.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door movement | | **Mappings:** | | MIXS:0000792 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 56 | +| | | Position: 56.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='swinging', description=None) | diff --git a/mixs6/door_size.md b/mixs6/door_size.md index 4c8ea631..57726e98 100644 --- a/mixs6/door_size.md +++ b/mixs6/door_size.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 51 | +| | | Position: 51.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2.5 square meter', description=None) | diff --git a/mixs6/door_type.md b/mixs6/door_type.md index 0d6eeb65..75f9558c 100644 --- a/mixs6/door_type.md +++ b/mixs6/door_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door type | | **Mappings:** | | MIXS:0000794 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 58 | +| | | Position: 58.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wooden', description=None) | diff --git a/mixs6/door_type_metal.md b/mixs6/door_type_metal.md index 7cdd369d..4921fda2 100644 --- a/mixs6/door_type_metal.md +++ b/mixs6/door_type_metal.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door type, metal | | **Mappings:** | | MIXS:0000796 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 60 | +| | | Position: 60.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='hollow', description=None) | diff --git a/mixs6/door_type_wood.md b/mixs6/door_type_wood.md index 874c2478..75aa86cb 100644 --- a/mixs6/door_type_wood.md +++ b/mixs6/door_type_wood.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | door type, wood | | **Mappings:** | | MIXS:0000797 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 61 | +| | | Position: 61.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='battened', description=None) | diff --git a/mixs6/door_water_mold.md b/mixs6/door_water_mold.md index b17c0d21..cb9361ee 100644 --- a/mixs6/door_water_mold.md +++ b/mixs6/door_water_mold.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | door signs of water/mold | | **Mappings:** | | MIXS:0000793 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 57 | +| | | Position: 57.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='presence of mold visible', description=None) | diff --git a/mixs6/douche.md b/mixs6/douche.md index 3d8fc7a0..2784edb7 100644 --- a/mixs6/douche.md +++ b/mixs6/douche.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:douche](https://w3id.org/mixs/vocab/douche) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | douche | | **Mappings:** | | MIXS:0000967 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 4 | +| | | Position: 4.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/down_par.md b/mixs6/down_par.md index 686b9a8f..5b49fda7 100644 --- a/mixs6/down_par.md +++ b/mixs6/down_par.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microEinstein per square meter per second, microEinstein per square centimeter per second | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='28.71 microEinstein per square meter per second', description=None) | diff --git a/mixs6/drainage_class.md b/mixs6/drainage_class.md index 38f62e78..1d381095 100644 --- a/mixs6/drainage_class.md +++ b/mixs6/drainage_class.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | drainage classification | | **Mappings:** | | MIXS:0001085 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 34 | +| | | Position: 34.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='well', description=None) | diff --git a/mixs6/drawings.md b/mixs6/drawings.md index 2a8456e4..550ee91c 100644 --- a/mixs6/drawings.md +++ b/mixs6/drawings.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | drawings | | **Mappings:** | | MIXS:0000798 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 62 | +| | | Position: 62.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='sketch', description=None) | diff --git a/mixs6/drug_usage.md b/mixs6/drug_usage.md index 02d850a4..1ff28ecf 100644 --- a/mixs6/drug_usage.md +++ b/mixs6/drug_usage.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | drug usage | | **Mappings:** | | MIXS:0000894 | | **Comments:** | | Expected value: drug name;frequency | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 19 | +| | | Position: 19.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='Lipitor;2/day', description=None) | diff --git a/mixs6/efficiency_percent.md b/mixs6/efficiency_percent.md index 5d0e785f..3f457c67 100644 --- a/mixs6/efficiency_percent.md +++ b/mixs6/efficiency_percent.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/elev.md b/mixs6/elev.md index 9b78443f..22a59058 100644 --- a/mixs6/elev.md +++ b/mixs6/elev.md @@ -232,7 +232,6 @@ None -> OPT [QuantityValue](QuantityValue.md) | --- | --- | --- | | **Aliases:** | | elevation | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Position: 7.0 | | | | This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, water | | **Examples:** | | Example(value='100 meter', description=None) | diff --git a/mixs6/elevator.md b/mixs6/elevator.md index f33a0dbf..3e825fd6 100644 --- a/mixs6/elevator.md +++ b/mixs6/elevator.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | elevator count | | **Mappings:** | | MIXS:0000799 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 63 | +| | | Position: 63.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2', description=None) | diff --git a/mixs6/emulsions.md b/mixs6/emulsions.md index 016f91ca..a00a23e4 100644 --- a/mixs6/emulsions.md +++ b/mixs6/emulsions.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: emulsion name;measurement value | | | | Preferred unit: gram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/encoded_traits.md b/mixs6/encoded_traits.md index 6116064c..42523109 100644 --- a/mixs6/encoded_traits.md +++ b/mixs6/encoded_traits.md @@ -31,7 +31,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | encoded traits | | **Comments:** | | Expected value: for plasmid: antibiotic resistance; for phage: converting genes | -| | | Preferred unit: | | | | Position: 28.0 | | **Examples:** | | Example(value='beta-lactamase class A', description=None) | diff --git a/mixs6/env_broad_scale.md b/mixs6/env_broad_scale.md index 9afd7322..ebb63c03 100644 --- a/mixs6/env_broad_scale.md +++ b/mixs6/env_broad_scale.md @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | broad-scale environmental context | | **Comments:** | | Expected value: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] | -| | | Preferred unit: | | | | Position: 10.0 | | **Examples:** | | Example(value='forest biome [ENVO:01000174]', description=None) | diff --git a/mixs6/env_local_scale.md b/mixs6/env_local_scale.md index 1835d064..c824110b 100644 --- a/mixs6/env_local_scale.md +++ b/mixs6/env_local_scale.md @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | local environmental context | | **Comments:** | | Expected value: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] | -| | | Preferred unit: | | | | Position: 11.0 | | **Examples:** | | Example(value='litter layer [ENVO:01000338]', description=None) | diff --git a/mixs6/env_medium.md b/mixs6/env_medium.md index c5122dc9..35591c84 100644 --- a/mixs6/env_medium.md +++ b/mixs6/env_medium.md @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | environmental medium | | **Comments:** | | Expected value: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] | -| | | Preferred unit: | | | | Position: 12.0 | | **Examples:** | | Example(value='soil [ENVO:00001998]', description=None) | diff --git a/mixs6/env_package.md b/mixs6/env_package.md index d49de2ea..872171ff 100644 --- a/mixs6/env_package.md +++ b/mixs6/env_package.md @@ -39,7 +39,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | environmental package | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 13.0 | | **Examples:** | | Example(value='soil', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/64 | diff --git a/mixs6/environment_field.md b/mixs6/environment_field.md index 22a2e196..f79c9ddd 100644 --- a/mixs6/environment_field.md +++ b/mixs6/environment_field.md @@ -233,6 +233,7 @@ None -> OPT [String](types/String.md) * [host_shape](host_shape.md) * [host_subject_id](host_subject_id.md) * [host_substrate](host_substrate.md) + * [host_symbiont](host_symbiont.md) * [host_taxid](host_taxid.md) * [host_tot_mass](host_tot_mass.md) * [host_wet_mass](host_wet_mass.md) @@ -250,6 +251,7 @@ None -> OPT [String](types/String.md) * [int_wall_cond](int_wall_cond.md) * [iw_bt_date_well](iw_bt_date_well.md) * [iwf](iwf.md) + * [kidney_disord](kidney_disord.md) * [last_clean](last_clean.md) * [lat_lon](lat_lon.md) * [light_intensity](light_intensity.md) diff --git a/mixs6/escalator.md b/mixs6/escalator.md index d69fbe22..f819dd25 100644 --- a/mixs6/escalator.md +++ b/mixs6/escalator.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | escalator count | | **Mappings:** | | MIXS:0000800 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 64 | +| | | Position: 64.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='4', description=None) | diff --git a/mixs6/estimated_size.md b/mixs6/estimated_size.md index 3644ffdb..d92bddec 100644 --- a/mixs6/estimated_size.md +++ b/mixs6/estimated_size.md @@ -34,7 +34,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | estimated size | | **Comments:** | | Expected value: number of base pairs | -| | | Preferred unit: | | | | Position: 18.0 | | **Examples:** | | Example(value='300000 bp', description=None) | diff --git a/mixs6/ethylbenzene.md b/mixs6/ethylbenzene.md index 420d3c5f..49ceb99e 100644 --- a/mixs6/ethylbenzene.md +++ b/mixs6/ethylbenzene.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 83 | +| | | Position: 83.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/exp_duct.md b/mixs6/exp_duct.md index 75e28fc0..19d1f2be 100644 --- a/mixs6/exp_duct.md +++ b/mixs6/exp_duct.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 65 | +| | | Position: 65.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/exp_pipe.md b/mixs6/exp_pipe.md index d460e03b..572707ee 100644 --- a/mixs6/exp_pipe.md +++ b/mixs6/exp_pipe.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | exposed pipes | | **Mappings:** | | MIXS:0000220 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 66 | +| | | Position: 66.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/experimental_factor.md b/mixs6/experimental_factor.md index 138dc29a..62063901 100644 --- a/mixs6/experimental_factor.md +++ b/mixs6/experimental_factor.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | experimental factor | | **Comments:** | | Expected value: text or EFO and/or OBI | -| | | Preferred unit: | | | | Position: 4.0 | | **Examples:** | | Example(value='time series design [EFO:EFO_0001779]', description=None) | diff --git a/mixs6/ext_door.md b/mixs6/ext_door.md index 2599ee16..474e604a 100644 --- a/mixs6/ext_door.md +++ b/mixs6/ext_door.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | exterior door count | | **Mappings:** | | MIXS:0000170 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 67 | +| | | Position: 67.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/ext_wall_orient.md b/mixs6/ext_wall_orient.md index 1534acde..cbebcd19 100644 --- a/mixs6/ext_wall_orient.md +++ b/mixs6/ext_wall_orient.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | orientations of exterior wall | | **Mappings:** | | MIXS:0000817 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 96 | +| | | Position: 96.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='northwest', description=None) | diff --git a/mixs6/ext_window_orient.md b/mixs6/ext_window_orient.md index badefdb7..f1899156 100644 --- a/mixs6/ext_window_orient.md +++ b/mixs6/ext_window_orient.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | orientations of exterior window | | **Mappings:** | | MIXS:0000818 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 97 | +| | | Position: 97.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='southwest', description=None) | diff --git a/mixs6/extrachrom_elements.md b/mixs6/extrachrom_elements.md index 0b76fdd6..65d97c26 100644 --- a/mixs6/extrachrom_elements.md +++ b/mixs6/extrachrom_elements.md @@ -32,7 +32,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | extrachromosomal elements | | **Comments:** | | Expected value: number of extrachromosmal elements | -| | | Preferred unit: | | | | Position: 17.0 | | **Examples:** | | Example(value='5', description=None) | diff --git a/mixs6/extreme_event.md b/mixs6/extreme_event.md index 8d8d1fb8..f92b79b2 100644 --- a/mixs6/extreme_event.md +++ b/mixs6/extreme_event.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:extreme_event](https://w3id.org/mixs/vocab/extreme_event) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/extreme events | | **Mappings:** | | MIXS:0000320 | | **Comments:** | | Expected value: date | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 11 | +| | | Position: 11.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/extreme_salinity.md b/mixs6/extreme_salinity.md index 56d12f9a..2a20916d 100644 --- a/mixs6/extreme_salinity.md +++ b/mixs6/extreme_salinity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millisiemens per meter | | | | Occurrence: 1 | -| | | Position: 46 | +| | | Position: 46.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/fao_class.md b/mixs6/fao_class.md index e73e92bc..38b6aff2 100644 --- a/mixs6/fao_class.md +++ b/mixs6/fao_class.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | soil_taxonomic/FAO classification | | **Mappings:** | | MIXS:0001083 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 26 | +| | | Position: 26.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='Luvisols', description=None) | diff --git a/mixs6/feat_pred.md b/mixs6/feat_pred.md index 8c27738d..2f98731e 100644 --- a/mixs6/feat_pred.md +++ b/mixs6/feat_pred.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | feature prediction | | **Comments:** | | Expected value: names and versions of software(s), parameters used | -| | | Preferred unit: | | | | Position: 59.0 | | **Examples:** | | Example(value='Prodigal;2.6.3;default parameters', description=None) | diff --git a/mixs6/fertilizer_regm.md b/mixs6/fertilizer_regm.md index 718f7634..01020148 100644 --- a/mixs6/fertilizer_regm.md +++ b/mixs6/fertilizer_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: fertilizer name;fertilizer amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/field.md b/mixs6/field.md index 908346ff..9e36c2e0 100644 --- a/mixs6/field.md +++ b/mixs6/field.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | field name | | **Mappings:** | | MIXS:0000291 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 4 | +| | | Position: 4.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/filter_type.md b/mixs6/filter_type.md index 5643ca53..f10e1221 100644 --- a/mixs6/filter_type.md +++ b/mixs6/filter_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | filter type | | **Mappings:** | | MIXS:0000765 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 17 | +| | | Position: 17.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='HEPA', description=None) | diff --git a/mixs6/fire.md b/mixs6/fire.md index b3299ae9..1aefb8dd 100644 --- a/mixs6/fire.md +++ b/mixs6/fire.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:fire](https://w3id.org/mixs/vocab/fire) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/fire | | **Mappings:** | | MIXS:0001086 | | **Comments:** | | Expected value: date | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 9 | +| | | Position: 9.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/fireplace_type.md b/mixs6/fireplace_type.md index 78de7cd4..d1c3f382 100644 --- a/mixs6/fireplace_type.md +++ b/mixs6/fireplace_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | fireplace type | | **Mappings:** | | MIXS:0000802 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 68 | +| | | Position: 68.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wood burning', description=None) | diff --git a/mixs6/flooding.md b/mixs6/flooding.md index 7d8311b9..ec726bc5 100644 --- a/mixs6/flooding.md +++ b/mixs6/flooding.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:flooding](https://w3id.org/mixs/vocab/flooding) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/flooding | | **Mappings:** | | MIXS:0000319 | | **Comments:** | | Expected value: date | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 10 | +| | | Position: 10.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/floor_age.md b/mixs6/floor_age.md index 978f27fc..6b90b689 100644 --- a/mixs6/floor_age.md +++ b/mixs6/floor_age.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: years, weeks, days | | | | Occurrence: 1 | -| | | Position: 69 | +| | | Position: 69.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/floor_area.md b/mixs6/floor_area.md index 801b852f..d178fb55 100644 --- a/mixs6/floor_area.md +++ b/mixs6/floor_area.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 70 | +| | | Position: 70.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/floor_cond.md b/mixs6/floor_cond.md index e2e22157..3fb6ff53 100644 --- a/mixs6/floor_cond.md +++ b/mixs6/floor_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | floor condition | | **Mappings:** | | MIXS:0000803 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 71 | +| | | Position: 71.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='new', description=None) | diff --git a/mixs6/floor_count.md b/mixs6/floor_count.md index f2d5a11b..b021aa11 100644 --- a/mixs6/floor_count.md +++ b/mixs6/floor_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | floor count | | **Mappings:** | | MIXS:0000225 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 72 | +| | | Position: 72.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/floor_finish_mat.md b/mixs6/floor_finish_mat.md index e41d8b77..68217df8 100644 --- a/mixs6/floor_finish_mat.md +++ b/mixs6/floor_finish_mat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | floor finish material | | **Mappings:** | | MIXS:0000804 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 73 | +| | | Position: 73.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='carpet', description=None) | diff --git a/mixs6/floor_struc.md b/mixs6/floor_struc.md index 9ec56e18..4e2a340b 100644 --- a/mixs6/floor_struc.md +++ b/mixs6/floor_struc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | floor structure | | **Mappings:** | | MIXS:0000806 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 75 | +| | | Position: 75.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='concrete', description=None) | diff --git a/mixs6/floor_thermal_mass.md b/mixs6/floor_thermal_mass.md index 2141422b..c5173ccc 100644 --- a/mixs6/floor_thermal_mass.md +++ b/mixs6/floor_thermal_mass.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: joule per degree Celsius | | | | Occurrence: 1 | -| | | Position: 76 | +| | | Position: 76.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/floor_water_mold.md b/mixs6/floor_water_mold.md index e5a30a5b..307f8a35 100644 --- a/mixs6/floor_water_mold.md +++ b/mixs6/floor_water_mold.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | floor signs of water/mold | | **Mappings:** | | MIXS:0000805 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 74 | +| | | Position: 74.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='ceiling discoloration', description=None) | diff --git a/mixs6/fluor.md b/mixs6/fluor.md index 7983ead9..2a3bc554 100644 --- a/mixs6/fluor.md +++ b/mixs6/fluor.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram chlorophyll a per cubic meter, volts | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='2.5 volts', description=None) | diff --git a/mixs6/foetal_health_stat.md b/mixs6/foetal_health_stat.md index ac8897d4..3ddbd1a6 100644 --- a/mixs6/foetal_health_stat.md +++ b/mixs6/foetal_health_stat.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | amniotic fluid/foetal health status | | **Mappings:** | | MIXS:0000275 | | **Comments:** | | Expected value: health status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 38 | +| | | Position: 38.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/freq_clean.md b/mixs6/freq_clean.md index b29c6191..71c28f02 100644 --- a/mixs6/freq_clean.md +++ b/mixs6/freq_clean.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | frequency of cleaning | | **Mappings:** | | MIXS:0000226 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 77 | +| | | Position: 77.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/freq_cook.md b/mixs6/freq_cook.md index 04e89d01..e6e6c3d3 100644 --- a/mixs6/freq_cook.md +++ b/mixs6/freq_cook.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | frequency of cooking | | **Mappings:** | | MIXS:0000227 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 78 | +| | | Position: 78.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/fungicide_regm.md b/mixs6/fungicide_regm.md index 28b93c47..38239a56 100644 --- a/mixs6/fungicide_regm.md +++ b/mixs6/fungicide_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: fungicide name;fungicide amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/furniture.md b/mixs6/furniture.md index c06ea3ff..22cfaf78 100644 --- a/mixs6/furniture.md +++ b/mixs6/furniture.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | furniture | | **Mappings:** | | MIXS:0000807 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 79 | +| | | Position: 79.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='chair', description=None) | diff --git a/mixs6/gaseous_environment.md b/mixs6/gaseous_environment.md index 73d8b0fd..afbe5c82 100644 --- a/mixs6/gaseous_environment.md +++ b/mixs6/gaseous_environment.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gaseous compound name;gaseous compound amount;treatment interval and duration | | | | Preferred unit: micromole per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/gaseous_substances.md b/mixs6/gaseous_substances.md index 8927a05a..a079a219 100644 --- a/mixs6/gaseous_substances.md +++ b/mixs6/gaseous_substances.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gaseous substance name;measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/gastrointest_disord.md b/mixs6/gastrointest_disord.md index af3ca822..486cb287 100644 --- a/mixs6/gastrointest_disord.md +++ b/mixs6/gastrointest_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | gastrointestinal tract disorder | | **Mappings:** | | MIXS:0000280 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: human-gut | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/gender_restroom.md b/mixs6/gender_restroom.md index cd8a4b1f..772290ac 100644 --- a/mixs6/gender_restroom.md +++ b/mixs6/gender_restroom.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | gender of restroom | | **Mappings:** | | MIXS:0000808 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 80 | +| | | Position: 80.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='male', description=None) | diff --git a/mixs6/genetic_mod.md b/mixs6/genetic_mod.md index adc06b42..6bc37490 100644 --- a/mixs6/genetic_mod.md +++ b/mixs6/genetic_mod.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | genetic modification | | **Mappings:** | | MIXS:0000859 | | **Comments:** | | Expected value: PMID,DOI,url or free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='aox1A transgenic', description=None) | diff --git a/mixs6/geo_loc_name.md b/mixs6/geo_loc_name.md index 9a057a46..09dc636a 100644 --- a/mixs6/geo_loc_name.md +++ b/mixs6/geo_loc_name.md @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | geographic location (country and/or sea,region) | | **Comments:** | | Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location name | -| | | Preferred unit: | | | | Position: 8.0 | | **Examples:** | | Example(value='Germany;North Rhine-Westphalia;Eifel National Park', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/17 | diff --git a/mixs6/gestation_state.md b/mixs6/gestation_state.md index bccec130..9e2c7046 100644 --- a/mixs6/gestation_state.md +++ b/mixs6/gestation_state.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | amniotic fluid/gestation state | | **Mappings:** | | MIXS:0000272 | | **Comments:** | | Expected value: gestation state | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 36 | +| | | Position: 36.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/glucosidase_act.md b/mixs6/glucosidase_act.md index 13722d14..ee1c35fb 100644 --- a/mixs6/glucosidase_act.md +++ b/mixs6/glucosidase_act.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: mol per liter per hour | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='5 mol per liter per hour', description=None) | diff --git a/mixs6/gravidity.md b/mixs6/gravidity.md index c49da4f8..6c55585e 100644 --- a/mixs6/gravidity.md +++ b/mixs6/gravidity.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | gravidity | | **Mappings:** | | MIXS:0000875 | | **Comments:** | | Expected value: gravidity status;timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 35 | +| | | Position: 35.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='yes;due date:2018-05-11', description=None) | diff --git a/mixs6/gravity.md b/mixs6/gravity.md index 131514e6..4c3e2c5c 100644 --- a/mixs6/gravity.md +++ b/mixs6/gravity.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gravity factor value;treatment interval and duration | | | | Preferred unit: meter per square second, g | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/growth_facil.md b/mixs6/growth_facil.md index 7e50da26..73a66397 100644 --- a/mixs6/growth_facil.md +++ b/mixs6/growth_facil.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | growth facility | | **Mappings:** | | MIXS:0001043 | | **Comments:** | | Expected value: free text or CO | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='Growth chamber [CO_715:0000189]', description=None) | diff --git a/mixs6/growth_habit.md b/mixs6/growth_habit.md index 14b3625b..84c7ba02 100644 --- a/mixs6/growth_habit.md +++ b/mixs6/growth_habit.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | growth habit | | **Mappings:** | | MIXS:0001044 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='spreading', description=None) | diff --git a/mixs6/growth_hormone_regm.md b/mixs6/growth_hormone_regm.md index d1d3ff70..d281763e 100644 --- a/mixs6/growth_hormone_regm.md +++ b/mixs6/growth_hormone_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: growth hormone name;growth hormone amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/gynecologic_disord.md b/mixs6/gynecologic_disord.md index bb4101dd..8d988444 100644 --- a/mixs6/gynecologic_disord.md +++ b/mixs6/gynecologic_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | gynecological disorder | | **Mappings:** | | MIXS:0000288 | | **Comments:** | | Expected value: gynecological disorder | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 9 | +| | | Position: 9.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/hall_count.md b/mixs6/hall_count.md index d01aec98..31e4d54c 100644 --- a/mixs6/hall_count.md +++ b/mixs6/hall_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | hallway/corridor count | | **Mappings:** | | MIXS:0000228 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 81 | +| | | Position: 81.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/handidness.md b/mixs6/handidness.md index c1d76548..61c5a807 100644 --- a/mixs6/handidness.md +++ b/mixs6/handidness.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | handidness | | **Mappings:** | | MIXS:0000809 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 82 | +| | | Position: 82.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='right handedness', description=None) | diff --git a/mixs6/hc_produced.md b/mixs6/hc_produced.md index d138fcfd..730e2423 100644 --- a/mixs6/hc_produced.md +++ b/mixs6/hc_produced.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | hydrocarbon type produced | | **Mappings:** | | MIXS:0000989 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Gas', description=None) | diff --git a/mixs6/hcr.md b/mixs6/hcr.md index d7c44faf..548eb929 100644 --- a/mixs6/hcr.md +++ b/mixs6/hcr.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | hydrocarbon resource type | | **Mappings:** | | MIXS:0000988 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Oil Sand', description=None) | diff --git a/mixs6/hcr_fw_salinity.md b/mixs6/hcr_fw_salinity.md index 2667d108..7ecac56f 100644 --- a/mixs6/hcr_fw_salinity.md +++ b/mixs6/hcr_fw_salinity.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 16 | +| | | Position: 16.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/hcr_geol_age.md b/mixs6/hcr_geol_age.md index 17882d43..7100eb7a 100644 --- a/mixs6/hcr_geol_age.md +++ b/mixs6/hcr_geol_age.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | hydrocarbon resource geological age | | **Mappings:** | | MIXS:0000993 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 14 | +| | | Position: 14.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Silurian', description=None) | diff --git a/mixs6/hcr_pressure.md b/mixs6/hcr_pressure.md index 227c8502..8130baa5 100644 --- a/mixs6/hcr_pressure.md +++ b/mixs6/hcr_pressure.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value range | | | | Preferred unit: atmosphere, kilopascal | | | | Occurrence: 1 | -| | | Position: 8 | +| | | Position: 8.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/hcr_temp.md b/mixs6/hcr_temp.md index 2f21b65b..1bb2dfe5 100644 --- a/mixs6/hcr_temp.md +++ b/mixs6/hcr_temp.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value range | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 6 | +| | | Position: 6.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='150-295 degree Celsius', description=None) | diff --git a/mixs6/health_disease_stat.md b/mixs6/health_disease_stat.md index c86da601..c269af6b 100644 --- a/mixs6/health_disease_stat.md +++ b/mixs6/health_disease_stat.md @@ -31,7 +31,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | health or disease status of specific host at time of collection | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 25.0 | | **Examples:** | | Example(value='dead', description=None) | diff --git a/mixs6/heat_cool_type.md b/mixs6/heat_cool_type.md index 3e0c0699..898f151e 100644 --- a/mixs6/heat_cool_type.md +++ b/mixs6/heat_cool_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | heating and cooling system type | | **Mappings:** | | MIXS:0000766 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 18 | +| | | Position: 18.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='heat pump', description=None) | diff --git a/mixs6/heat_deliv_loc.md b/mixs6/heat_deliv_loc.md index cc4311b3..87859c31 100644 --- a/mixs6/heat_deliv_loc.md +++ b/mixs6/heat_deliv_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | heating delivery locations | | **Mappings:** | | MIXS:0000810 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 83 | +| | | Position: 83.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='north', description=None) | diff --git a/mixs6/heat_system_deliv_meth.md b/mixs6/heat_system_deliv_meth.md index c97543d7..6123ad24 100644 --- a/mixs6/heat_system_deliv_meth.md +++ b/mixs6/heat_system_deliv_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | heating system delivery method | | **Mappings:** | | MIXS:0000812 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 84 | +| | | Position: 84.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='radiant', description=None) | diff --git a/mixs6/heat_system_id.md b/mixs6/heat_system_id.md index c95b6d06..398c1fb0 100644 --- a/mixs6/heat_system_id.md +++ b/mixs6/heat_system_id.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | heating system identifier | | **Mappings:** | | MIXS:0000833 | | **Comments:** | | Expected value: unique identifier | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 85 | +| | | Position: 85.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/heavy_metals.md b/mixs6/heavy_metals.md index 73587be8..936fb920 100644 --- a/mixs6/heavy_metals.md +++ b/mixs6/heavy_metals.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: heavy metal name;measurement value | | | | Preferred unit: microgram per gram | | | | Occurrence: m | -| | | Position: 48 | +| | | Position: 48.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/heavy_metals_meth.md b/mixs6/heavy_metals_meth.md index 666c564a..1c42a529 100644 --- a/mixs6/heavy_metals_meth.md +++ b/mixs6/heavy_metals_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | extreme_unusual_properties/heavy metals method | | **Mappings:** | | MIXS:0000343 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 49 | +| | | Position: 49.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/height_carper_fiber.md b/mixs6/height_carper_fiber.md index de9662ea..a4e7e7ce 100644 --- a/mixs6/height_carper_fiber.md +++ b/mixs6/height_carper_fiber.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: centimeter | | | | Occurrence: 1 | -| | | Position: 86 | +| | | Position: 86.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/herbicide_regm.md b/mixs6/herbicide_regm.md index ab186797..d94ee4cd 100644 --- a/mixs6/herbicide_regm.md +++ b/mixs6/herbicide_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: herbicide name;herbicide amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/horizon.md b/mixs6/horizon.md index f2cd1b1f..cf2fdaad 100644 --- a/mixs6/horizon.md +++ b/mixs6/horizon.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | horizon | | **Mappings:** | | MIXS:0001082 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 12 | +| | | Position: 12.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='A horizon', description=None) | diff --git a/mixs6/horizon_meth.md b/mixs6/horizon_meth.md index 93eb6e42..a1c729fc 100644 --- a/mixs6/horizon_meth.md +++ b/mixs6/horizon_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | horizon method | | **Mappings:** | | MIXS:0000321 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 13 | +| | | Position: 13.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/host_age.md b/mixs6/host_age.md index a270f7b2..c5ce9f0e 100644 --- a/mixs6/host_age.md +++ b/mixs6/host_age.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: year, day, hour | | | | Occurrence: 1 | -| | | Position: 9 | +| | | Position: 9.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='10 days', description=None) | diff --git a/mixs6/host_blood_press_diast.md b/mixs6/host_blood_press_diast.md index 396c307e..6f6c1207 100644 --- a/mixs6/host_blood_press_diast.md +++ b/mixs6/host_blood_press_diast.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millimeter mercury | | | | Occurrence: 1 | -| | | Position: 31 | +| | | Position: 31.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/host_blood_press_syst.md b/mixs6/host_blood_press_syst.md index f159d87e..06d9888a 100644 --- a/mixs6/host_blood_press_syst.md +++ b/mixs6/host_blood_press_syst.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millimeter mercury | | | | Occurrence: 1 | -| | | Position: 32 | +| | | Position: 32.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/host_body_habitat.md b/mixs6/host_body_habitat.md index c2e584d0..f7fcb755 100644 --- a/mixs6/host_body_habitat.md +++ b/mixs6/host_body_habitat.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host body habitat | | **Mappings:** | | MIXS:0000866 | | **Comments:** | | Expected value: free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 14 | +| | | Position: 14.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='nasopharynx', description=None) | diff --git a/mixs6/host_body_mass_index.md b/mixs6/host_body_mass_index.md index 93b1d543..5822e2bd 100644 --- a/mixs6/host_body_mass_index.md +++ b/mixs6/host_body_mass_index.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilogram per square meter | | | | Occurrence: 1 | -| | | Position: 20 | +| | | Position: 20.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='22 kilogram per square meter', description=None) | diff --git a/mixs6/host_body_product.md b/mixs6/host_body_product.md index c683c72a..6bd1a45b 100644 --- a/mixs6/host_body_product.md +++ b/mixs6/host_body_product.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host body product | | **Mappings:** | | MIXS:0000888 | | **Comments:** | | Expected value: FMA or UBERON | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 16 | +| | | Position: 16.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='Portion of mucus [fma66938]', description=None) | diff --git a/mixs6/host_body_site.md b/mixs6/host_body_site.md index 14318e23..ac527c7a 100644 --- a/mixs6/host_body_site.md +++ b/mixs6/host_body_site.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host body site | | **Mappings:** | | MIXS:0000867 | | **Comments:** | | Expected value: FMA or UBERON | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 15 | +| | | Position: 15.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='gill [UBERON:0002535]', description=None) | diff --git a/mixs6/host_body_temp.md b/mixs6/host_body_temp.md index e8080437..09964e25 100644 --- a/mixs6/host_body_temp.md +++ b/mixs6/host_body_temp.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 29 | +| | | Position: 29.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='15 degree Celsius', description=None) | diff --git a/mixs6/host_color.md b/mixs6/host_color.md index f24afc35..e82a6612 100644 --- a/mixs6/host_color.md +++ b/mixs6/host_color.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host color | | **Mappings:** | | MIXS:0000260 | | **Comments:** | | Expected value: color | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 33 | +| | | Position: 33.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/host_common_name.md b/mixs6/host_common_name.md index fc22c21f..ddced188 100644 --- a/mixs6/host_common_name.md +++ b/mixs6/host_common_name.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host common name | | **Mappings:** | | MIXS:0000248 | | **Comments:** | | Expected value: common name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 4 | +| | | Position: 4.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='mussel', description=None) | diff --git a/mixs6/host_diet.md b/mixs6/host_diet.md index 0f4bbe4a..dc87246d 100644 --- a/mixs6/host_diet.md +++ b/mixs6/host_diet.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host diet | | **Mappings:** | | MIXS:0000869 | | **Comments:** | | Expected value: diet type | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 20 | +| | | Position: 20.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='herbivore', description=None) | diff --git a/mixs6/host_disease_stat.md b/mixs6/host_disease_stat.md index 65b3e1d0..e70890e9 100644 --- a/mixs6/host_disease_stat.md +++ b/mixs6/host_disease_stat.md @@ -112,9 +112,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host disease status | | **Mappings:** | | MIXS:0000031 | | **Comments:** | | Expected value: disease name or DO | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 12 | +| | | Position: 12.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='rabies [DOID:11260]', description=None) | diff --git a/mixs6/host_dry_mass.md b/mixs6/host_dry_mass.md index 0e393bd9..84b93496 100644 --- a/mixs6/host_dry_mass.md +++ b/mixs6/host_dry_mass.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilogram, gram | | | | Occurrence: 1 | -| | | Position: 30 | +| | | Position: 30.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='500 gram', description=None) | diff --git a/mixs6/host_family_relationship.md b/mixs6/host_family_relationship.md index a1768590..792a5e91 100644 --- a/mixs6/host_family_relationship.md +++ b/mixs6/host_family_relationship.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host family relationship | | **Mappings:** | | MIXS:0000872 | | **Comments:** | | Expected value: relationship type;arbitrary identifier | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 24 | +| | | Position: 24.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='offspring;Mussel25', description=None) | diff --git a/mixs6/host_genotype.md b/mixs6/host_genotype.md index 1bce480e..b104145f 100644 --- a/mixs6/host_genotype.md +++ b/mixs6/host_genotype.md @@ -112,9 +112,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host genotype | | **Mappings:** | | MIXS:0000365 | | **Comments:** | | Expected value: genotype | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 27 | +| | | Position: 27.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='C57BL/6', description=None) | diff --git a/mixs6/host_growth_cond.md b/mixs6/host_growth_cond.md index 4671f26d..ff0a887e 100644 --- a/mixs6/host_growth_cond.md +++ b/mixs6/host_growth_cond.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host growth conditions | | **Mappings:** | | MIXS:0000871 | | **Comments:** | | Expected value: PMID,DOI,url or free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 22 | +| | | Position: 22.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='https://academic.oup.com/icesjms/article/68/2/349/617247', description=None) | diff --git a/mixs6/host_height.md b/mixs6/host_height.md index 89444236..7d0578f3 100644 --- a/mixs6/host_height.md +++ b/mixs6/host_height.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: centimeter, millimeter, meter | | | | Occurrence: 1 | -| | | Position: 18 | +| | | Position: 18.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='0.1 meter', description=None) | diff --git a/mixs6/host_hiv_stat.md b/mixs6/host_hiv_stat.md index 049b1e47..69c59820 100644 --- a/mixs6/host_hiv_stat.md +++ b/mixs6/host_hiv_stat.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host HIV status | | **Mappings:** | | MIXS:0000265 | | **Comments:** | | Expected value: HIV status;HAART initiation status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 18 | +| | | Position: 18.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes;yes', description=None) | diff --git a/mixs6/host_infra_specific_name.md b/mixs6/host_infra_specific_name.md index 00bc2ab9..3590705c 100644 --- a/mixs6/host_infra_specific_name.md +++ b/mixs6/host_infra_specific_name.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host infra-specific name | | **Mappings:** | | MIXS:0000253 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 25 | +| | | Position: 25.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='borealis', description=None) | diff --git a/mixs6/host_infra_specific_rank.md b/mixs6/host_infra_specific_rank.md index 085ef2ae..0d71f079 100644 --- a/mixs6/host_infra_specific_rank.md +++ b/mixs6/host_infra_specific_rank.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host infra-specific rank | | **Mappings:** | | MIXS:0000254 | | **Comments:** | | Expected value: rank | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 26 | +| | | Position: 26.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='subspecies', description=None) | diff --git a/mixs6/host_last_meal.md b/mixs6/host_last_meal.md index a1353f06..956f7f2d 100644 --- a/mixs6/host_last_meal.md +++ b/mixs6/host_last_meal.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host last meal | | **Mappings:** | | MIXS:0000870 | | **Comments:** | | Expected value: content;duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 21 | +| | | Position: 21.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='corn feed;P2H', description=None) | diff --git a/mixs6/host_length.md b/mixs6/host_length.md index bf535024..2422cc87 100644 --- a/mixs6/host_length.md +++ b/mixs6/host_length.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: centimeter, millimeter, meter | | | | Occurrence: 1 | -| | | Position: 19 | +| | | Position: 19.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='1 meter', description=None) | diff --git a/mixs6/host_life_stage.md b/mixs6/host_life_stage.md index 8fe0a7c4..c4089d97 100644 --- a/mixs6/host_life_stage.md +++ b/mixs6/host_life_stage.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host life stage | | **Mappings:** | | MIXS:0000251 | | **Comments:** | | Expected value: stage | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 10 | +| | | Position: 10.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='adult', description=None) | diff --git a/mixs6/host_occupation.md b/mixs6/host_occupation.md index d8683d7d..d1ddc1fe 100644 --- a/mixs6/host_occupation.md +++ b/mixs6/host_occupation.md @@ -88,9 +88,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host occupation | | **Mappings:** | | MIXS:0000896 | | **Comments:** | | Expected value: IHMC code | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 24 | +| | | Position: 24.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='veterinary', description=None) | diff --git a/mixs6/host_phenotype.md b/mixs6/host_phenotype.md index 97e88954..2ba2d358 100644 --- a/mixs6/host_phenotype.md +++ b/mixs6/host_phenotype.md @@ -112,9 +112,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host phenotype | | **Mappings:** | | MIXS:0000874 | | **Comments:** | | Expected value: PATO or HP | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 28 | +| | | Position: 28.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='elongated [PATO:0001154]', description=None) | diff --git a/mixs6/host_pred_appr.md b/mixs6/host_pred_appr.md index 0cd7066a..81696362 100644 --- a/mixs6/host_pred_appr.md +++ b/mixs6/host_pred_appr.md @@ -29,7 +29,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | host prediction approach | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 90.0 | | **Examples:** | | Example(value='CRISPR spacer match', description=None) | diff --git a/mixs6/host_pred_est_acc.md b/mixs6/host_pred_est_acc.md index 09051028..3738cc6f 100644 --- a/mixs6/host_pred_est_acc.md +++ b/mixs6/host_pred_est_acc.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | host prediction estimated accuracy | | **Comments:** | | Expected value: false discovery rate | -| | | Preferred unit: | | | | Position: 91.0 | | **Examples:** | | Example(value='CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)', description=None) | diff --git a/mixs6/host_pulse.md b/mixs6/host_pulse.md index 1df4295c..38c32af4 100644 --- a/mixs6/host_pulse.md +++ b/mixs6/host_pulse.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: beats per minute | | | | Occurrence: 1 | -| | | Position: 35 | +| | | Position: 35.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='65 beats per minute', description=None) | diff --git a/mixs6/host_sex.md b/mixs6/host_sex.md index eb965052..4be83934 100644 --- a/mixs6/host_sex.md +++ b/mixs6/host_sex.md @@ -100,9 +100,8 @@ None -> OPT | **Aliases:** | | host sex | | **Mappings:** | | MIXS:0000811 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 11 | +| | | Position: 11.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='female', description=None) | diff --git a/mixs6/host_shape.md b/mixs6/host_shape.md index 43913364..5bcb39a4 100644 --- a/mixs6/host_shape.md +++ b/mixs6/host_shape.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host shape | | **Mappings:** | | MIXS:0000261 | | **Comments:** | | Expected value: shape | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 34 | +| | | Position: 34.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='round', description=None) | diff --git a/mixs6/host_spec_range.md b/mixs6/host_spec_range.md index 60d81251..a3d13af8 100644 --- a/mixs6/host_spec_range.md +++ b/mixs6/host_spec_range.md @@ -33,7 +33,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | host specificity or range | | **Comments:** | | Expected value: NCBI taxid | -| | | Preferred unit: | | | | Position: 24.0 | | **Examples:** | | Example(value='9606', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/66 | diff --git a/mixs6/host_subject_id.md b/mixs6/host_subject_id.md index dfe62039..f7b59b74 100644 --- a/mixs6/host_subject_id.md +++ b/mixs6/host_subject_id.md @@ -100,9 +100,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host subject id | | **Mappings:** | | MIXS:0000861 | | **Comments:** | | Expected value: unique identifier | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 8 | +| | | Position: 8.0 | | | | This field is used in: 6 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='MPI123', description=None) | diff --git a/mixs6/host_substrate.md b/mixs6/host_substrate.md index 0d2c8ffd..fe8647e8 100644 --- a/mixs6/host_substrate.md +++ b/mixs6/host_substrate.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host substrate | | **Mappings:** | | MIXS:0000252 | | **Comments:** | | Expected value: substrate name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 23 | +| | | Position: 23.0 | | | | This field is used uniquely in: host-associated | | **Examples:** | | Example(value='rock', description=None) | diff --git a/mixs6/host_symbiont.md b/mixs6/host_symbiont.md new file mode 100644 index 00000000..9eb46abb --- /dev/null +++ b/mixs6/host_symbiont.md @@ -0,0 +1,117 @@ + +# Slot: host_symbiont + + +The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + +URI: [mixs.vocab:host_symbiont](https://w3id.org/mixs/vocab/host_symbiont) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Host-associated](Host-associated.md) + * [Host-associatedME](Host-associatedME.md) + * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md) + * [Host-associatedMIGSEukaryote](Host-associatedMIGSEukaryote.md) + * [Host-associatedMIGSOrg](Host-associatedMIGSOrg.md) + * [Host-associatedMIGSPlant](Host-associatedMIGSPlant.md) + * [Host-associatedMIGSVirus](Host-associatedMIGSVirus.md) + * [Host-associatedMIMAG](Host-associatedMIMAG.md) + * [Host-associatedMIMARKSSpecimen](Host-associatedMIMARKSSpecimen.md) + * [Host-associatedMIMARKSSurvey](Host-associatedMIMARKSSurvey.md) + * [Host-associatedMISAG](Host-associatedMISAG.md) + * [Host-associatedMIUVIG](Host-associatedMIUVIG.md) + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + * [Human-gut](Human-gut.md) + * [Human-gutME](Human-gutME.md) + * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md) + * [Human-gutMIGSEukaryote](Human-gutMIGSEukaryote.md) + * [Human-gutMIGSOrg](Human-gutMIGSOrg.md) + * [Human-gutMIGSPlant](Human-gutMIGSPlant.md) + * [Human-gutMIGSVirus](Human-gutMIGSVirus.md) + * [Human-gutMIMAG](Human-gutMIMAG.md) + * [Human-gutMIMARKSSpecimen](Human-gutMIMARKSSpecimen.md) + * [Human-gutMIMARKSSurvey](Human-gutMIMARKSSurvey.md) + * [Human-gutMISAG](Human-gutMISAG.md) + * [Human-gutMIUVIG](Human-gutMIUVIG.md) + * [Human-oral](Human-oral.md) + * [Human-oralME](Human-oralME.md) + * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md) + * [Human-oralMIGSEukaryote](Human-oralMIGSEukaryote.md) + * [Human-oralMIGSOrg](Human-oralMIGSOrg.md) + * [Human-oralMIGSPlant](Human-oralMIGSPlant.md) + * [Human-oralMIGSVirus](Human-oralMIGSVirus.md) + * [Human-oralMIMAG](Human-oralMIMAG.md) + * [Human-oralMIMARKSSpecimen](Human-oralMIMARKSSpecimen.md) + * [Human-oralMIMARKSSurvey](Human-oralMIMARKSSurvey.md) + * [Human-oralMISAG](Human-oralMISAG.md) + * [Human-oralMIUVIG](Human-oralMIUVIG.md) + * [Human-skin](Human-skin.md) + * [Human-skinME](Human-skinME.md) + * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md) + * [Human-skinMIGSEukaryote](Human-skinMIGSEukaryote.md) + * [Human-skinMIGSOrg](Human-skinMIGSOrg.md) + * [Human-skinMIGSPlant](Human-skinMIGSPlant.md) + * [Human-skinMIGSVirus](Human-skinMIGSVirus.md) + * [Human-skinMIMAG](Human-skinMIMAG.md) + * [Human-skinMIMARKSSpecimen](Human-skinMIMARKSSpecimen.md) + * [Human-skinMIMARKSSurvey](Human-skinMIMARKSSurvey.md) + * [Human-skinMISAG](Human-skinMISAG.md) + * [Human-skinMIUVIG](Human-skinMIUVIG.md) + * [Human-vaginal](Human-vaginal.md) + * [Human-vaginalME](Human-vaginalME.md) + * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md) + * [Human-vaginalMIGSEukaryote](Human-vaginalMIGSEukaryote.md) + * [Human-vaginalMIGSOrg](Human-vaginalMIGSOrg.md) + * [Human-vaginalMIGSPlant](Human-vaginalMIGSPlant.md) + * [Human-vaginalMIGSVirus](Human-vaginalMIGSVirus.md) + * [Human-vaginalMIMAG](Human-vaginalMIMAG.md) + * [Human-vaginalMIMARKSSpecimen](Human-vaginalMIMARKSSpecimen.md) + * [Human-vaginalMIMARKSSurvey](Human-vaginalMIMARKSSurvey.md) + * [Human-vaginalMISAG](Human-vaginalMISAG.md) + * [Human-vaginalMIUVIG](Human-vaginalMIUVIG.md) + * [Plant-associated](Plant-associated.md) + * [Plant-associatedME](Plant-associatedME.md) + * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md) + * [Plant-associatedMIGSEukaryote](Plant-associatedMIGSEukaryote.md) + * [Plant-associatedMIGSOrg](Plant-associatedMIGSOrg.md) + * [Plant-associatedMIGSPlant](Plant-associatedMIGSPlant.md) + * [Plant-associatedMIGSVirus](Plant-associatedMIGSVirus.md) + * [Plant-associatedMIMAG](Plant-associatedMIMAG.md) + * [Plant-associatedMIMARKSSpecimen](Plant-associatedMIMARKSSpecimen.md) + * [Plant-associatedMIMARKSSurvey](Plant-associatedMIMARKSSurvey.md) + * [Plant-associatedMISAG](Plant-associatedMISAG.md) + * [Plant-associatedMIUVIG](Plant-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | observed host symbionts | +| **Comments:** | | Expected value: species name or common name | +| | | Occurrence: m | +| | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | +| **Examples:** | | Example(value='flukeworms', description=None) | + diff --git a/mixs6/host_taxid.md b/mixs6/host_taxid.md index 8f3dce1c..b9708a09 100644 --- a/mixs6/host_taxid.md +++ b/mixs6/host_taxid.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | host taxid | | **Mappings:** | | MIXS:0000250 | | **Comments:** | | Expected value: NCBI taxon identifier | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 7 | +| | | Position: 7.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='7955', description=None) | diff --git a/mixs6/host_tot_mass.md b/mixs6/host_tot_mass.md index 748f559b..699df932 100644 --- a/mixs6/host_tot_mass.md +++ b/mixs6/host_tot_mass.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilogram, gram | | | | Occurrence: 1 | -| | | Position: 17 | +| | | Position: 17.0 | | | | This field is used in: 7 packages: host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, plant-associated | | **Examples:** | | Example(value='2500 gram', description=None) | diff --git a/mixs6/host_wet_mass.md b/mixs6/host_wet_mass.md index 2f683df2..1e0f2d97 100644 --- a/mixs6/host_wet_mass.md +++ b/mixs6/host_wet_mass.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilogram, gram | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='1500 gram', description=None) | diff --git a/mixs6/hrt.md b/mixs6/hrt.md index 03aaa9ec..413bbc93 100644 --- a/mixs6/hrt.md +++ b/mixs6/hrt.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:hrt](https://w3id.org/mixs/vocab/hrt) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | HRT | | **Mappings:** | | MIXS:0000969 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 7 | +| | | Position: 7.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/humidity.md b/mixs6/humidity.md index 13fd8237..bc036ab1 100644 --- a/mixs6/humidity.md +++ b/mixs6/humidity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram per cubic meter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='25 gram per cubic meter', description=None) | diff --git a/mixs6/humidity_regm.md b/mixs6/humidity_regm.md index 5d804f97..30015aa4 100644 --- a/mixs6/humidity_regm.md +++ b/mixs6/humidity_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: humidity value;treatment interval and duration | | | | Preferred unit: gram per cubic meter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/hysterectomy.md b/mixs6/hysterectomy.md index a003a702..470c3841 100644 --- a/mixs6/hysterectomy.md +++ b/mixs6/hysterectomy.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | hysterectomy | | **Mappings:** | | MIXS:0000287 | | **Comments:** | | Expected value: hysterectomy status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 8 | +| | | Position: 8.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='no', description=None) | diff --git a/mixs6/ihmc_ethnicity.md b/mixs6/ihmc_ethnicity.md index 4e94adfa..844a7619 100644 --- a/mixs6/ihmc_ethnicity.md +++ b/mixs6/ihmc_ethnicity.md @@ -88,9 +88,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | IHMC ethnicity | | **Mappings:** | | MIXS:0000895 | | **Comments:** | | Expected value: IHMC code or free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 23 | +| | | Position: 23.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='caucasian', description=None) | diff --git a/mixs6/ihmc_medication_code.md b/mixs6/ihmc_medication_code.md index 5abcdb78..7b541595 100644 --- a/mixs6/ihmc_medication_code.md +++ b/mixs6/ihmc_medication_code.md @@ -88,9 +88,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | IHMC medication code | | **Mappings:** | | MIXS:0000884 | | **Comments:** | | Expected value: IHMC code | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='810', description=None) | diff --git a/mixs6/index.md b/mixs6/index.md index 694b39c1..14ad1538 100644 --- a/mixs6/index.md +++ b/mixs6/index.md @@ -1,8 +1,8 @@ -# Mixs6 schema +# Mixs schema -MIxS 6 linkml rendering +Minimal Information about any Sequence Standard ### Classes @@ -231,18 +231,6 @@ MIxS 6 linkml rendering ### Slots * [core field](core_field.md) - basic fields - * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. - * [ME➞sample_name](ME_sample_name.md) - * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) - * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) - * [MIGS org➞sample_name](MIGS_org_sample_name.md) - * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) - * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) - * [MIMAG➞sample_name](MIMAG_sample_name.md) - * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) - * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) - * [MISAG➞sample_name](MISAG_sample_name.md) - * [MIUVIG➞sample_name](MIUVIG_sample_name.md) * [environment field](environment_field.md) - field describing environmental aspect of a sample * [abs_air_humidity](abs_air_humidity.md) - Actual mass of water vapor - mh20 - present in the air water vapor mixture * [add_recov_method](add_recov_method.md) - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field @@ -258,7 +246,7 @@ MIxS 6 linkml rendering * [alkalinity](alkalinity.md) - Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate * [alkalinity_method](alkalinity_method.md) - Method used for alkalinity measurement * [alkyl_diethers](alkyl_diethers.md) - Concentration of alkyl diethers - * [alt](alt.md) - Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth‚Äôs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + * [alt](alt.md) - Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air * [aminopept_act](aminopept_act.md) - Measurement of aminopeptidase activity * [ammonium](ammonium.md) - Concentration of ammonium in the sample * [amniotic_fluid_color](amniotic_fluid_color.md) - Specification of the color of the amniotic fluid sample @@ -286,7 +274,7 @@ MIxS 6 linkml rendering * [biochem_oxygen_dem](biochem_oxygen_dem.md) - Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period * [biocide](biocide.md) - List of biocides (commercial name of product and supplier) and date of administration * [biocide_admin_method](biocide_admin_method.md) - Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) - * [biol_stat](biol_stat.md) - The level of genome modification + * [biol_stat](biol_stat.md) - The level of genome modification. * [biomass](biomass.md) - Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements * [biotic_regm](biotic_regm.md) - Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. * [birth_control](birth_control.md) - Specification of birth control medication used @@ -341,7 +329,7 @@ MIxS 6 linkml rendering * [date_last_rain](date_last_rain.md) - The date of the last time it rained * [density](density.md) - Density of the sample, which is its mass per unit volume (aka volumetric mass density) * [depos_env](depos_env.md) - Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field - * [depth](depth.md) - Please refer to the definitions of depth in the environmental packages + * [depth](depth.md) - The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. * [dermatology_disord](dermatology_disord.md) - History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37). * [dew_point](dew_point.md) - The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. * [diet_last_six_month](diet_last_six_month.md) - Specification of major diet changes in the last six months, if yes the change should be specified @@ -516,6 +504,7 @@ MIxS 6 linkml rendering * [host_shape](host_shape.md) - Morphological shape of host * [host_subject_id](host_subject_id.md) - A unique identifier by which each subject can be referred to, de-identified, e.g. #131 * [host_substrate](host_substrate.md) - The growth substrate of the host + * [host_symbiont](host_symbiont.md) - The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. * [host_taxid](host_taxid.md) - NCBI taxon id of the host, e.g. 9606 * [host_tot_mass](host_tot_mass.md) - Total mass of the host at collection, the unit depends on host * [host_wet_mass](host_wet_mass.md) - Measurement of wet mass @@ -533,6 +522,7 @@ MIxS 6 linkml rendering * [int_wall_cond](int_wall_cond.md) - The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas * [iw_bt_date_well](iw_bt_date_well.md) - Injection water breakthrough date per well following a secondary and/or tertiary recovery * [iwf](iwf.md) - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + * [kidney_disord](kidney_disord.md) - History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). * [last_clean](last_clean.md) - The last time the floor was cleaned (swept, mopped, vacuumed) * [lat_lon](lat_lon.md) - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system * [ME➞lat_lon](ME_lat_lon.md) @@ -774,8 +764,8 @@ MIxS 6 linkml rendering * [train_stop_loc](train_stop_loc.md) - The train stop collection location * [travel_out_six_month](travel_out_six_month.md) - Specification of the countries travelled in the last six months; can include multiple travels * [turbidity](turbidity.md) - Measure of the amount of cloudiness or haziness in water caused by individual particles - * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) - * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + * [tvdss_of_hcr_pressure](tvdss_of_hcr_pressure.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + * [tvdss_of_hcr_temp](tvdss_of_hcr_temp.md) - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). * [twin_sibling](twin_sibling.md) - Specification of twin sibling presence * [typ_occup_density](typ_occup_density.md) - Customary or normal density of occupants * [urine_collect_meth](urine_collect_meth.md) - Specification of urine collection method @@ -861,6 +851,18 @@ MIxS 6 linkml rendering * [MIMARKS survey➞project_name](MIMARKS_survey_project_name.md) * [MISAG➞project_name](MISAG_project_name.md) * [MIUVIG➞project_name](MIUVIG_project_name.md) + * [sample_name](sample_name.md) - Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. + * [ME➞sample_name](ME_sample_name.md) + * [MIGS bacteria➞sample_name](MIGS_bacteria_sample_name.md) + * [MIGS eukaryote➞sample_name](MIGS_eukaryote_sample_name.md) + * [MIGS org➞sample_name](MIGS_org_sample_name.md) + * [MIGS plant➞sample_name](MIGS_plant_sample_name.md) + * [MIGS virus➞sample_name](MIGS_virus_sample_name.md) + * [MIMAG➞sample_name](MIMAG_sample_name.md) + * [MIMARKS specimen➞sample_name](MIMARKS_specimen_sample_name.md) + * [MIMARKS survey➞sample_name](MIMARKS_survey_sample_name.md) + * [MISAG➞sample_name](MISAG_sample_name.md) + * [MIUVIG➞sample_name](MIUVIG_sample_name.md) * [submitted_to_insdc](submitted_to_insdc.md) - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases * [ME➞submitted_to_insdc](ME_submitted_to_insdc.md) * [MIGS bacteria➞submitted_to_insdc](MIGS_bacteria_submitted_to_insdc.md) @@ -958,19 +960,7 @@ MIxS 6 linkml rendering * [MIMARKS specimen➞rel_to_oxygen](MIMARKS_specimen_rel_to_oxygen.md) * [MIMARKS survey➞rel_to_oxygen](MIMARKS_survey_rel_to_oxygen.md) * [MISAG➞rel_to_oxygen](MISAG_rel_to_oxygen.md) - * [samp_collect_device](samp_collect_device.md) - The method or device employed for collecting the sample - * [ME➞samp_collect_device](ME_samp_collect_device.md) - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) - * [samp_mat_process](samp_mat_process.md) - Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + * [samp_mat_process](samp_mat_process.md) - A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. * [ME➞samp_mat_process](ME_samp_mat_process.md) * [MIGS bacteria➞samp_mat_process](MIGS_bacteria_samp_mat_process.md) * [MIGS eukaryote➞samp_mat_process](MIGS_eukaryote_samp_mat_process.md) @@ -994,6 +984,30 @@ MIxS 6 linkml rendering * [MIMARKS survey➞samp_size](MIMARKS_survey_samp_size.md) * [MISAG➞samp_size](MISAG_samp_size.md) * [MIUVIG➞samp_size](MIUVIG_samp_size.md) + * [sample_collect_device](sample_collect_device.md) - The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + * [ME➞sample_collect_device](ME_sample_collect_device.md) + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) + * [sample_collect_method](sample_collect_method.md) - The method employed for collecting the sample. + * [ME➞sample_collect_method](ME_sample_collect_method.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) * [size_frac](size_frac.md) - Filtering pore size used in sample preparation * [ME➞size_frac](ME_size_frac.md) * [MIMAG➞size_frac](MIMAG_size_frac.md) @@ -1378,9 +1392,138 @@ MIxS 6 linkml rendering * [x_16s_recover](x_16s_recover.md) - Can a 16S gene be recovered from the submitted SAG or MAG? * [MIMAG➞x_16s_recover](MIMAG_x_16s_recover.md) * [MISAG➞x_16s_recover](MISAG_x_16s_recover.md) - * [x_16s_recover_software](x_16s_recover_software.md) - Tools used for 16S rRNA gene extraction - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) + +### Enums + + * [add_recov_method_enum](add_recov_method_enum.md) + * [arch_struc_enum](arch_struc_enum.md) + * [assembly_qual_enum](assembly_qual_enum.md) + * [bin_param_enum](bin_param_enum.md) + * [bin_software_enum](bin_software_enum.md) + * [biol_stat_enum](biol_stat_enum.md) + * [biotic_relationship_enum](biotic_relationship_enum.md) + * [build_docs_enum](build_docs_enum.md) + * [build_occup_type_enum](build_occup_type_enum.md) + * [building_setting_enum](building_setting_enum.md) + * [ceil_cond_enum](ceil_cond_enum.md) + * [ceil_finish_mat_enum](ceil_finish_mat_enum.md) + * [ceil_texture_enum](ceil_texture_enum.md) + * [ceil_type_enum](ceil_type_enum.md) + * [compl_appr_enum](compl_appr_enum.md) + * [compl_score_enum](compl_score_enum.md) + * [contam_screen_param_enum](contam_screen_param_enum.md) + * [cur_land_use_enum](cur_land_use_enum.md) + * [decontam_software_enum](decontam_software_enum.md) + * [depos_env_enum](depos_env_enum.md) + * [dominant_hand_enum](dominant_hand_enum.md) + * [door_comp_type_enum](door_comp_type_enum.md) + * [door_cond_enum](door_cond_enum.md) + * [door_direct_enum](door_direct_enum.md) + * [door_loc_enum](door_loc_enum.md) + * [door_mat_enum](door_mat_enum.md) + * [door_move_enum](door_move_enum.md) + * [door_type_enum](door_type_enum.md) + * [door_type_metal_enum](door_type_metal_enum.md) + * [door_type_wood_enum](door_type_wood_enum.md) + * [drainage_class_enum](drainage_class_enum.md) + * [drawings_enum](drawings_enum.md) + * [drug_usage_enum](drug_usage_enum.md) + * [env_package_enum](env_package_enum.md) + * [ext_wall_orient_enum](ext_wall_orient_enum.md) + * [ext_window_orient_enum](ext_window_orient_enum.md) + * [fao_class_enum](fao_class_enum.md) + * [filter_type_enum](filter_type_enum.md) + * [floor_cond_enum](floor_cond_enum.md) + * [floor_finish_mat_enum](floor_finish_mat_enum.md) + * [floor_struc_enum](floor_struc_enum.md) + * [floor_water_mold_enum](floor_water_mold_enum.md) + * [furniture_enum](furniture_enum.md) + * [growth_habit_enum](growth_habit_enum.md) + * [handidness_enum](handidness_enum.md) + * [hc_produced_enum](hc_produced_enum.md) + * [hcr_enum](hcr_enum.md) + * [hcr_geol_age_enum](hcr_geol_age_enum.md) + * [health_disease_stat_enum](health_disease_stat_enum.md) + * [heat_cool_type_enum](heat_cool_type_enum.md) + * [heat_deliv_loc_enum](heat_deliv_loc_enum.md) + * [horizon_enum](horizon_enum.md) + * [host_pred_appr_enum](host_pred_appr_enum.md) + * [host_sex_enum](host_sex_enum.md) + * [indoor_space_enum](indoor_space_enum.md) + * [indoor_surf_enum](indoor_surf_enum.md) + * [int_wall_cond_enum](int_wall_cond_enum.md) + * [investigation_type_enum](investigation_type_enum.md) + * [lib_layout_enum](lib_layout_enum.md) + * [light_type_enum](light_type_enum.md) + * [lithology_enum](lithology_enum.md) + * [mag_cov_software_enum](mag_cov_software_enum.md) + * [mech_struc_enum](mech_struc_enum.md) + * [occup_document_enum](occup_document_enum.md) + * [organism_count_enum](organism_count_enum.md) + * [oxy_stat_samp_enum](oxy_stat_samp_enum.md) + * [plant_growth_med_enum](plant_growth_med_enum.md) + * [plant_sex_enum](plant_sex_enum.md) + * [pred_genome_struc_enum](pred_genome_struc_enum.md) + * [pred_genome_type_enum](pred_genome_type_enum.md) + * [pres_animal_enum](pres_animal_enum.md) + * [profile_position_enum](profile_position_enum.md) + * [quad_pos_enum](quad_pos_enum.md) + * [rel_samp_loc_enum](rel_samp_loc_enum.md) + * [rel_to_oxygen_enum](rel_to_oxygen_enum.md) + * [room_condt_enum](room_condt_enum.md) + * [room_connected_enum](room_connected_enum.md) + * [room_loc_enum](room_loc_enum.md) + * [room_samp_pos_enum](room_samp_pos_enum.md) + * [room_type_enum](room_type_enum.md) + * [samp_capt_status_enum](samp_capt_status_enum.md) + * [samp_collection_point_enum](samp_collection_point_enum.md) + * [samp_dis_stage_enum](samp_dis_stage_enum.md) + * [samp_floor_enum](samp_floor_enum.md) + * [samp_md_enum](samp_md_enum.md) + * [samp_subtype_enum](samp_subtype_enum.md) + * [samp_type_enum](samp_type_enum.md) + * [samp_weather_enum](samp_weather_enum.md) + * [season_use_enum](season_use_enum.md) + * [sediment_type_enum](sediment_type_enum.md) + * [seq_meth_enum](seq_meth_enum.md) + * [shading_device_cond_enum](shading_device_cond_enum.md) + * [shading_device_type_enum](shading_device_type_enum.md) + * [single_cell_lysis_appr_enum](single_cell_lysis_appr_enum.md) + * [sort_tech_enum](sort_tech_enum.md) + * [source_uvig_enum](source_uvig_enum.md) + * [special_diet_enum](special_diet_enum.md) + * [specific_enum](specific_enum.md) + * [sr_dep_env_enum](sr_dep_env_enum.md) + * [sr_geol_age_enum](sr_geol_age_enum.md) + * [sr_kerog_type_enum](sr_kerog_type_enum.md) + * [sr_lithology_enum](sr_lithology_enum.md) + * [study_complt_stat_enum](study_complt_stat_enum.md) + * [substructure_type_enum](substructure_type_enum.md) + * [surf_air_cont_enum](surf_air_cont_enum.md) + * [surf_material_enum](surf_material_enum.md) + * [tax_ident_enum](tax_ident_enum.md) + * [tidal_stage_enum](tidal_stage_enum.md) + * [tillage_enum](tillage_enum.md) + * [train_line_enum](train_line_enum.md) + * [train_stat_loc_enum](train_stat_loc_enum.md) + * [train_stop_loc_enum](train_stop_loc_enum.md) + * [trophic_level_enum](trophic_level_enum.md) + * [virus_enrich_appr_enum](virus_enrich_appr_enum.md) + * [vis_media_enum](vis_media_enum.md) + * [wall_const_type_enum](wall_const_type_enum.md) + * [wall_finish_mat_enum](wall_finish_mat_enum.md) + * [wall_loc_enum](wall_loc_enum.md) + * [wall_surf_treatment_enum](wall_surf_treatment_enum.md) + * [wall_texture_enum](wall_texture_enum.md) + * [water_feat_type_enum](water_feat_type_enum.md) + * [weekday_enum](weekday_enum.md) + * [window_cond_enum](window_cond_enum.md) + * [window_cover_enum](window_cover_enum.md) + * [window_horiz_pos_enum](window_horiz_pos_enum.md) + * [window_loc_enum](window_loc_enum.md) + * [window_mat_enum](window_mat_enum.md) + * [window_type_enum](window_type_enum.md) + * [window_vert_pos_enum](window_vert_pos_enum.md) ### Types diff --git a/mixs6/indoor_space.md b/mixs6/indoor_space.md index 69cfb616..a6314ef6 100644 --- a/mixs6/indoor_space.md +++ b/mixs6/indoor_space.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | indoor space | | **Mappings:** | | MIXS:0000763 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 15 | +| | | Position: 15.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='foyer', description=None) | diff --git a/mixs6/indoor_surf.md b/mixs6/indoor_surf.md index 1f291ce5..740be8b6 100644 --- a/mixs6/indoor_surf.md +++ b/mixs6/indoor_surf.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | indoor surface | | **Mappings:** | | MIXS:0000764 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 16 | +| | | Position: 16.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wall', description=None) | diff --git a/mixs6/indust_eff_percent.md b/mixs6/indust_eff_percent.md index ff3d740c..0ed84035 100644 --- a/mixs6/indust_eff_percent.md +++ b/mixs6/indust_eff_percent.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/inorg_particles.md b/mixs6/inorg_particles.md index 23618072..a2155917 100644 --- a/mixs6/inorg_particles.md +++ b/mixs6/inorg_particles.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: inorganic particle name;measurement value | | | | Preferred unit: mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/inside_lux.md b/mixs6/inside_lux.md index 2817e59c..92515128 100644 --- a/mixs6/inside_lux.md +++ b/mixs6/inside_lux.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilowatt per square metre | | | | Occurrence: 1 | -| | | Position: 87 | +| | | Position: 87.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/int_wall_cond.md b/mixs6/int_wall_cond.md index bf11725f..8772d356 100644 --- a/mixs6/int_wall_cond.md +++ b/mixs6/int_wall_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | interior wall condition | | **Mappings:** | | MIXS:0000813 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 88 | +| | | Position: 88.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='damaged', description=None) | diff --git a/mixs6/investigation_field.md b/mixs6/investigation_field.md index f8e785ee..96f6808f 100644 --- a/mixs6/investigation_field.md +++ b/mixs6/investigation_field.md @@ -19,6 +19,7 @@ None -> OPT [String](types/String.md) * [experimental_factor](experimental_factor.md) * [investigation_type](investigation_type.md) * [project_name](project_name.md) + * [sample_name](sample_name.md) * [submitted_to_insdc](submitted_to_insdc.md) ## Used by diff --git a/mixs6/investigation_type.md b/mixs6/investigation_type.md index 0ddf3662..10d4647b 100644 --- a/mixs6/investigation_type.md +++ b/mixs6/investigation_type.md @@ -39,7 +39,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | investigation type | | **Comments:** | | Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genomes | -| | | Preferred unit: | | | | Position: 2.0 | | **Examples:** | | Example(value='metagenome', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/60 | diff --git a/mixs6/isol_growth_condt.md b/mixs6/isol_growth_condt.md index 923d6ef8..67b453a9 100644 --- a/mixs6/isol_growth_condt.md +++ b/mixs6/isol_growth_condt.md @@ -34,7 +34,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | isolation and growth condition | | **Comments:** | | Expected value: PMID,DOI or URL | -| | | Preferred unit: | | | | Position: 30.0 | | **Examples:** | | Example(value='doi: 10.1016/j.syapm.2018.01.009', description=None) | diff --git a/mixs6/iw_bt_date_well.md b/mixs6/iw_bt_date_well.md index b77d48c4..07824676 100644 --- a/mixs6/iw_bt_date_well.md +++ b/mixs6/iw_bt_date_well.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:iw_bt_date_well](https://w3id.org/mixs/vocab/iw_bt_date_well) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | injection water breakthrough date of specific well | | **Mappings:** | | MIXS:0001010 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 29 | +| | | Position: 29.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/iwf.md b/mixs6/iwf.md index 85a1a71d..1c441ad6 100644 --- a/mixs6/iwf.md +++ b/mixs6/iwf.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 27 | +| | | Position: 27.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/kidney_disord.md b/mixs6/kidney_disord.md new file mode 100644 index 00000000..ef63a25f --- /dev/null +++ b/mixs6/kidney_disord.md @@ -0,0 +1,47 @@ + +# Slot: kidney_disord + + +History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). + +URI: [mixs.vocab:kidney_disord](https://w3id.org/mixs/vocab/kidney_disord) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [environment field](environment_field.md) + +## Children + + +## Used by + + * [Human-associated](Human-associated.md) + * [Human-associatedME](Human-associatedME.md) + * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md) + * [Human-associatedMIGSEukaryote](Human-associatedMIGSEukaryote.md) + * [Human-associatedMIGSOrg](Human-associatedMIGSOrg.md) + * [Human-associatedMIGSPlant](Human-associatedMIGSPlant.md) + * [Human-associatedMIGSVirus](Human-associatedMIGSVirus.md) + * [Human-associatedMIMAG](Human-associatedMIMAG.md) + * [Human-associatedMIMARKSSpecimen](Human-associatedMIMARKSSpecimen.md) + * [Human-associatedMIMARKSSurvey](Human-associatedMIMARKSSurvey.md) + * [Human-associatedMISAG](Human-associatedMISAG.md) + * [Human-associatedMIUVIG](Human-associatedMIUVIG.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | urine/kidney disorder | +| **Mappings:** | | MIXS:0000277 | +| **Comments:** | | Expected value: disorder name | +| | | Occurrence: m | +| | | Position: 40.0 | +| | | This field is used uniquely in: human-associated | +| **Examples:** | | Example(value='', description=None) | + diff --git a/mixs6/last_clean.md b/mixs6/last_clean.md index eee67a47..3ac71306 100644 --- a/mixs6/last_clean.md +++ b/mixs6/last_clean.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:last_clean](https://w3id.org/mixs/vocab/last_clean) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | last time swept/mopped/vacuumed | | **Mappings:** | | MIXS:0000814 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 89 | +| | | Position: 89.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='2018-05-11:T14:30Z', description=None) | diff --git a/mixs6/lat_lon.md b/mixs6/lat_lon.md index c1650030..160fcf6e 100644 --- a/mixs6/lat_lon.md +++ b/mixs6/lat_lon.md @@ -243,7 +243,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | geographic location (latitude and longitude) | | **Comments:** | | Expected value: decimal degrees | -| | | Preferred unit: | | | | Position: 5.0 | | **Examples:** | | Example(value='50.586825 6.408977', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/62 | diff --git a/mixs6/lib_layout.md b/mixs6/lib_layout.md index 5ad862b5..eb667bbb 100644 --- a/mixs6/lib_layout.md +++ b/mixs6/lib_layout.md @@ -38,7 +38,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | library layout | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 41.0 | | **Examples:** | | Example(value='paired', description=None) | diff --git a/mixs6/lib_reads_seqd.md b/mixs6/lib_reads_seqd.md index 2c0606d5..656f1d10 100644 --- a/mixs6/lib_reads_seqd.md +++ b/mixs6/lib_reads_seqd.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | library reads sequenced | | **Comments:** | | Expected value: number of reads sequenced | -| | | Preferred unit: | | | | Position: 40.0 | | **Examples:** | | Example(value='20', description=None) | diff --git a/mixs6/lib_screen.md b/mixs6/lib_screen.md index 1280445b..577fd0aa 100644 --- a/mixs6/lib_screen.md +++ b/mixs6/lib_screen.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | library screening strategy | | **Comments:** | | Expected value: screening strategy name | -| | | Preferred unit: | | | | Position: 43.0 | | **Examples:** | | Example(value='enriched, screened, normalized', description=None) | diff --git a/mixs6/lib_size.md b/mixs6/lib_size.md index 410443ad..8b9400a2 100644 --- a/mixs6/lib_size.md +++ b/mixs6/lib_size.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | library size | | **Comments:** | | Expected value: number of clones | -| | | Preferred unit: | | | | Position: 39.0 | | **Examples:** | | Example(value='50', description=None) | diff --git a/mixs6/lib_vector.md b/mixs6/lib_vector.md index 7fb8c386..ed175c6a 100644 --- a/mixs6/lib_vector.md +++ b/mixs6/lib_vector.md @@ -38,7 +38,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | library vector | | **Comments:** | | Expected value: vector | -| | | Preferred unit: | | | | Position: 42.0 | | **Examples:** | | Example(value='Bacteriophage P1', description=None) | diff --git a/mixs6/light_intensity.md b/mixs6/light_intensity.md index 0f9887aa..4e527bc5 100644 --- a/mixs6/light_intensity.md +++ b/mixs6/light_intensity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: lux | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='0.3 lux', description=None) | diff --git a/mixs6/light_regm.md b/mixs6/light_regm.md index 6c3e54f3..c33d4e51 100644 --- a/mixs6/light_regm.md +++ b/mixs6/light_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: exposure type;light intensity;light quality | | | | Preferred unit: lux; micrometer, nanometer, angstrom | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='incandescant light;10 lux;450 nanometer', description=None) | diff --git a/mixs6/light_type.md b/mixs6/light_type.md index 3978cb36..3e617938 100644 --- a/mixs6/light_type.md +++ b/mixs6/light_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | light type | | **Mappings:** | | MIXS:0000769 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 21 | +| | | Position: 21.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='desk lamp', description=None) | diff --git a/mixs6/link_addit_analys.md b/mixs6/link_addit_analys.md index 49ba804f..04d9c501 100644 --- a/mixs6/link_addit_analys.md +++ b/mixs6/link_addit_analys.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | links to additional analysis | | **Mappings:** | | MIXS:0000340 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 45 | +| | | Position: 45.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/link_class_info.md b/mixs6/link_class_info.md index 1f7d3219..dd7dfb21 100644 --- a/mixs6/link_class_info.md +++ b/mixs6/link_class_info.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | link to classification information | | **Mappings:** | | MIXS:0000329 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 25 | +| | | Position: 25.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/link_climate_info.md b/mixs6/link_climate_info.md index 6f44bada..9cf5d4d9 100644 --- a/mixs6/link_climate_info.md +++ b/mixs6/link_climate_info.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | link to climate information | | **Mappings:** | | MIXS:0000328 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 20 | +| | | Position: 20.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/lithology.md b/mixs6/lithology.md index 8da76645..95a86c18 100644 --- a/mixs6/lithology.md +++ b/mixs6/lithology.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | lithology | | **Mappings:** | | MIXS:0000990 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 12 | +| | | Position: 12.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='Volcanic', description=None) | diff --git a/mixs6/liver_disord.md b/mixs6/liver_disord.md index 8d5add52..1edbc172 100644 --- a/mixs6/liver_disord.md +++ b/mixs6/liver_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | liver disorder | | **Mappings:** | | MIXS:0000282 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: human-gut | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/local_class.md b/mixs6/local_class.md index 88cdcfdb..d9470282 100644 --- a/mixs6/local_class.md +++ b/mixs6/local_class.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | soil_taxonomic/local classification | | **Mappings:** | | MIXS:0000330 | | **Comments:** | | Expected value: local classification name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 27 | +| | | Position: 27.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/local_class_meth.md b/mixs6/local_class_meth.md index 0e612c53..cc3da0c6 100644 --- a/mixs6/local_class_meth.md +++ b/mixs6/local_class_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | soil_taxonomic/local classification method | | **Mappings:** | | MIXS:0000331 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 28 | +| | | Position: 28.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/mag_cov_software.md b/mixs6/mag_cov_software.md index d9447aab..355ac8f7 100644 --- a/mixs6/mag_cov_software.md +++ b/mixs6/mag_cov_software.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | MAG coverage software | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 82.0 | | **Examples:** | | Example(value='bbmap', description=None) | diff --git a/mixs6/magnesium.md b/mixs6/magnesium.md index e165270a..810cca11 100644 --- a/mixs6/magnesium.md +++ b/mixs6/magnesium.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: mole per liter, milligram per liter, parts per million, micromole per kilogram | | | | Occurrence: 1 | -| | | Position: 69 | +| | | Position: 69.0 | | | | This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='52.8 micromole per kilogram', description=None) | diff --git a/mixs6/maternal_health_stat.md b/mixs6/maternal_health_stat.md index 4d538bd7..1fac52f5 100644 --- a/mixs6/maternal_health_stat.md +++ b/mixs6/maternal_health_stat.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | amniotic fluid/maternal health status | | **Mappings:** | | MIXS:0000273 | | **Comments:** | | Expected value: health status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 37 | +| | | Position: 37.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/max_occup.md b/mixs6/max_occup.md index 22a84b07..c3c33e8e 100644 --- a/mixs6/max_occup.md +++ b/mixs6/max_occup.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | maximum occupancy | | **Mappings:** | | MIXS:0000229 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 90 | +| | | Position: 90.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/me_collection_date.md b/mixs6/me_collection_date.md index b36dbb32..36cf2144 100644 --- a/mixs6/me_collection_date.md +++ b/mixs6/me_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ME_collection_date](https://w3id.org/mixs/vocab/ME_collection_d ## Domain and Range -[ME](ME.md) -> REQ [String](types/String.md) +[ME](ME.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/me_sample_name.md b/mixs6/me_sample_name.md index 261b70fa..251b038f 100644 --- a/mixs6/me_sample_name.md +++ b/mixs6/me_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:ME_sample_name](https://w3id.org/mixs/vocab/ME_sample_name) ## Domain and Range -[ME](ME.md) -> OPT [String](types/String.md) +[ME](ME.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/mean_frict_vel.md b/mixs6/mean_frict_vel.md index ad91c28e..47448218 100644 --- a/mixs6/mean_frict_vel.md +++ b/mixs6/mean_frict_vel.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter per second | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.5 meter per second', description=None) | diff --git a/mixs6/mean_peak_frict_vel.md b/mixs6/mean_peak_frict_vel.md index 7082cb35..db04b786 100644 --- a/mixs6/mean_peak_frict_vel.md +++ b/mixs6/mean_peak_frict_vel.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter per second | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='1 meter per second', description=None) | diff --git a/mixs6/mech_struc.md b/mixs6/mech_struc.md index b080f73a..2aff3998 100644 --- a/mixs6/mech_struc.md +++ b/mixs6/mech_struc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | mechanical structure | | **Mappings:** | | MIXS:0000815 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 91 | +| | | Position: 91.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='elevator', description=None) | diff --git a/mixs6/mechanical_damage.md b/mixs6/mechanical_damage.md index 76fe7967..d8986e86 100644 --- a/mixs6/mechanical_damage.md +++ b/mixs6/mechanical_damage.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | mechanical damage | | **Mappings:** | | MIXS:0001052 | | **Comments:** | | Expected value: damage type;body site | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='pruning;bark', description=None) | diff --git a/mixs6/medic_hist_perform.md b/mixs6/medic_hist_perform.md index 87911c14..c31d1b68 100644 --- a/mixs6/medic_hist_perform.md +++ b/mixs6/medic_hist_perform.md @@ -88,9 +88,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | medical history performed | | **Mappings:** | | MIXS:0000897 | | **Comments:** | | Expected value: true or false | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 28 | +| | | Position: 28.0 | | | | This field is used in: 5 packages: human-associated, human-gut, human-oral, human-skin, human-vaginal | | **Examples:** | | Example(value='TRUE', description=None) | diff --git a/mixs6/menarche.md b/mixs6/menarche.md index 5d19a012..0b113c28 100644 --- a/mixs6/menarche.md +++ b/mixs6/menarche.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:menarche](https://w3id.org/mixs/vocab/menarche) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | menarche | | **Mappings:** | | MIXS:0000965 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/menopause.md b/mixs6/menopause.md index c585d5a8..7aa150d6 100644 --- a/mixs6/menopause.md +++ b/mixs6/menopause.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:menopause](https://w3id.org/mixs/vocab/menopause) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | menopause | | **Mappings:** | | MIXS:0000968 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 6 | +| | | Position: 6.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/methane.md b/mixs6/methane.md index 0a397bca..68917fb0 100644 --- a/mixs6/methane.md +++ b/mixs6/methane.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, parts per billion, parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: air, microbial mat_biofilm, sediment | | **Examples:** | | Example(value='1800 parts per billion', description=None) | diff --git a/mixs6/microbial_biomass.md b/mixs6/microbial_biomass.md index 1743fc16..8b376cb5 100644 --- a/mixs6/microbial_biomass.md +++ b/mixs6/microbial_biomass.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: ton, kilogram, gram per kilogram soil | | | | Occurrence: 1 | -| | | Position: 43 | +| | | Position: 43.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/microbial_biomass_meth.md b/mixs6/microbial_biomass_meth.md index 32829c87..d3878f35 100644 --- a/mixs6/microbial_biomass_meth.md +++ b/mixs6/microbial_biomass_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | microbial biomass method | | **Mappings:** | | MIXS:0000339 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 44 | +| | | Position: 44.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/mid.md b/mixs6/mid.md index 35e3119e..90b166e3 100644 --- a/mixs6/mid.md +++ b/mixs6/mid.md @@ -33,7 +33,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | multiplex identifiers | | **Comments:** | | Expected value: multiplex identifier sequence | -| | | Preferred unit: | | | | Position: 47.0 | | **Examples:** | | Example(value='GTGAATAT', description=None) | diff --git a/mixs6/migs_ba_adapters.md b/mixs6/migs_ba_adapters.md deleted file mode 100644 index 202a624f..00000000 --- a/mixs6/migs_ba_adapters.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_adapters - - - - -URI: [mixs.vocab:migs_ba_adapters](https://w3id.org/mixs/vocab/migs_ba_adapters) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [adapters](adapters.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_annot.md b/mixs6/migs_ba_annot.md deleted file mode 100644 index 17b9c14b..00000000 --- a/mixs6/migs_ba_annot.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_annot - - - - -URI: [mixs.vocab:migs_ba_annot](https://w3id.org/mixs/vocab/migs_ba_annot) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [annot](annot.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_assembly_name.md b/mixs6/migs_ba_assembly_name.md deleted file mode 100644 index 550d47b6..00000000 --- a/mixs6/migs_ba_assembly_name.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_assembly_name - - - - -URI: [mixs.vocab:migs_ba_assembly_name](https://w3id.org/mixs/vocab/migs_ba_assembly_name) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [assembly_name](assembly_name.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_assembly_qual.md b/mixs6/migs_ba_assembly_qual.md deleted file mode 100644 index 53fa4d3c..00000000 --- a/mixs6/migs_ba_assembly_qual.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_assembly_qual - - - - -URI: [mixs.vocab:migs_ba_assembly_qual](https://w3id.org/mixs/vocab/migs_ba_assembly_qual) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ - -## Parents - - * is_a: [assembly_qual](assembly_qual.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_assembly_software.md b/mixs6/migs_ba_assembly_software.md deleted file mode 100644 index 4d8fc32f..00000000 --- a/mixs6/migs_ba_assembly_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_assembly_software - - - - -URI: [mixs.vocab:migs_ba_assembly_software](https://w3id.org/mixs/vocab/migs_ba_assembly_software) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [assembly_software](assembly_software.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_biotic_relationship.md b/mixs6/migs_ba_biotic_relationship.md deleted file mode 100644 index cf26cd5d..00000000 --- a/mixs6/migs_ba_biotic_relationship.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_biotic_relationship - - - - -URI: [mixs.vocab:migs_ba_biotic_relationship](https://w3id.org/mixs/vocab/migs_ba_biotic_relationship) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [biotic_relationship](biotic_relationship.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_collection_date.md b/mixs6/migs_ba_collection_date.md deleted file mode 100644 index 643cc548..00000000 --- a/mixs6/migs_ba_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_collection_date - - - - -URI: [mixs.vocab:migs_ba_collection_date](https://w3id.org/mixs/vocab/migs_ba_collection_date) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_compl_score.md b/mixs6/migs_ba_compl_score.md deleted file mode 100644 index bae3d1dd..00000000 --- a/mixs6/migs_ba_compl_score.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_compl_score - - - - -URI: [mixs.vocab:migs_ba_compl_score](https://w3id.org/mixs/vocab/migs_ba_compl_score) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [compl_score](compl_score.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_compl_software.md b/mixs6/migs_ba_compl_software.md deleted file mode 100644 index 8566283a..00000000 --- a/mixs6/migs_ba_compl_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_compl_software - - - - -URI: [mixs.vocab:migs_ba_compl_software](https://w3id.org/mixs/vocab/migs_ba_compl_software) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [compl_software](compl_software.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_encoded_traits.md b/mixs6/migs_ba_encoded_traits.md deleted file mode 100644 index 5df21614..00000000 --- a/mixs6/migs_ba_encoded_traits.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_encoded_traits - - - - -URI: [mixs.vocab:migs_ba_encoded_traits](https://w3id.org/mixs/vocab/migs_ba_encoded_traits) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [encoded_traits](encoded_traits.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_env_broad_scale.md b/mixs6/migs_ba_env_broad_scale.md deleted file mode 100644 index 9ff91f7b..00000000 --- a/mixs6/migs_ba_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_env_broad_scale - - - - -URI: [mixs.vocab:migs_ba_env_broad_scale](https://w3id.org/mixs/vocab/migs_ba_env_broad_scale) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_local_scale.md b/mixs6/migs_ba_env_local_scale.md deleted file mode 100644 index 06d6ecf2..00000000 --- a/mixs6/migs_ba_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_env_local_scale - - - - -URI: [mixs.vocab:migs_ba_env_local_scale](https://w3id.org/mixs/vocab/migs_ba_env_local_scale) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_medium.md b/mixs6/migs_ba_env_medium.md deleted file mode 100644 index a73b2b86..00000000 --- a/mixs6/migs_ba_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_env_medium - - - - -URI: [mixs.vocab:migs_ba_env_medium](https://w3id.org/mixs/vocab/migs_ba_env_medium) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_env_package.md b/mixs6/migs_ba_env_package.md deleted file mode 100644 index 073e3fe7..00000000 --- a/mixs6/migs_ba_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_env_package - - - - -URI: [mixs.vocab:migs_ba_env_package](https://w3id.org/mixs/vocab/migs_ba_env_package) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_estimated_size.md b/mixs6/migs_ba_estimated_size.md deleted file mode 100644 index fdaaeb89..00000000 --- a/mixs6/migs_ba_estimated_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_estimated_size - - - - -URI: [mixs.vocab:migs_ba_estimated_size](https://w3id.org/mixs/vocab/migs_ba_estimated_size) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [estimated_size](estimated_size.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_experimental_factor.md b/mixs6/migs_ba_experimental_factor.md deleted file mode 100644 index 54f48a26..00000000 --- a/mixs6/migs_ba_experimental_factor.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_experimental_factor - - - - -URI: [mixs.vocab:migs_ba_experimental_factor](https://w3id.org/mixs/vocab/migs_ba_experimental_factor) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_extrachrom_elements.md b/mixs6/migs_ba_extrachrom_elements.md deleted file mode 100644 index b3f7c8cd..00000000 --- a/mixs6/migs_ba_extrachrom_elements.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_extrachrom_elements - - - - -URI: [mixs.vocab:migs_ba_extrachrom_elements](https://w3id.org/mixs/vocab/migs_ba_extrachrom_elements) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [extrachrom_elements](extrachrom_elements.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_feat_pred.md b/mixs6/migs_ba_feat_pred.md deleted file mode 100644 index c44b9fc0..00000000 --- a/mixs6/migs_ba_feat_pred.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_feat_pred - - - - -URI: [mixs.vocab:migs_ba_feat_pred](https://w3id.org/mixs/vocab/migs_ba_feat_pred) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [feat_pred](feat_pred.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_geo_loc_name.md b/mixs6/migs_ba_geo_loc_name.md deleted file mode 100644 index a9af3ee3..00000000 --- a/mixs6/migs_ba_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_geo_loc_name - - - - -URI: [mixs.vocab:migs_ba_geo_loc_name](https://w3id.org/mixs/vocab/migs_ba_geo_loc_name) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_health_disease_stat.md b/mixs6/migs_ba_health_disease_stat.md deleted file mode 100644 index 675f6fe7..00000000 --- a/mixs6/migs_ba_health_disease_stat.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_health_disease_stat - - - - -URI: [mixs.vocab:migs_ba_health_disease_stat](https://w3id.org/mixs/vocab/migs_ba_health_disease_stat) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [health_disease_stat](health_disease_stat.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_host_spec_range.md b/mixs6/migs_ba_host_spec_range.md deleted file mode 100644 index 4a91bdad..00000000 --- a/mixs6/migs_ba_host_spec_range.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_host_spec_range - - - - -URI: [mixs.vocab:migs_ba_host_spec_range](https://w3id.org/mixs/vocab/migs_ba_host_spec_range) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [host_spec_range](host_spec_range.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_investigation_type.md b/mixs6/migs_ba_investigation_type.md deleted file mode 100644 index 9f9ba46d..00000000 --- a/mixs6/migs_ba_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_investigation_type - - - - -URI: [mixs.vocab:migs_ba_investigation_type](https://w3id.org/mixs/vocab/migs_ba_investigation_type) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_isol_growth_condt.md b/mixs6/migs_ba_isol_growth_condt.md deleted file mode 100644 index 5de15014..00000000 --- a/mixs6/migs_ba_isol_growth_condt.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_isol_growth_condt - - - - -URI: [mixs.vocab:migs_ba_isol_growth_condt](https://w3id.org/mixs/vocab/migs_ba_isol_growth_condt) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [isol_growth_condt](isol_growth_condt.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lat_lon.md b/mixs6/migs_ba_lat_lon.md deleted file mode 100644 index 4259c437..00000000 --- a/mixs6/migs_ba_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_ba_lat_lon - - - - -URI: [mixs.vocab:migs_ba_lat_lon](https://w3id.org/mixs/vocab/migs_ba_lat_lon) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MigsBa](MigsBa.md) diff --git a/mixs6/migs_ba_lib_layout.md b/mixs6/migs_ba_lib_layout.md deleted file mode 100644 index 2829bd6f..00000000 --- a/mixs6/migs_ba_lib_layout.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_lib_layout - - - - -URI: [mixs.vocab:migs_ba_lib_layout](https://w3id.org/mixs/vocab/migs_ba_lib_layout) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [lib_layout](lib_layout.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_reads_seqd.md b/mixs6/migs_ba_lib_reads_seqd.md deleted file mode 100644 index 1c8271d9..00000000 --- a/mixs6/migs_ba_lib_reads_seqd.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_lib_reads_seqd - - - - -URI: [mixs.vocab:migs_ba_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_ba_lib_reads_seqd) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_reads_seqd](lib_reads_seqd.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_screen.md b/mixs6/migs_ba_lib_screen.md deleted file mode 100644 index 213ecc7a..00000000 --- a/mixs6/migs_ba_lib_screen.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_lib_screen - - - - -URI: [mixs.vocab:migs_ba_lib_screen](https://w3id.org/mixs/vocab/migs_ba_lib_screen) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_screen](lib_screen.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_size.md b/mixs6/migs_ba_lib_size.md deleted file mode 100644 index 71698443..00000000 --- a/mixs6/migs_ba_lib_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_lib_size - - - - -URI: [mixs.vocab:migs_ba_lib_size](https://w3id.org/mixs/vocab/migs_ba_lib_size) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_size](lib_size.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_lib_vector.md b/mixs6/migs_ba_lib_vector.md deleted file mode 100644 index 3c371ef5..00000000 --- a/mixs6/migs_ba_lib_vector.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_lib_vector - - - - -URI: [mixs.vocab:migs_ba_lib_vector](https://w3id.org/mixs/vocab/migs_ba_lib_vector) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_vector](lib_vector.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_nucl_acid_amp.md b/mixs6/migs_ba_nucl_acid_amp.md deleted file mode 100644 index a07917c5..00000000 --- a/mixs6/migs_ba_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_nucl_acid_amp - - - - -URI: [mixs.vocab:migs_ba_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_ba_nucl_acid_amp) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_nucl_acid_ext.md b/mixs6/migs_ba_nucl_acid_ext.md deleted file mode 100644 index 2821f8c1..00000000 --- a/mixs6/migs_ba_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_nucl_acid_ext - - - - -URI: [mixs.vocab:migs_ba_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_ba_nucl_acid_ext) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_num_replicons.md b/mixs6/migs_ba_num_replicons.md deleted file mode 100644 index 76a293ba..00000000 --- a/mixs6/migs_ba_num_replicons.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_num_replicons - - - - -URI: [mixs.vocab:migs_ba_num_replicons](https://w3id.org/mixs/vocab/migs_ba_num_replicons) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [num_replicons](num_replicons.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_number_contig.md b/mixs6/migs_ba_number_contig.md deleted file mode 100644 index f21eb0a8..00000000 --- a/mixs6/migs_ba_number_contig.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_number_contig - - - - -URI: [mixs.vocab:migs_ba_number_contig](https://w3id.org/mixs/vocab/migs_ba_number_contig) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [number_contig](number_contig.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_pathogenicity.md b/mixs6/migs_ba_pathogenicity.md deleted file mode 100644 index 87a65c57..00000000 --- a/mixs6/migs_ba_pathogenicity.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_pathogenicity - - - - -URI: [mixs.vocab:migs_ba_pathogenicity](https://w3id.org/mixs/vocab/migs_ba_pathogenicity) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pathogenicity](pathogenicity.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_project_name.md b/mixs6/migs_ba_project_name.md deleted file mode 100644 index 78c6be58..00000000 --- a/mixs6/migs_ba_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_project_name - - - - -URI: [mixs.vocab:migs_ba_project_name](https://w3id.org/mixs/vocab/migs_ba_project_name) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_ref_biomaterial.md b/mixs6/migs_ba_ref_biomaterial.md deleted file mode 100644 index e812c69e..00000000 --- a/mixs6/migs_ba_ref_biomaterial.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_ref_biomaterial - - - - -URI: [mixs.vocab:migs_ba_ref_biomaterial](https://w3id.org/mixs/vocab/migs_ba_ref_biomaterial) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [ref_biomaterial](ref_biomaterial.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_ref_db.md b/mixs6/migs_ba_ref_db.md deleted file mode 100644 index 040f9750..00000000 --- a/mixs6/migs_ba_ref_db.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_ref_db - - - - -URI: [mixs.vocab:migs_ba_ref_db](https://w3id.org/mixs/vocab/migs_ba_ref_db) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_db](ref_db.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_rel_to_oxygen.md b/mixs6/migs_ba_rel_to_oxygen.md deleted file mode 100644 index 5f1585f4..00000000 --- a/mixs6/migs_ba_rel_to_oxygen.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_rel_to_oxygen - - - - -URI: [mixs.vocab:migs_ba_rel_to_oxygen](https://w3id.org/mixs/vocab/migs_ba_rel_to_oxygen) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [rel_to_oxygen](rel_to_oxygen.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_samp_collect_device.md b/mixs6/migs_ba_samp_collect_device.md deleted file mode 100644 index 07b9ddca..00000000 --- a/mixs6/migs_ba_samp_collect_device.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_samp_collect_device - - - - -URI: [mixs.vocab:migs_ba_samp_collect_device](https://w3id.org/mixs/vocab/migs_ba_samp_collect_device) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_samp_mat_process.md b/mixs6/migs_ba_samp_mat_process.md deleted file mode 100644 index 2c50d118..00000000 --- a/mixs6/migs_ba_samp_mat_process.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_samp_mat_process - - - - -URI: [mixs.vocab:migs_ba_samp_mat_process](https://w3id.org/mixs/vocab/migs_ba_samp_mat_process) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_samp_size.md b/mixs6/migs_ba_samp_size.md deleted file mode 100644 index 5f2ffc11..00000000 --- a/mixs6/migs_ba_samp_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_samp_size - - - - -URI: [mixs.vocab:migs_ba_samp_size](https://w3id.org/mixs/vocab/migs_ba_samp_size) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sample_name.md b/mixs6/migs_ba_sample_name.md deleted file mode 100644 index ecd122ec..00000000 --- a/mixs6/migs_ba_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_sample_name - - - - -URI: [mixs.vocab:migs_ba_sample_name](https://w3id.org/mixs/vocab/migs_ba_sample_name) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_seq_meth.md b/mixs6/migs_ba_seq_meth.md deleted file mode 100644 index 4fbf26cc..00000000 --- a/mixs6/migs_ba_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_seq_meth - - - - -URI: [mixs.vocab:migs_ba_seq_meth](https://w3id.org/mixs/vocab/migs_ba_seq_meth) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sim_search_meth.md b/mixs6/migs_ba_sim_search_meth.md deleted file mode 100644 index 5e86deda..00000000 --- a/mixs6/migs_ba_sim_search_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_sim_search_meth - - - - -URI: [mixs.vocab:migs_ba_sim_search_meth](https://w3id.org/mixs/vocab/migs_ba_sim_search_meth) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sim_search_meth](sim_search_meth.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_sop.md b/mixs6/migs_ba_sop.md deleted file mode 100644 index 416172cb..00000000 --- a/mixs6/migs_ba_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_sop - - - - -URI: [mixs.vocab:migs_ba_sop](https://w3id.org/mixs/vocab/migs_ba_sop) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_source_mat_id.md b/mixs6/migs_ba_source_mat_id.md deleted file mode 100644 index 074ad9fb..00000000 --- a/mixs6/migs_ba_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_source_mat_id - - - - -URI: [mixs.vocab:migs_ba_source_mat_id](https://w3id.org/mixs/vocab/migs_ba_source_mat_id) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_specific_host.md b/mixs6/migs_ba_specific_host.md deleted file mode 100644 index e8f56721..00000000 --- a/mixs6/migs_ba_specific_host.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_specific_host - - - - -URI: [mixs.vocab:migs_ba_specific_host](https://w3id.org/mixs/vocab/migs_ba_specific_host) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [specific_host](specific_host.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_submitted_to_insdc.md b/mixs6/migs_ba_submitted_to_insdc.md deleted file mode 100644 index 78f42bb7..00000000 --- a/mixs6/migs_ba_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_submitted_to_insdc - - - - -URI: [mixs.vocab:migs_ba_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_ba_submitted_to_insdc) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_subspecf_gen_lin.md b/mixs6/migs_ba_subspecf_gen_lin.md deleted file mode 100644 index e4619438..00000000 --- a/mixs6/migs_ba_subspecf_gen_lin.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_subspecf_gen_lin - - - - -URI: [mixs.vocab:migs_ba_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_ba_subspecf_gen_lin) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_tax_class.md b/mixs6/migs_ba_tax_class.md deleted file mode 100644 index 9518f918..00000000 --- a/mixs6/migs_ba_tax_class.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_ba_tax_class - - - - -URI: [mixs.vocab:migs_ba_tax_class](https://w3id.org/mixs/vocab/migs_ba_tax_class) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [tax_class](tax_class.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) diff --git a/mixs6/migs_ba_tax_ident.md b/mixs6/migs_ba_tax_ident.md deleted file mode 100644 index 823bbfbc..00000000 --- a/mixs6/migs_ba_tax_ident.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_tax_ident - - - - -URI: [mixs.vocab:migs_ba_tax_ident](https://w3id.org/mixs/vocab/migs_ba_tax_ident) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [tax_ident](tax_ident.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_trophic_level.md b/mixs6/migs_ba_trophic_level.md deleted file mode 100644 index 69867451..00000000 --- a/mixs6/migs_ba_trophic_level.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_trophic_level - - - - -URI: [mixs.vocab:migs_ba_trophic_level](https://w3id.org/mixs/vocab/migs_ba_trophic_level) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT - -## Parents - - * is_a: [trophic_level](trophic_level.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_ba_url.md b/mixs6/migs_ba_url.md deleted file mode 100644 index e4af5a2f..00000000 --- a/mixs6/migs_ba_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_ba_url - - - - -URI: [mixs.vocab:migs_ba_url](https://w3id.org/mixs/vocab/migs_ba_url) - - -## Domain and Range - -[MigsBa](MigsBa.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMigsBa](AirMigsBa.md) - * [BuiltEnvironmentMigsBa](BuiltEnvironmentMigsBa.md) - * [Host-associatedMigsBa](Host-associatedMigsBa.md) - * [Human-associatedMigsBa](Human-associatedMigsBa.md) - * [Human-gutMigsBa](Human-gutMigsBa.md) - * [Human-oralMigsBa](Human-oralMigsBa.md) - * [Human-skinMigsBa](Human-skinMigsBa.md) - * [Human-vaginalMigsBa](Human-vaginalMigsBa.md) - * [HydrocarbonResources-coresMigsBa](HydrocarbonResources-coresMigsBa.md) - * [HydrocarbonResources-fluidsSwabsMigsBa](HydrocarbonResources-fluidsSwabsMigsBa.md) - * [MicrobialMatBiofilmMigsBa](MicrobialMatBiofilmMigsBa.md) - * [MigsBa](MigsBa.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsBa](MiscellaneousNaturalOrArtificialEnvironmentMigsBa.md) - * [Plant-associatedMigsBa](Plant-associatedMigsBa.md) - * [SedimentMigsBa](SedimentMigsBa.md) - * [SoilMigsBa](SoilMigsBa.md) - * [WastewaterSludgeMigsBa](WastewaterSludgeMigsBa.md) - * [WaterMigsBa](WaterMigsBa.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_adapters.md b/mixs6/migs_eu_adapters.md deleted file mode 100644 index d69ed764..00000000 --- a/mixs6/migs_eu_adapters.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_adapters - - - - -URI: [mixs.vocab:migs_eu_adapters](https://w3id.org/mixs/vocab/migs_eu_adapters) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [adapters](adapters.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_annot.md b/mixs6/migs_eu_annot.md deleted file mode 100644 index c96d5ea1..00000000 --- a/mixs6/migs_eu_annot.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_annot - - - - -URI: [mixs.vocab:migs_eu_annot](https://w3id.org/mixs/vocab/migs_eu_annot) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [annot](annot.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_assembly_name.md b/mixs6/migs_eu_assembly_name.md deleted file mode 100644 index 16f06f78..00000000 --- a/mixs6/migs_eu_assembly_name.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_assembly_name - - - - -URI: [mixs.vocab:migs_eu_assembly_name](https://w3id.org/mixs/vocab/migs_eu_assembly_name) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [assembly_name](assembly_name.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_assembly_qual.md b/mixs6/migs_eu_assembly_qual.md deleted file mode 100644 index 20266c8f..00000000 --- a/mixs6/migs_eu_assembly_qual.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_assembly_qual - - - - -URI: [mixs.vocab:migs_eu_assembly_qual](https://w3id.org/mixs/vocab/migs_eu_assembly_qual) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ - -## Parents - - * is_a: [assembly_qual](assembly_qual.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_assembly_software.md b/mixs6/migs_eu_assembly_software.md deleted file mode 100644 index 683886b5..00000000 --- a/mixs6/migs_eu_assembly_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_assembly_software - - - - -URI: [mixs.vocab:migs_eu_assembly_software](https://w3id.org/mixs/vocab/migs_eu_assembly_software) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [assembly_software](assembly_software.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_biotic_relationship.md b/mixs6/migs_eu_biotic_relationship.md deleted file mode 100644 index 5d6aa601..00000000 --- a/mixs6/migs_eu_biotic_relationship.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_biotic_relationship - - - - -URI: [mixs.vocab:migs_eu_biotic_relationship](https://w3id.org/mixs/vocab/migs_eu_biotic_relationship) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [biotic_relationship](biotic_relationship.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_collection_date.md b/mixs6/migs_eu_collection_date.md deleted file mode 100644 index a965176c..00000000 --- a/mixs6/migs_eu_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_collection_date - - - - -URI: [mixs.vocab:migs_eu_collection_date](https://w3id.org/mixs/vocab/migs_eu_collection_date) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_compl_score.md b/mixs6/migs_eu_compl_score.md deleted file mode 100644 index 7b08ab18..00000000 --- a/mixs6/migs_eu_compl_score.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_compl_score - - - - -URI: [mixs.vocab:migs_eu_compl_score](https://w3id.org/mixs/vocab/migs_eu_compl_score) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [compl_score](compl_score.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_compl_software.md b/mixs6/migs_eu_compl_software.md deleted file mode 100644 index 4cb9ba0d..00000000 --- a/mixs6/migs_eu_compl_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_compl_software - - - - -URI: [mixs.vocab:migs_eu_compl_software](https://w3id.org/mixs/vocab/migs_eu_compl_software) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [compl_software](compl_software.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_env_broad_scale.md b/mixs6/migs_eu_env_broad_scale.md deleted file mode 100644 index 60eed904..00000000 --- a/mixs6/migs_eu_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_env_broad_scale - - - - -URI: [mixs.vocab:migs_eu_env_broad_scale](https://w3id.org/mixs/vocab/migs_eu_env_broad_scale) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_local_scale.md b/mixs6/migs_eu_env_local_scale.md deleted file mode 100644 index 2537a8d5..00000000 --- a/mixs6/migs_eu_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_env_local_scale - - - - -URI: [mixs.vocab:migs_eu_env_local_scale](https://w3id.org/mixs/vocab/migs_eu_env_local_scale) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_medium.md b/mixs6/migs_eu_env_medium.md deleted file mode 100644 index 4cb33473..00000000 --- a/mixs6/migs_eu_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_env_medium - - - - -URI: [mixs.vocab:migs_eu_env_medium](https://w3id.org/mixs/vocab/migs_eu_env_medium) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_env_package.md b/mixs6/migs_eu_env_package.md deleted file mode 100644 index e36475d2..00000000 --- a/mixs6/migs_eu_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_env_package - - - - -URI: [mixs.vocab:migs_eu_env_package](https://w3id.org/mixs/vocab/migs_eu_env_package) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_estimated_size.md b/mixs6/migs_eu_estimated_size.md deleted file mode 100644 index d271aa07..00000000 --- a/mixs6/migs_eu_estimated_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_estimated_size - - - - -URI: [mixs.vocab:migs_eu_estimated_size](https://w3id.org/mixs/vocab/migs_eu_estimated_size) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [estimated_size](estimated_size.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_experimental_factor.md b/mixs6/migs_eu_experimental_factor.md deleted file mode 100644 index d51ac899..00000000 --- a/mixs6/migs_eu_experimental_factor.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_experimental_factor - - - - -URI: [mixs.vocab:migs_eu_experimental_factor](https://w3id.org/mixs/vocab/migs_eu_experimental_factor) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_extrachrom_elements.md b/mixs6/migs_eu_extrachrom_elements.md deleted file mode 100644 index 3b733b18..00000000 --- a/mixs6/migs_eu_extrachrom_elements.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_extrachrom_elements - - - - -URI: [mixs.vocab:migs_eu_extrachrom_elements](https://w3id.org/mixs/vocab/migs_eu_extrachrom_elements) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [extrachrom_elements](extrachrom_elements.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_feat_pred.md b/mixs6/migs_eu_feat_pred.md deleted file mode 100644 index fac65b4a..00000000 --- a/mixs6/migs_eu_feat_pred.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_feat_pred - - - - -URI: [mixs.vocab:migs_eu_feat_pred](https://w3id.org/mixs/vocab/migs_eu_feat_pred) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [feat_pred](feat_pred.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_geo_loc_name.md b/mixs6/migs_eu_geo_loc_name.md deleted file mode 100644 index 90e28e73..00000000 --- a/mixs6/migs_eu_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_geo_loc_name - - - - -URI: [mixs.vocab:migs_eu_geo_loc_name](https://w3id.org/mixs/vocab/migs_eu_geo_loc_name) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_health_disease_stat.md b/mixs6/migs_eu_health_disease_stat.md deleted file mode 100644 index 808269b4..00000000 --- a/mixs6/migs_eu_health_disease_stat.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_health_disease_stat - - - - -URI: [mixs.vocab:migs_eu_health_disease_stat](https://w3id.org/mixs/vocab/migs_eu_health_disease_stat) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [health_disease_stat](health_disease_stat.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_host_spec_range.md b/mixs6/migs_eu_host_spec_range.md deleted file mode 100644 index a3d93322..00000000 --- a/mixs6/migs_eu_host_spec_range.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_host_spec_range - - - - -URI: [mixs.vocab:migs_eu_host_spec_range](https://w3id.org/mixs/vocab/migs_eu_host_spec_range) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [host_spec_range](host_spec_range.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_investigation_type.md b/mixs6/migs_eu_investigation_type.md deleted file mode 100644 index ac4a6de6..00000000 --- a/mixs6/migs_eu_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_investigation_type - - - - -URI: [mixs.vocab:migs_eu_investigation_type](https://w3id.org/mixs/vocab/migs_eu_investigation_type) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_isol_growth_condt.md b/mixs6/migs_eu_isol_growth_condt.md deleted file mode 100644 index 78536e14..00000000 --- a/mixs6/migs_eu_isol_growth_condt.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_isol_growth_condt - - - - -URI: [mixs.vocab:migs_eu_isol_growth_condt](https://w3id.org/mixs/vocab/migs_eu_isol_growth_condt) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [isol_growth_condt](isol_growth_condt.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lat_lon.md b/mixs6/migs_eu_lat_lon.md deleted file mode 100644 index 7b2e5ad2..00000000 --- a/mixs6/migs_eu_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_eu_lat_lon - - - - -URI: [mixs.vocab:migs_eu_lat_lon](https://w3id.org/mixs/vocab/migs_eu_lat_lon) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MigsEu](MigsEu.md) diff --git a/mixs6/migs_eu_lib_layout.md b/mixs6/migs_eu_lib_layout.md deleted file mode 100644 index ccf40b9e..00000000 --- a/mixs6/migs_eu_lib_layout.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_lib_layout - - - - -URI: [mixs.vocab:migs_eu_lib_layout](https://w3id.org/mixs/vocab/migs_eu_lib_layout) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [lib_layout](lib_layout.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_reads_seqd.md b/mixs6/migs_eu_lib_reads_seqd.md deleted file mode 100644 index 802ae9b6..00000000 --- a/mixs6/migs_eu_lib_reads_seqd.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_lib_reads_seqd - - - - -URI: [mixs.vocab:migs_eu_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_eu_lib_reads_seqd) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_reads_seqd](lib_reads_seqd.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_screen.md b/mixs6/migs_eu_lib_screen.md deleted file mode 100644 index 75f6ce55..00000000 --- a/mixs6/migs_eu_lib_screen.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_lib_screen - - - - -URI: [mixs.vocab:migs_eu_lib_screen](https://w3id.org/mixs/vocab/migs_eu_lib_screen) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_screen](lib_screen.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_size.md b/mixs6/migs_eu_lib_size.md deleted file mode 100644 index 57b3b2f5..00000000 --- a/mixs6/migs_eu_lib_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_lib_size - - - - -URI: [mixs.vocab:migs_eu_lib_size](https://w3id.org/mixs/vocab/migs_eu_lib_size) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_size](lib_size.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_lib_vector.md b/mixs6/migs_eu_lib_vector.md deleted file mode 100644 index 4c4e9180..00000000 --- a/mixs6/migs_eu_lib_vector.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_lib_vector - - - - -URI: [mixs.vocab:migs_eu_lib_vector](https://w3id.org/mixs/vocab/migs_eu_lib_vector) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_vector](lib_vector.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_nucl_acid_amp.md b/mixs6/migs_eu_nucl_acid_amp.md deleted file mode 100644 index ac30966a..00000000 --- a/mixs6/migs_eu_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_nucl_acid_amp - - - - -URI: [mixs.vocab:migs_eu_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_eu_nucl_acid_amp) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_nucl_acid_ext.md b/mixs6/migs_eu_nucl_acid_ext.md deleted file mode 100644 index d12607e1..00000000 --- a/mixs6/migs_eu_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_nucl_acid_ext - - - - -URI: [mixs.vocab:migs_eu_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_eu_nucl_acid_ext) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_num_replicons.md b/mixs6/migs_eu_num_replicons.md deleted file mode 100644 index 54b2e149..00000000 --- a/mixs6/migs_eu_num_replicons.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_num_replicons - - - - -URI: [mixs.vocab:migs_eu_num_replicons](https://w3id.org/mixs/vocab/migs_eu_num_replicons) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [num_replicons](num_replicons.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_number_contig.md b/mixs6/migs_eu_number_contig.md deleted file mode 100644 index fd77b8f2..00000000 --- a/mixs6/migs_eu_number_contig.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_number_contig - - - - -URI: [mixs.vocab:migs_eu_number_contig](https://w3id.org/mixs/vocab/migs_eu_number_contig) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [number_contig](number_contig.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_pathogenicity.md b/mixs6/migs_eu_pathogenicity.md deleted file mode 100644 index a49e6b96..00000000 --- a/mixs6/migs_eu_pathogenicity.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_pathogenicity - - - - -URI: [mixs.vocab:migs_eu_pathogenicity](https://w3id.org/mixs/vocab/migs_eu_pathogenicity) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pathogenicity](pathogenicity.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_ploidy.md b/mixs6/migs_eu_ploidy.md deleted file mode 100644 index 7e8d9385..00000000 --- a/mixs6/migs_eu_ploidy.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_ploidy - - - - -URI: [mixs.vocab:migs_eu_ploidy](https://w3id.org/mixs/vocab/migs_eu_ploidy) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ploidy](ploidy.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_project_name.md b/mixs6/migs_eu_project_name.md deleted file mode 100644 index f45e5ae0..00000000 --- a/mixs6/migs_eu_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_project_name - - - - -URI: [mixs.vocab:migs_eu_project_name](https://w3id.org/mixs/vocab/migs_eu_project_name) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_propagation.md b/mixs6/migs_eu_propagation.md deleted file mode 100644 index 5879bb44..00000000 --- a/mixs6/migs_eu_propagation.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_propagation - - - - -URI: [mixs.vocab:migs_eu_propagation](https://w3id.org/mixs/vocab/migs_eu_propagation) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [propagation](propagation.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_ref_biomaterial.md b/mixs6/migs_eu_ref_biomaterial.md deleted file mode 100644 index f09f5bb4..00000000 --- a/mixs6/migs_eu_ref_biomaterial.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_ref_biomaterial - - - - -URI: [mixs.vocab:migs_eu_ref_biomaterial](https://w3id.org/mixs/vocab/migs_eu_ref_biomaterial) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_biomaterial](ref_biomaterial.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_ref_db.md b/mixs6/migs_eu_ref_db.md deleted file mode 100644 index 52a10dd3..00000000 --- a/mixs6/migs_eu_ref_db.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_ref_db - - - - -URI: [mixs.vocab:migs_eu_ref_db](https://w3id.org/mixs/vocab/migs_eu_ref_db) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_db](ref_db.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_collect_device.md b/mixs6/migs_eu_samp_collect_device.md deleted file mode 100644 index 2c98c723..00000000 --- a/mixs6/migs_eu_samp_collect_device.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_samp_collect_device - - - - -URI: [mixs.vocab:migs_eu_samp_collect_device](https://w3id.org/mixs/vocab/migs_eu_samp_collect_device) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_mat_process.md b/mixs6/migs_eu_samp_mat_process.md deleted file mode 100644 index 04b56a2f..00000000 --- a/mixs6/migs_eu_samp_mat_process.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_samp_mat_process - - - - -URI: [mixs.vocab:migs_eu_samp_mat_process](https://w3id.org/mixs/vocab/migs_eu_samp_mat_process) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_samp_size.md b/mixs6/migs_eu_samp_size.md deleted file mode 100644 index 1864507e..00000000 --- a/mixs6/migs_eu_samp_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_samp_size - - - - -URI: [mixs.vocab:migs_eu_samp_size](https://w3id.org/mixs/vocab/migs_eu_samp_size) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sample_name.md b/mixs6/migs_eu_sample_name.md deleted file mode 100644 index 79acd46f..00000000 --- a/mixs6/migs_eu_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_sample_name - - - - -URI: [mixs.vocab:migs_eu_sample_name](https://w3id.org/mixs/vocab/migs_eu_sample_name) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_seq_meth.md b/mixs6/migs_eu_seq_meth.md deleted file mode 100644 index 6ff99b4c..00000000 --- a/mixs6/migs_eu_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_seq_meth - - - - -URI: [mixs.vocab:migs_eu_seq_meth](https://w3id.org/mixs/vocab/migs_eu_seq_meth) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sim_search_meth.md b/mixs6/migs_eu_sim_search_meth.md deleted file mode 100644 index 5e139a86..00000000 --- a/mixs6/migs_eu_sim_search_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_sim_search_meth - - - - -URI: [mixs.vocab:migs_eu_sim_search_meth](https://w3id.org/mixs/vocab/migs_eu_sim_search_meth) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sim_search_meth](sim_search_meth.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_sop.md b/mixs6/migs_eu_sop.md deleted file mode 100644 index c9299a5e..00000000 --- a/mixs6/migs_eu_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_sop - - - - -URI: [mixs.vocab:migs_eu_sop](https://w3id.org/mixs/vocab/migs_eu_sop) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_source_mat_id.md b/mixs6/migs_eu_source_mat_id.md deleted file mode 100644 index 252c0d41..00000000 --- a/mixs6/migs_eu_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_source_mat_id - - - - -URI: [mixs.vocab:migs_eu_source_mat_id](https://w3id.org/mixs/vocab/migs_eu_source_mat_id) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_specific_host.md b/mixs6/migs_eu_specific_host.md deleted file mode 100644 index 542ac0e4..00000000 --- a/mixs6/migs_eu_specific_host.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_specific_host - - - - -URI: [mixs.vocab:migs_eu_specific_host](https://w3id.org/mixs/vocab/migs_eu_specific_host) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [specific_host](specific_host.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_submitted_to_insdc.md b/mixs6/migs_eu_submitted_to_insdc.md deleted file mode 100644 index 469ff0e4..00000000 --- a/mixs6/migs_eu_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_submitted_to_insdc - - - - -URI: [mixs.vocab:migs_eu_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_eu_submitted_to_insdc) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_subspecf_gen_lin.md b/mixs6/migs_eu_subspecf_gen_lin.md deleted file mode 100644 index 91ea5605..00000000 --- a/mixs6/migs_eu_subspecf_gen_lin.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_subspecf_gen_lin - - - - -URI: [mixs.vocab:migs_eu_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_eu_subspecf_gen_lin) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_tax_class.md b/mixs6/migs_eu_tax_class.md deleted file mode 100644 index 92632da9..00000000 --- a/mixs6/migs_eu_tax_class.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_eu_tax_class - - - - -URI: [mixs.vocab:migs_eu_tax_class](https://w3id.org/mixs/vocab/migs_eu_tax_class) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [tax_class](tax_class.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) diff --git a/mixs6/migs_eu_tax_ident.md b/mixs6/migs_eu_tax_ident.md deleted file mode 100644 index ee9ab943..00000000 --- a/mixs6/migs_eu_tax_ident.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_tax_ident - - - - -URI: [mixs.vocab:migs_eu_tax_ident](https://w3id.org/mixs/vocab/migs_eu_tax_ident) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [tax_ident](tax_ident.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_trophic_level.md b/mixs6/migs_eu_trophic_level.md deleted file mode 100644 index 5c6fac76..00000000 --- a/mixs6/migs_eu_trophic_level.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_trophic_level - - - - -URI: [mixs.vocab:migs_eu_trophic_level](https://w3id.org/mixs/vocab/migs_eu_trophic_level) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT - -## Parents - - * is_a: [trophic_level](trophic_level.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_eu_url.md b/mixs6/migs_eu_url.md deleted file mode 100644 index 6a7a49b6..00000000 --- a/mixs6/migs_eu_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_eu_url - - - - -URI: [mixs.vocab:migs_eu_url](https://w3id.org/mixs/vocab/migs_eu_url) - - -## Domain and Range - -[MigsEu](MigsEu.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMigsEu](AirMigsEu.md) - * [BuiltEnvironmentMigsEu](BuiltEnvironmentMigsEu.md) - * [Host-associatedMigsEu](Host-associatedMigsEu.md) - * [Human-associatedMigsEu](Human-associatedMigsEu.md) - * [Human-gutMigsEu](Human-gutMigsEu.md) - * [Human-oralMigsEu](Human-oralMigsEu.md) - * [Human-skinMigsEu](Human-skinMigsEu.md) - * [Human-vaginalMigsEu](Human-vaginalMigsEu.md) - * [HydrocarbonResources-coresMigsEu](HydrocarbonResources-coresMigsEu.md) - * [HydrocarbonResources-fluidsSwabsMigsEu](HydrocarbonResources-fluidsSwabsMigsEu.md) - * [MicrobialMatBiofilmMigsEu](MicrobialMatBiofilmMigsEu.md) - * [MigsEu](MigsEu.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsEu](MiscellaneousNaturalOrArtificialEnvironmentMigsEu.md) - * [Plant-associatedMigsEu](Plant-associatedMigsEu.md) - * [SedimentMigsEu](SedimentMigsEu.md) - * [SoilMigsEu](SoilMigsEu.md) - * [WastewaterSludgeMigsEu](WastewaterSludgeMigsEu.md) - * [WaterMigsEu](WaterMigsEu.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_org_collection_date.md b/mixs6/migs_org_collection_date.md index ea3647f7..ef25e3a7 100644 --- a/mixs6/migs_org_collection_date.md +++ b/mixs6/migs_org_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_org_collection_date](https://w3id.org/mixs/vocab/MIGS_org_ ## Domain and Range -[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) +[MIGSOrg](MIGSOrg.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/migs_org_sample_name.md b/mixs6/migs_org_sample_name.md index 5e52d127..d4e3f0c3 100644 --- a/mixs6/migs_org_sample_name.md +++ b/mixs6/migs_org_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIGS_org_sample_name](https://w3id.org/mixs/vocab/MIGS_org_samp ## Domain and Range -[MIGSOrg](MIGSOrg.md) -> OPT [String](types/String.md) +[MIGSOrg](MIGSOrg.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/migs_pl_adapters.md b/mixs6/migs_pl_adapters.md deleted file mode 100644 index 944c2422..00000000 --- a/mixs6/migs_pl_adapters.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_adapters - - - - -URI: [mixs.vocab:migs_pl_adapters](https://w3id.org/mixs/vocab/migs_pl_adapters) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [adapters](adapters.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_annot.md b/mixs6/migs_pl_annot.md deleted file mode 100644 index 5b3849c4..00000000 --- a/mixs6/migs_pl_annot.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_annot - - - - -URI: [mixs.vocab:migs_pl_annot](https://w3id.org/mixs/vocab/migs_pl_annot) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [annot](annot.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_assembly_name.md b/mixs6/migs_pl_assembly_name.md deleted file mode 100644 index ca345509..00000000 --- a/mixs6/migs_pl_assembly_name.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_assembly_name - - - - -URI: [mixs.vocab:migs_pl_assembly_name](https://w3id.org/mixs/vocab/migs_pl_assembly_name) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [assembly_name](assembly_name.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_assembly_qual.md b/mixs6/migs_pl_assembly_qual.md deleted file mode 100644 index 645db662..00000000 --- a/mixs6/migs_pl_assembly_qual.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_assembly_qual - - - - -URI: [mixs.vocab:migs_pl_assembly_qual](https://w3id.org/mixs/vocab/migs_pl_assembly_qual) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT - -## Parents - - * is_a: [assembly_qual](assembly_qual.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_assembly_software.md b/mixs6/migs_pl_assembly_software.md deleted file mode 100644 index 7c4c61af..00000000 --- a/mixs6/migs_pl_assembly_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_assembly_software - - - - -URI: [mixs.vocab:migs_pl_assembly_software](https://w3id.org/mixs/vocab/migs_pl_assembly_software) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [assembly_software](assembly_software.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_collection_date.md b/mixs6/migs_pl_collection_date.md deleted file mode 100644 index 58bcba22..00000000 --- a/mixs6/migs_pl_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_collection_date - - - - -URI: [mixs.vocab:migs_pl_collection_date](https://w3id.org/mixs/vocab/migs_pl_collection_date) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_compl_score.md b/mixs6/migs_pl_compl_score.md deleted file mode 100644 index 4bc74c96..00000000 --- a/mixs6/migs_pl_compl_score.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_compl_score - - - - -URI: [mixs.vocab:migs_pl_compl_score](https://w3id.org/mixs/vocab/migs_pl_compl_score) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT - -## Parents - - * is_a: [compl_score](compl_score.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_compl_software.md b/mixs6/migs_pl_compl_software.md deleted file mode 100644 index cfb9b8cb..00000000 --- a/mixs6/migs_pl_compl_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_compl_software - - - - -URI: [mixs.vocab:migs_pl_compl_software](https://w3id.org/mixs/vocab/migs_pl_compl_software) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [compl_software](compl_software.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_encoded_traits.md b/mixs6/migs_pl_encoded_traits.md deleted file mode 100644 index cb56c959..00000000 --- a/mixs6/migs_pl_encoded_traits.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_encoded_traits - - - - -URI: [mixs.vocab:migs_pl_encoded_traits](https://w3id.org/mixs/vocab/migs_pl_encoded_traits) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [encoded_traits](encoded_traits.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_env_broad_scale.md b/mixs6/migs_pl_env_broad_scale.md deleted file mode 100644 index cec8b9ee..00000000 --- a/mixs6/migs_pl_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_env_broad_scale - - - - -URI: [mixs.vocab:migs_pl_env_broad_scale](https://w3id.org/mixs/vocab/migs_pl_env_broad_scale) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_local_scale.md b/mixs6/migs_pl_env_local_scale.md deleted file mode 100644 index a0bbfafd..00000000 --- a/mixs6/migs_pl_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_env_local_scale - - - - -URI: [mixs.vocab:migs_pl_env_local_scale](https://w3id.org/mixs/vocab/migs_pl_env_local_scale) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_medium.md b/mixs6/migs_pl_env_medium.md deleted file mode 100644 index 470e9c8a..00000000 --- a/mixs6/migs_pl_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_env_medium - - - - -URI: [mixs.vocab:migs_pl_env_medium](https://w3id.org/mixs/vocab/migs_pl_env_medium) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_env_package.md b/mixs6/migs_pl_env_package.md deleted file mode 100644 index a73e86d9..00000000 --- a/mixs6/migs_pl_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_env_package - - - - -URI: [mixs.vocab:migs_pl_env_package](https://w3id.org/mixs/vocab/migs_pl_env_package) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_estimated_size.md b/mixs6/migs_pl_estimated_size.md deleted file mode 100644 index 9272d555..00000000 --- a/mixs6/migs_pl_estimated_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_estimated_size - - - - -URI: [mixs.vocab:migs_pl_estimated_size](https://w3id.org/mixs/vocab/migs_pl_estimated_size) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [estimated_size](estimated_size.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_experimental_factor.md b/mixs6/migs_pl_experimental_factor.md deleted file mode 100644 index f9bc24b9..00000000 --- a/mixs6/migs_pl_experimental_factor.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_experimental_factor - - - - -URI: [mixs.vocab:migs_pl_experimental_factor](https://w3id.org/mixs/vocab/migs_pl_experimental_factor) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_feat_pred.md b/mixs6/migs_pl_feat_pred.md deleted file mode 100644 index 96a16907..00000000 --- a/mixs6/migs_pl_feat_pred.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_feat_pred - - - - -URI: [mixs.vocab:migs_pl_feat_pred](https://w3id.org/mixs/vocab/migs_pl_feat_pred) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [feat_pred](feat_pred.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_geo_loc_name.md b/mixs6/migs_pl_geo_loc_name.md deleted file mode 100644 index 16cea806..00000000 --- a/mixs6/migs_pl_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_geo_loc_name - - - - -URI: [mixs.vocab:migs_pl_geo_loc_name](https://w3id.org/mixs/vocab/migs_pl_geo_loc_name) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_host_spec_range.md b/mixs6/migs_pl_host_spec_range.md deleted file mode 100644 index 3be75f87..00000000 --- a/mixs6/migs_pl_host_spec_range.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_host_spec_range - - - - -URI: [mixs.vocab:migs_pl_host_spec_range](https://w3id.org/mixs/vocab/migs_pl_host_spec_range) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [host_spec_range](host_spec_range.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_investigation_type.md b/mixs6/migs_pl_investigation_type.md deleted file mode 100644 index c4a61019..00000000 --- a/mixs6/migs_pl_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_investigation_type - - - - -URI: [mixs.vocab:migs_pl_investigation_type](https://w3id.org/mixs/vocab/migs_pl_investigation_type) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_isol_growth_condt.md b/mixs6/migs_pl_isol_growth_condt.md deleted file mode 100644 index 1d02df0f..00000000 --- a/mixs6/migs_pl_isol_growth_condt.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_isol_growth_condt - - - - -URI: [mixs.vocab:migs_pl_isol_growth_condt](https://w3id.org/mixs/vocab/migs_pl_isol_growth_condt) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [isol_growth_condt](isol_growth_condt.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lat_lon.md b/mixs6/migs_pl_lat_lon.md deleted file mode 100644 index 9734ed6f..00000000 --- a/mixs6/migs_pl_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_pl_lat_lon - - - - -URI: [mixs.vocab:migs_pl_lat_lon](https://w3id.org/mixs/vocab/migs_pl_lat_lon) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MigsPl](MigsPl.md) diff --git a/mixs6/migs_pl_lib_layout.md b/mixs6/migs_pl_lib_layout.md deleted file mode 100644 index 86d02d4e..00000000 --- a/mixs6/migs_pl_lib_layout.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_lib_layout - - - - -URI: [mixs.vocab:migs_pl_lib_layout](https://w3id.org/mixs/vocab/migs_pl_lib_layout) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT - -## Parents - - * is_a: [lib_layout](lib_layout.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_reads_seqd.md b/mixs6/migs_pl_lib_reads_seqd.md deleted file mode 100644 index 22d638a4..00000000 --- a/mixs6/migs_pl_lib_reads_seqd.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_lib_reads_seqd - - - - -URI: [mixs.vocab:migs_pl_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_pl_lib_reads_seqd) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_reads_seqd](lib_reads_seqd.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_screen.md b/mixs6/migs_pl_lib_screen.md deleted file mode 100644 index 5dadacba..00000000 --- a/mixs6/migs_pl_lib_screen.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_lib_screen - - - - -URI: [mixs.vocab:migs_pl_lib_screen](https://w3id.org/mixs/vocab/migs_pl_lib_screen) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_screen](lib_screen.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_size.md b/mixs6/migs_pl_lib_size.md deleted file mode 100644 index 43e18625..00000000 --- a/mixs6/migs_pl_lib_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_lib_size - - - - -URI: [mixs.vocab:migs_pl_lib_size](https://w3id.org/mixs/vocab/migs_pl_lib_size) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_size](lib_size.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_lib_vector.md b/mixs6/migs_pl_lib_vector.md deleted file mode 100644 index 43c2db4f..00000000 --- a/mixs6/migs_pl_lib_vector.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_lib_vector - - - - -URI: [mixs.vocab:migs_pl_lib_vector](https://w3id.org/mixs/vocab/migs_pl_lib_vector) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_vector](lib_vector.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_nucl_acid_amp.md b/mixs6/migs_pl_nucl_acid_amp.md deleted file mode 100644 index 0d12aac3..00000000 --- a/mixs6/migs_pl_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_nucl_acid_amp - - - - -URI: [mixs.vocab:migs_pl_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_pl_nucl_acid_amp) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_nucl_acid_ext.md b/mixs6/migs_pl_nucl_acid_ext.md deleted file mode 100644 index a9ced933..00000000 --- a/mixs6/migs_pl_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_nucl_acid_ext - - - - -URI: [mixs.vocab:migs_pl_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_pl_nucl_acid_ext) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_number_contig.md b/mixs6/migs_pl_number_contig.md deleted file mode 100644 index 9d503dda..00000000 --- a/mixs6/migs_pl_number_contig.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_number_contig - - - - -URI: [mixs.vocab:migs_pl_number_contig](https://w3id.org/mixs/vocab/migs_pl_number_contig) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [number_contig](number_contig.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_project_name.md b/mixs6/migs_pl_project_name.md deleted file mode 100644 index 996c6ad3..00000000 --- a/mixs6/migs_pl_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_project_name - - - - -URI: [mixs.vocab:migs_pl_project_name](https://w3id.org/mixs/vocab/migs_pl_project_name) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_propagation.md b/mixs6/migs_pl_propagation.md deleted file mode 100644 index ae2cac79..00000000 --- a/mixs6/migs_pl_propagation.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_propagation - - - - -URI: [mixs.vocab:migs_pl_propagation](https://w3id.org/mixs/vocab/migs_pl_propagation) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [propagation](propagation.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_ref_biomaterial.md b/mixs6/migs_pl_ref_biomaterial.md deleted file mode 100644 index 6c766345..00000000 --- a/mixs6/migs_pl_ref_biomaterial.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_ref_biomaterial - - - - -URI: [mixs.vocab:migs_pl_ref_biomaterial](https://w3id.org/mixs/vocab/migs_pl_ref_biomaterial) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_biomaterial](ref_biomaterial.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_ref_db.md b/mixs6/migs_pl_ref_db.md deleted file mode 100644 index 6de82e45..00000000 --- a/mixs6/migs_pl_ref_db.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_ref_db - - - - -URI: [mixs.vocab:migs_pl_ref_db](https://w3id.org/mixs/vocab/migs_pl_ref_db) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_db](ref_db.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_collect_device.md b/mixs6/migs_pl_samp_collect_device.md deleted file mode 100644 index 8d164472..00000000 --- a/mixs6/migs_pl_samp_collect_device.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_samp_collect_device - - - - -URI: [mixs.vocab:migs_pl_samp_collect_device](https://w3id.org/mixs/vocab/migs_pl_samp_collect_device) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_mat_process.md b/mixs6/migs_pl_samp_mat_process.md deleted file mode 100644 index 64420e94..00000000 --- a/mixs6/migs_pl_samp_mat_process.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_samp_mat_process - - - - -URI: [mixs.vocab:migs_pl_samp_mat_process](https://w3id.org/mixs/vocab/migs_pl_samp_mat_process) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_samp_size.md b/mixs6/migs_pl_samp_size.md deleted file mode 100644 index a028a032..00000000 --- a/mixs6/migs_pl_samp_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_samp_size - - - - -URI: [mixs.vocab:migs_pl_samp_size](https://w3id.org/mixs/vocab/migs_pl_samp_size) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sample_name.md b/mixs6/migs_pl_sample_name.md deleted file mode 100644 index 7f48e3ee..00000000 --- a/mixs6/migs_pl_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_sample_name - - - - -URI: [mixs.vocab:migs_pl_sample_name](https://w3id.org/mixs/vocab/migs_pl_sample_name) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_seq_meth.md b/mixs6/migs_pl_seq_meth.md deleted file mode 100644 index 88490b4d..00000000 --- a/mixs6/migs_pl_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_seq_meth - - - - -URI: [mixs.vocab:migs_pl_seq_meth](https://w3id.org/mixs/vocab/migs_pl_seq_meth) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sim_search_meth.md b/mixs6/migs_pl_sim_search_meth.md deleted file mode 100644 index 04219948..00000000 --- a/mixs6/migs_pl_sim_search_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_sim_search_meth - - - - -URI: [mixs.vocab:migs_pl_sim_search_meth](https://w3id.org/mixs/vocab/migs_pl_sim_search_meth) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sim_search_meth](sim_search_meth.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_sop.md b/mixs6/migs_pl_sop.md deleted file mode 100644 index b5dc7e06..00000000 --- a/mixs6/migs_pl_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_sop - - - - -URI: [mixs.vocab:migs_pl_sop](https://w3id.org/mixs/vocab/migs_pl_sop) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_source_mat_id.md b/mixs6/migs_pl_source_mat_id.md deleted file mode 100644 index 8db66956..00000000 --- a/mixs6/migs_pl_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_source_mat_id - - - - -URI: [mixs.vocab:migs_pl_source_mat_id](https://w3id.org/mixs/vocab/migs_pl_source_mat_id) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_specific_host.md b/mixs6/migs_pl_specific_host.md deleted file mode 100644 index 9b9051a5..00000000 --- a/mixs6/migs_pl_specific_host.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_specific_host - - - - -URI: [mixs.vocab:migs_pl_specific_host](https://w3id.org/mixs/vocab/migs_pl_specific_host) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [specific_host](specific_host.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_submitted_to_insdc.md b/mixs6/migs_pl_submitted_to_insdc.md deleted file mode 100644 index 0b12e93d..00000000 --- a/mixs6/migs_pl_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_submitted_to_insdc - - - - -URI: [mixs.vocab:migs_pl_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_pl_submitted_to_insdc) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_subspecf_gen_lin.md b/mixs6/migs_pl_subspecf_gen_lin.md deleted file mode 100644 index 15c0df49..00000000 --- a/mixs6/migs_pl_subspecf_gen_lin.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_subspecf_gen_lin - - - - -URI: [mixs.vocab:migs_pl_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_pl_subspecf_gen_lin) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_tax_class.md b/mixs6/migs_pl_tax_class.md deleted file mode 100644 index 89cb9134..00000000 --- a/mixs6/migs_pl_tax_class.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_pl_tax_class - - - - -URI: [mixs.vocab:migs_pl_tax_class](https://w3id.org/mixs/vocab/migs_pl_tax_class) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [tax_class](tax_class.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) diff --git a/mixs6/migs_pl_tax_ident.md b/mixs6/migs_pl_tax_ident.md deleted file mode 100644 index 0f48b229..00000000 --- a/mixs6/migs_pl_tax_ident.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_tax_ident - - - - -URI: [mixs.vocab:migs_pl_tax_ident](https://w3id.org/mixs/vocab/migs_pl_tax_ident) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT - -## Parents - - * is_a: [tax_ident](tax_ident.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_pl_url.md b/mixs6/migs_pl_url.md deleted file mode 100644 index b1bee8c2..00000000 --- a/mixs6/migs_pl_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_pl_url - - - - -URI: [mixs.vocab:migs_pl_url](https://w3id.org/mixs/vocab/migs_pl_url) - - -## Domain and Range - -[MigsPl](MigsPl.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMigsPl](AirMigsPl.md) - * [BuiltEnvironmentMigsPl](BuiltEnvironmentMigsPl.md) - * [Host-associatedMigsPl](Host-associatedMigsPl.md) - * [Human-associatedMigsPl](Human-associatedMigsPl.md) - * [Human-gutMigsPl](Human-gutMigsPl.md) - * [Human-oralMigsPl](Human-oralMigsPl.md) - * [Human-skinMigsPl](Human-skinMigsPl.md) - * [Human-vaginalMigsPl](Human-vaginalMigsPl.md) - * [HydrocarbonResources-coresMigsPl](HydrocarbonResources-coresMigsPl.md) - * [HydrocarbonResources-fluidsSwabsMigsPl](HydrocarbonResources-fluidsSwabsMigsPl.md) - * [MicrobialMatBiofilmMigsPl](MicrobialMatBiofilmMigsPl.md) - * [MigsPl](MigsPl.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsPl](MiscellaneousNaturalOrArtificialEnvironmentMigsPl.md) - * [Plant-associatedMigsPl](Plant-associatedMigsPl.md) - * [SedimentMigsPl](SedimentMigsPl.md) - * [SoilMigsPl](SoilMigsPl.md) - * [WastewaterSludgeMigsPl](WastewaterSludgeMigsPl.md) - * [WaterMigsPl](WaterMigsPl.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_adapters.md b/mixs6/migs_vi_adapters.md deleted file mode 100644 index efdf0cb6..00000000 --- a/mixs6/migs_vi_adapters.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_adapters - - - - -URI: [mixs.vocab:migs_vi_adapters](https://w3id.org/mixs/vocab/migs_vi_adapters) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [adapters](adapters.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_annot.md b/mixs6/migs_vi_annot.md deleted file mode 100644 index fb2c3632..00000000 --- a/mixs6/migs_vi_annot.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_annot - - - - -URI: [mixs.vocab:migs_vi_annot](https://w3id.org/mixs/vocab/migs_vi_annot) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [annot](annot.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_assembly_name.md b/mixs6/migs_vi_assembly_name.md deleted file mode 100644 index 736d5151..00000000 --- a/mixs6/migs_vi_assembly_name.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_assembly_name - - - - -URI: [mixs.vocab:migs_vi_assembly_name](https://w3id.org/mixs/vocab/migs_vi_assembly_name) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [assembly_name](assembly_name.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_assembly_qual.md b/mixs6/migs_vi_assembly_qual.md deleted file mode 100644 index 5453b781..00000000 --- a/mixs6/migs_vi_assembly_qual.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_assembly_qual - - - - -URI: [mixs.vocab:migs_vi_assembly_qual](https://w3id.org/mixs/vocab/migs_vi_assembly_qual) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [assembly_qual](assembly_qual.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_assembly_software.md b/mixs6/migs_vi_assembly_software.md deleted file mode 100644 index 87ff40ad..00000000 --- a/mixs6/migs_vi_assembly_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_assembly_software - - - - -URI: [mixs.vocab:migs_vi_assembly_software](https://w3id.org/mixs/vocab/migs_vi_assembly_software) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [assembly_software](assembly_software.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_biotic_relationship.md b/mixs6/migs_vi_biotic_relationship.md deleted file mode 100644 index e721549e..00000000 --- a/mixs6/migs_vi_biotic_relationship.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_biotic_relationship - - - - -URI: [mixs.vocab:migs_vi_biotic_relationship](https://w3id.org/mixs/vocab/migs_vi_biotic_relationship) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [biotic_relationship](biotic_relationship.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_collection_date.md b/mixs6/migs_vi_collection_date.md deleted file mode 100644 index 659f29d4..00000000 --- a/mixs6/migs_vi_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_collection_date - - - - -URI: [mixs.vocab:migs_vi_collection_date](https://w3id.org/mixs/vocab/migs_vi_collection_date) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_compl_score.md b/mixs6/migs_vi_compl_score.md deleted file mode 100644 index c9b27db7..00000000 --- a/mixs6/migs_vi_compl_score.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_compl_score - - - - -URI: [mixs.vocab:migs_vi_compl_score](https://w3id.org/mixs/vocab/migs_vi_compl_score) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [compl_score](compl_score.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_compl_software.md b/mixs6/migs_vi_compl_software.md deleted file mode 100644 index c98a0c06..00000000 --- a/mixs6/migs_vi_compl_software.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_compl_software - - - - -URI: [mixs.vocab:migs_vi_compl_software](https://w3id.org/mixs/vocab/migs_vi_compl_software) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [compl_software](compl_software.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_encoded_traits.md b/mixs6/migs_vi_encoded_traits.md deleted file mode 100644 index 7d318a7e..00000000 --- a/mixs6/migs_vi_encoded_traits.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_encoded_traits - - - - -URI: [mixs.vocab:migs_vi_encoded_traits](https://w3id.org/mixs/vocab/migs_vi_encoded_traits) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [encoded_traits](encoded_traits.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_env_broad_scale.md b/mixs6/migs_vi_env_broad_scale.md deleted file mode 100644 index 90179a66..00000000 --- a/mixs6/migs_vi_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_env_broad_scale - - - - -URI: [mixs.vocab:migs_vi_env_broad_scale](https://w3id.org/mixs/vocab/migs_vi_env_broad_scale) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_local_scale.md b/mixs6/migs_vi_env_local_scale.md deleted file mode 100644 index b274d51c..00000000 --- a/mixs6/migs_vi_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_env_local_scale - - - - -URI: [mixs.vocab:migs_vi_env_local_scale](https://w3id.org/mixs/vocab/migs_vi_env_local_scale) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_medium.md b/mixs6/migs_vi_env_medium.md deleted file mode 100644 index 03d4a7af..00000000 --- a/mixs6/migs_vi_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_env_medium - - - - -URI: [mixs.vocab:migs_vi_env_medium](https://w3id.org/mixs/vocab/migs_vi_env_medium) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_env_package.md b/mixs6/migs_vi_env_package.md deleted file mode 100644 index e4b1d1e9..00000000 --- a/mixs6/migs_vi_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_env_package - - - - -URI: [mixs.vocab:migs_vi_env_package](https://w3id.org/mixs/vocab/migs_vi_env_package) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_estimated_size.md b/mixs6/migs_vi_estimated_size.md deleted file mode 100644 index 5aebe8c3..00000000 --- a/mixs6/migs_vi_estimated_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_estimated_size - - - - -URI: [mixs.vocab:migs_vi_estimated_size](https://w3id.org/mixs/vocab/migs_vi_estimated_size) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [estimated_size](estimated_size.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_experimental_factor.md b/mixs6/migs_vi_experimental_factor.md deleted file mode 100644 index 87c4f7ab..00000000 --- a/mixs6/migs_vi_experimental_factor.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_experimental_factor - - - - -URI: [mixs.vocab:migs_vi_experimental_factor](https://w3id.org/mixs/vocab/migs_vi_experimental_factor) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_feat_pred.md b/mixs6/migs_vi_feat_pred.md deleted file mode 100644 index e6b3da8f..00000000 --- a/mixs6/migs_vi_feat_pred.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_feat_pred - - - - -URI: [mixs.vocab:migs_vi_feat_pred](https://w3id.org/mixs/vocab/migs_vi_feat_pred) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [feat_pred](feat_pred.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_geo_loc_name.md b/mixs6/migs_vi_geo_loc_name.md deleted file mode 100644 index e9710dbe..00000000 --- a/mixs6/migs_vi_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_geo_loc_name - - - - -URI: [mixs.vocab:migs_vi_geo_loc_name](https://w3id.org/mixs/vocab/migs_vi_geo_loc_name) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_health_disease_stat.md b/mixs6/migs_vi_health_disease_stat.md deleted file mode 100644 index 5fa7d4c5..00000000 --- a/mixs6/migs_vi_health_disease_stat.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_health_disease_stat - - - - -URI: [mixs.vocab:migs_vi_health_disease_stat](https://w3id.org/mixs/vocab/migs_vi_health_disease_stat) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [health_disease_stat](health_disease_stat.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_host_spec_range.md b/mixs6/migs_vi_host_spec_range.md deleted file mode 100644 index 4a5d3190..00000000 --- a/mixs6/migs_vi_host_spec_range.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_host_spec_range - - - - -URI: [mixs.vocab:migs_vi_host_spec_range](https://w3id.org/mixs/vocab/migs_vi_host_spec_range) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [host_spec_range](host_spec_range.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_investigation_type.md b/mixs6/migs_vi_investigation_type.md deleted file mode 100644 index 2c56ce70..00000000 --- a/mixs6/migs_vi_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_investigation_type - - - - -URI: [mixs.vocab:migs_vi_investigation_type](https://w3id.org/mixs/vocab/migs_vi_investigation_type) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_isol_growth_condt.md b/mixs6/migs_vi_isol_growth_condt.md deleted file mode 100644 index 13fb2b04..00000000 --- a/mixs6/migs_vi_isol_growth_condt.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_isol_growth_condt - - - - -URI: [mixs.vocab:migs_vi_isol_growth_condt](https://w3id.org/mixs/vocab/migs_vi_isol_growth_condt) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [isol_growth_condt](isol_growth_condt.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lat_lon.md b/mixs6/migs_vi_lat_lon.md deleted file mode 100644 index b0e195f1..00000000 --- a/mixs6/migs_vi_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: migs_vi_lat_lon - - - - -URI: [mixs.vocab:migs_vi_lat_lon](https://w3id.org/mixs/vocab/migs_vi_lat_lon) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MigsVi](MigsVi.md) diff --git a/mixs6/migs_vi_lib_layout.md b/mixs6/migs_vi_lib_layout.md deleted file mode 100644 index 2def1775..00000000 --- a/mixs6/migs_vi_lib_layout.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_lib_layout - - - - -URI: [mixs.vocab:migs_vi_lib_layout](https://w3id.org/mixs/vocab/migs_vi_lib_layout) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [lib_layout](lib_layout.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_reads_seqd.md b/mixs6/migs_vi_lib_reads_seqd.md deleted file mode 100644 index 8a9dfebe..00000000 --- a/mixs6/migs_vi_lib_reads_seqd.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_lib_reads_seqd - - - - -URI: [mixs.vocab:migs_vi_lib_reads_seqd](https://w3id.org/mixs/vocab/migs_vi_lib_reads_seqd) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_reads_seqd](lib_reads_seqd.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_screen.md b/mixs6/migs_vi_lib_screen.md deleted file mode 100644 index fd862f04..00000000 --- a/mixs6/migs_vi_lib_screen.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_lib_screen - - - - -URI: [mixs.vocab:migs_vi_lib_screen](https://w3id.org/mixs/vocab/migs_vi_lib_screen) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_screen](lib_screen.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_size.md b/mixs6/migs_vi_lib_size.md deleted file mode 100644 index df2b6dce..00000000 --- a/mixs6/migs_vi_lib_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_lib_size - - - - -URI: [mixs.vocab:migs_vi_lib_size](https://w3id.org/mixs/vocab/migs_vi_lib_size) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_size](lib_size.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_lib_vector.md b/mixs6/migs_vi_lib_vector.md deleted file mode 100644 index 24de264c..00000000 --- a/mixs6/migs_vi_lib_vector.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_lib_vector - - - - -URI: [mixs.vocab:migs_vi_lib_vector](https://w3id.org/mixs/vocab/migs_vi_lib_vector) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_vector](lib_vector.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_nucl_acid_amp.md b/mixs6/migs_vi_nucl_acid_amp.md deleted file mode 100644 index fd54de7e..00000000 --- a/mixs6/migs_vi_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_nucl_acid_amp - - - - -URI: [mixs.vocab:migs_vi_nucl_acid_amp](https://w3id.org/mixs/vocab/migs_vi_nucl_acid_amp) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_nucl_acid_ext.md b/mixs6/migs_vi_nucl_acid_ext.md deleted file mode 100644 index a00e5ede..00000000 --- a/mixs6/migs_vi_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_nucl_acid_ext - - - - -URI: [mixs.vocab:migs_vi_nucl_acid_ext](https://w3id.org/mixs/vocab/migs_vi_nucl_acid_ext) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_num_replicons.md b/mixs6/migs_vi_num_replicons.md deleted file mode 100644 index 5e6749b2..00000000 --- a/mixs6/migs_vi_num_replicons.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_num_replicons - - - - -URI: [mixs.vocab:migs_vi_num_replicons](https://w3id.org/mixs/vocab/migs_vi_num_replicons) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [num_replicons](num_replicons.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_number_contig.md b/mixs6/migs_vi_number_contig.md deleted file mode 100644 index 82e79e12..00000000 --- a/mixs6/migs_vi_number_contig.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_number_contig - - - - -URI: [mixs.vocab:migs_vi_number_contig](https://w3id.org/mixs/vocab/migs_vi_number_contig) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [number_contig](number_contig.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_pathogenicity.md b/mixs6/migs_vi_pathogenicity.md deleted file mode 100644 index 0a9e7b93..00000000 --- a/mixs6/migs_vi_pathogenicity.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_pathogenicity - - - - -URI: [mixs.vocab:migs_vi_pathogenicity](https://w3id.org/mixs/vocab/migs_vi_pathogenicity) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pathogenicity](pathogenicity.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_project_name.md b/mixs6/migs_vi_project_name.md deleted file mode 100644 index b0315090..00000000 --- a/mixs6/migs_vi_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_project_name - - - - -URI: [mixs.vocab:migs_vi_project_name](https://w3id.org/mixs/vocab/migs_vi_project_name) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_propagation.md b/mixs6/migs_vi_propagation.md deleted file mode 100644 index 4ff00178..00000000 --- a/mixs6/migs_vi_propagation.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_propagation - - - - -URI: [mixs.vocab:migs_vi_propagation](https://w3id.org/mixs/vocab/migs_vi_propagation) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [propagation](propagation.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_ref_biomaterial.md b/mixs6/migs_vi_ref_biomaterial.md deleted file mode 100644 index e19d83fa..00000000 --- a/mixs6/migs_vi_ref_biomaterial.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_ref_biomaterial - - - - -URI: [mixs.vocab:migs_vi_ref_biomaterial](https://w3id.org/mixs/vocab/migs_vi_ref_biomaterial) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_biomaterial](ref_biomaterial.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_ref_db.md b/mixs6/migs_vi_ref_db.md deleted file mode 100644 index a91a4e21..00000000 --- a/mixs6/migs_vi_ref_db.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_ref_db - - - - -URI: [mixs.vocab:migs_vi_ref_db](https://w3id.org/mixs/vocab/migs_vi_ref_db) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [ref_db](ref_db.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_collect_device.md b/mixs6/migs_vi_samp_collect_device.md deleted file mode 100644 index fdc01030..00000000 --- a/mixs6/migs_vi_samp_collect_device.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_samp_collect_device - - - - -URI: [mixs.vocab:migs_vi_samp_collect_device](https://w3id.org/mixs/vocab/migs_vi_samp_collect_device) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_mat_process.md b/mixs6/migs_vi_samp_mat_process.md deleted file mode 100644 index d67bdf69..00000000 --- a/mixs6/migs_vi_samp_mat_process.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_samp_mat_process - - - - -URI: [mixs.vocab:migs_vi_samp_mat_process](https://w3id.org/mixs/vocab/migs_vi_samp_mat_process) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_samp_size.md b/mixs6/migs_vi_samp_size.md deleted file mode 100644 index cc7cc740..00000000 --- a/mixs6/migs_vi_samp_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_samp_size - - - - -URI: [mixs.vocab:migs_vi_samp_size](https://w3id.org/mixs/vocab/migs_vi_samp_size) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sample_name.md b/mixs6/migs_vi_sample_name.md deleted file mode 100644 index 29ac0ecf..00000000 --- a/mixs6/migs_vi_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_sample_name - - - - -URI: [mixs.vocab:migs_vi_sample_name](https://w3id.org/mixs/vocab/migs_vi_sample_name) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_seq_meth.md b/mixs6/migs_vi_seq_meth.md deleted file mode 100644 index 2eff2c0e..00000000 --- a/mixs6/migs_vi_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_seq_meth - - - - -URI: [mixs.vocab:migs_vi_seq_meth](https://w3id.org/mixs/vocab/migs_vi_seq_meth) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sim_search_meth.md b/mixs6/migs_vi_sim_search_meth.md deleted file mode 100644 index 1ce26ef0..00000000 --- a/mixs6/migs_vi_sim_search_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_sim_search_meth - - - - -URI: [mixs.vocab:migs_vi_sim_search_meth](https://w3id.org/mixs/vocab/migs_vi_sim_search_meth) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sim_search_meth](sim_search_meth.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_sop.md b/mixs6/migs_vi_sop.md deleted file mode 100644 index 4698f009..00000000 --- a/mixs6/migs_vi_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_sop - - - - -URI: [mixs.vocab:migs_vi_sop](https://w3id.org/mixs/vocab/migs_vi_sop) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_source_mat_id.md b/mixs6/migs_vi_source_mat_id.md deleted file mode 100644 index 473569c4..00000000 --- a/mixs6/migs_vi_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_source_mat_id - - - - -URI: [mixs.vocab:migs_vi_source_mat_id](https://w3id.org/mixs/vocab/migs_vi_source_mat_id) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_specific_host.md b/mixs6/migs_vi_specific_host.md deleted file mode 100644 index 9028a162..00000000 --- a/mixs6/migs_vi_specific_host.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_specific_host - - - - -URI: [mixs.vocab:migs_vi_specific_host](https://w3id.org/mixs/vocab/migs_vi_specific_host) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [specific_host](specific_host.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_submitted_to_insdc.md b/mixs6/migs_vi_submitted_to_insdc.md deleted file mode 100644 index 59d3c3e4..00000000 --- a/mixs6/migs_vi_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_submitted_to_insdc - - - - -URI: [mixs.vocab:migs_vi_submitted_to_insdc](https://w3id.org/mixs/vocab/migs_vi_submitted_to_insdc) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_subspecf_gen_lin.md b/mixs6/migs_vi_subspecf_gen_lin.md deleted file mode 100644 index c9b3d5ee..00000000 --- a/mixs6/migs_vi_subspecf_gen_lin.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_subspecf_gen_lin - - - - -URI: [mixs.vocab:migs_vi_subspecf_gen_lin](https://w3id.org/mixs/vocab/migs_vi_subspecf_gen_lin) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_tax_class.md b/mixs6/migs_vi_tax_class.md deleted file mode 100644 index 0faa9072..00000000 --- a/mixs6/migs_vi_tax_class.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: migs_vi_tax_class - - - - -URI: [mixs.vocab:migs_vi_tax_class](https://w3id.org/mixs/vocab/migs_vi_tax_class) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [tax_class](tax_class.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) diff --git a/mixs6/migs_vi_tax_ident.md b/mixs6/migs_vi_tax_ident.md deleted file mode 100644 index 2fc7500b..00000000 --- a/mixs6/migs_vi_tax_ident.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_tax_ident - - - - -URI: [mixs.vocab:migs_vi_tax_ident](https://w3id.org/mixs/vocab/migs_vi_tax_ident) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [tax_ident](tax_ident.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_url.md b/mixs6/migs_vi_url.md deleted file mode 100644 index dcf986ec..00000000 --- a/mixs6/migs_vi_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_url - - - - -URI: [mixs.vocab:migs_vi_url](https://w3id.org/mixs/vocab/migs_vi_url) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/migs_vi_virus_enrich_appr.md b/mixs6/migs_vi_virus_enrich_appr.md deleted file mode 100644 index 83390996..00000000 --- a/mixs6/migs_vi_virus_enrich_appr.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: migs_vi_virus_enrich_appr - - - - -URI: [mixs.vocab:migs_vi_virus_enrich_appr](https://w3id.org/mixs/vocab/migs_vi_virus_enrich_appr) - - -## Domain and Range - -[MigsVi](MigsVi.md) -> OPT - -## Parents - - * is_a: [virus_enrich_appr](virus_enrich_appr.md) - -## Children - - -## Used by - - * [AirMigsVi](AirMigsVi.md) - * [BuiltEnvironmentMigsVi](BuiltEnvironmentMigsVi.md) - * [Host-associatedMigsVi](Host-associatedMigsVi.md) - * [Human-associatedMigsVi](Human-associatedMigsVi.md) - * [Human-gutMigsVi](Human-gutMigsVi.md) - * [Human-oralMigsVi](Human-oralMigsVi.md) - * [Human-skinMigsVi](Human-skinMigsVi.md) - * [Human-vaginalMigsVi](Human-vaginalMigsVi.md) - * [HydrocarbonResources-coresMigsVi](HydrocarbonResources-coresMigsVi.md) - * [HydrocarbonResources-fluidsSwabsMigsVi](HydrocarbonResources-fluidsSwabsMigsVi.md) - * [MicrobialMatBiofilmMigsVi](MicrobialMatBiofilmMigsVi.md) - * [MigsVi](MigsVi.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMigsVi](MiscellaneousNaturalOrArtificialEnvironmentMigsVi.md) - * [Plant-associatedMigsVi](Plant-associatedMigsVi.md) - * [SedimentMigsVi](SedimentMigsVi.md) - * [SoilMigsVi](SoilMigsVi.md) - * [WastewaterSludgeMigsVi](WastewaterSludgeMigsVi.md) - * [WaterMigsVi](WaterMigsVi.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimag_collection_date.md b/mixs6/mimag_collection_date.md index e5500089..6aaedfb9 100644 --- a/mixs6/mimag_collection_date.md +++ b/mixs6/mimag_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMAG_collection_date](https://w3id.org/mixs/vocab/MIMAG_collec ## Domain and Range -[MIMAG](MIMAG.md) -> REQ [String](types/String.md) +[MIMAG](MIMAG.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/mimag_sample_name.md b/mixs6/mimag_sample_name.md index a73fa25e..a150cce3 100644 --- a/mixs6/mimag_sample_name.md +++ b/mixs6/mimag_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIMAG_sample_name](https://w3id.org/mixs/vocab/MIMAG_sample_nam ## Domain and Range -[MIMAG](MIMAG.md) -> OPT [String](types/String.md) +[MIMAG](MIMAG.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/mimarks_c_biotic_relationship.md b/mixs6/mimarks_c_biotic_relationship.md deleted file mode 100644 index 9350b59f..00000000 --- a/mixs6/mimarks_c_biotic_relationship.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_biotic_relationship - - - - -URI: [mixs.vocab:mimarks_c_biotic_relationship](https://w3id.org/mixs/vocab/mimarks_c_biotic_relationship) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT - -## Parents - - * is_a: [biotic_relationship](biotic_relationship.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_chimera_check.md b/mixs6/mimarks_c_chimera_check.md deleted file mode 100644 index 8acfe8fa..00000000 --- a/mixs6/mimarks_c_chimera_check.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_chimera_check - - - - -URI: [mixs.vocab:mimarks_c_chimera_check](https://w3id.org/mixs/vocab/mimarks_c_chimera_check) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [chimera_check](chimera_check.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_collection_date.md b/mixs6/mimarks_c_collection_date.md deleted file mode 100644 index 1d90d71d..00000000 --- a/mixs6/mimarks_c_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_collection_date - - - - -URI: [mixs.vocab:mimarks_c_collection_date](https://w3id.org/mixs/vocab/mimarks_c_collection_date) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_broad_scale.md b/mixs6/mimarks_c_env_broad_scale.md deleted file mode 100644 index 5df4a781..00000000 --- a/mixs6/mimarks_c_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_env_broad_scale - - - - -URI: [mixs.vocab:mimarks_c_env_broad_scale](https://w3id.org/mixs/vocab/mimarks_c_env_broad_scale) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_local_scale.md b/mixs6/mimarks_c_env_local_scale.md deleted file mode 100644 index efa8b90c..00000000 --- a/mixs6/mimarks_c_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_env_local_scale - - - - -URI: [mixs.vocab:mimarks_c_env_local_scale](https://w3id.org/mixs/vocab/mimarks_c_env_local_scale) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_medium.md b/mixs6/mimarks_c_env_medium.md deleted file mode 100644 index 1249b0d5..00000000 --- a/mixs6/mimarks_c_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_env_medium - - - - -URI: [mixs.vocab:mimarks_c_env_medium](https://w3id.org/mixs/vocab/mimarks_c_env_medium) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_env_package.md b/mixs6/mimarks_c_env_package.md deleted file mode 100644 index ebf7d669..00000000 --- a/mixs6/mimarks_c_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_env_package - - - - -URI: [mixs.vocab:mimarks_c_env_package](https://w3id.org/mixs/vocab/mimarks_c_env_package) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_experimental_factor.md b/mixs6/mimarks_c_experimental_factor.md deleted file mode 100644 index f00839f8..00000000 --- a/mixs6/mimarks_c_experimental_factor.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_experimental_factor - - - - -URI: [mixs.vocab:mimarks_c_experimental_factor](https://w3id.org/mixs/vocab/mimarks_c_experimental_factor) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_extrachrom_elements.md b/mixs6/mimarks_c_extrachrom_elements.md deleted file mode 100644 index 6fd2d180..00000000 --- a/mixs6/mimarks_c_extrachrom_elements.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_extrachrom_elements - - - - -URI: [mixs.vocab:mimarks_c_extrachrom_elements](https://w3id.org/mixs/vocab/mimarks_c_extrachrom_elements) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [extrachrom_elements](extrachrom_elements.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_geo_loc_name.md b/mixs6/mimarks_c_geo_loc_name.md deleted file mode 100644 index bbd3cef2..00000000 --- a/mixs6/mimarks_c_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_geo_loc_name - - - - -URI: [mixs.vocab:mimarks_c_geo_loc_name](https://w3id.org/mixs/vocab/mimarks_c_geo_loc_name) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_investigation_type.md b/mixs6/mimarks_c_investigation_type.md deleted file mode 100644 index e5f4009c..00000000 --- a/mixs6/mimarks_c_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_investigation_type - - - - -URI: [mixs.vocab:mimarks_c_investigation_type](https://w3id.org/mixs/vocab/mimarks_c_investigation_type) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_isol_growth_condt.md b/mixs6/mimarks_c_isol_growth_condt.md deleted file mode 100644 index 32f03ddb..00000000 --- a/mixs6/mimarks_c_isol_growth_condt.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_isol_growth_condt - - - - -URI: [mixs.vocab:mimarks_c_isol_growth_condt](https://w3id.org/mixs/vocab/mimarks_c_isol_growth_condt) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [isol_growth_condt](isol_growth_condt.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_lat_lon.md b/mixs6/mimarks_c_lat_lon.md deleted file mode 100644 index 18d53c49..00000000 --- a/mixs6/mimarks_c_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_c_lat_lon - - - - -URI: [mixs.vocab:mimarks_c_lat_lon](https://w3id.org/mixs/vocab/mimarks_c_lat_lon) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MimarksC](MimarksC.md) diff --git a/mixs6/mimarks_c_nucl_acid_amp.md b/mixs6/mimarks_c_nucl_acid_amp.md deleted file mode 100644 index 188f89f7..00000000 --- a/mixs6/mimarks_c_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_nucl_acid_amp - - - - -URI: [mixs.vocab:mimarks_c_nucl_acid_amp](https://w3id.org/mixs/vocab/mimarks_c_nucl_acid_amp) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_nucl_acid_ext.md b/mixs6/mimarks_c_nucl_acid_ext.md deleted file mode 100644 index 1a3eee85..00000000 --- a/mixs6/mimarks_c_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_nucl_acid_ext - - - - -URI: [mixs.vocab:mimarks_c_nucl_acid_ext](https://w3id.org/mixs/vocab/mimarks_c_nucl_acid_ext) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_pcr_cond.md b/mixs6/mimarks_c_pcr_cond.md deleted file mode 100644 index 8361cddd..00000000 --- a/mixs6/mimarks_c_pcr_cond.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_pcr_cond - - - - -URI: [mixs.vocab:mimarks_c_pcr_cond](https://w3id.org/mixs/vocab/mimarks_c_pcr_cond) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pcr_cond](pcr_cond.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_pcr_primers.md b/mixs6/mimarks_c_pcr_primers.md deleted file mode 100644 index 53e87436..00000000 --- a/mixs6/mimarks_c_pcr_primers.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_pcr_primers - - - - -URI: [mixs.vocab:mimarks_c_pcr_primers](https://w3id.org/mixs/vocab/mimarks_c_pcr_primers) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pcr_primers](pcr_primers.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_project_name.md b/mixs6/mimarks_c_project_name.md deleted file mode 100644 index 4da8637b..00000000 --- a/mixs6/mimarks_c_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_project_name - - - - -URI: [mixs.vocab:mimarks_c_project_name](https://w3id.org/mixs/vocab/mimarks_c_project_name) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_rel_to_oxygen.md b/mixs6/mimarks_c_rel_to_oxygen.md deleted file mode 100644 index e1f2cdaa..00000000 --- a/mixs6/mimarks_c_rel_to_oxygen.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_rel_to_oxygen - - - - -URI: [mixs.vocab:mimarks_c_rel_to_oxygen](https://w3id.org/mixs/vocab/mimarks_c_rel_to_oxygen) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT - -## Parents - - * is_a: [rel_to_oxygen](rel_to_oxygen.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_samp_collect_device.md b/mixs6/mimarks_c_samp_collect_device.md deleted file mode 100644 index 8c4a28f2..00000000 --- a/mixs6/mimarks_c_samp_collect_device.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_samp_collect_device - - - - -URI: [mixs.vocab:mimarks_c_samp_collect_device](https://w3id.org/mixs/vocab/mimarks_c_samp_collect_device) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_samp_mat_process.md b/mixs6/mimarks_c_samp_mat_process.md deleted file mode 100644 index 7e194cbb..00000000 --- a/mixs6/mimarks_c_samp_mat_process.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_samp_mat_process - - - - -URI: [mixs.vocab:mimarks_c_samp_mat_process](https://w3id.org/mixs/vocab/mimarks_c_samp_mat_process) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_samp_size.md b/mixs6/mimarks_c_samp_size.md deleted file mode 100644 index b5187114..00000000 --- a/mixs6/mimarks_c_samp_size.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_samp_size - - - - -URI: [mixs.vocab:mimarks_c_samp_size](https://w3id.org/mixs/vocab/mimarks_c_samp_size) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_sample_name.md b/mixs6/mimarks_c_sample_name.md deleted file mode 100644 index 5975c748..00000000 --- a/mixs6/mimarks_c_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_sample_name - - - - -URI: [mixs.vocab:mimarks_c_sample_name](https://w3id.org/mixs/vocab/mimarks_c_sample_name) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_seq_meth.md b/mixs6/mimarks_c_seq_meth.md deleted file mode 100644 index d823808f..00000000 --- a/mixs6/mimarks_c_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_seq_meth - - - - -URI: [mixs.vocab:mimarks_c_seq_meth](https://w3id.org/mixs/vocab/mimarks_c_seq_meth) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_seq_quality_check.md b/mixs6/mimarks_c_seq_quality_check.md deleted file mode 100644 index da7b6fe9..00000000 --- a/mixs6/mimarks_c_seq_quality_check.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_seq_quality_check - - - - -URI: [mixs.vocab:mimarks_c_seq_quality_check](https://w3id.org/mixs/vocab/mimarks_c_seq_quality_check) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [seq_quality_check](seq_quality_check.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_sop.md b/mixs6/mimarks_c_sop.md deleted file mode 100644 index 7bc4d927..00000000 --- a/mixs6/mimarks_c_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_sop - - - - -URI: [mixs.vocab:mimarks_c_sop](https://w3id.org/mixs/vocab/mimarks_c_sop) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_source_mat_id.md b/mixs6/mimarks_c_source_mat_id.md deleted file mode 100644 index 3eb109b7..00000000 --- a/mixs6/mimarks_c_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_source_mat_id - - - - -URI: [mixs.vocab:mimarks_c_source_mat_id](https://w3id.org/mixs/vocab/mimarks_c_source_mat_id) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_submitted_to_insdc.md b/mixs6/mimarks_c_submitted_to_insdc.md deleted file mode 100644 index 7275dfed..00000000 --- a/mixs6/mimarks_c_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_submitted_to_insdc - - - - -URI: [mixs.vocab:mimarks_c_submitted_to_insdc](https://w3id.org/mixs/vocab/mimarks_c_submitted_to_insdc) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_subspecf_gen_lin.md b/mixs6/mimarks_c_subspecf_gen_lin.md deleted file mode 100644 index 9929caf2..00000000 --- a/mixs6/mimarks_c_subspecf_gen_lin.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_subspecf_gen_lin - - - - -URI: [mixs.vocab:mimarks_c_subspecf_gen_lin](https://w3id.org/mixs/vocab/mimarks_c_subspecf_gen_lin) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [subspecf_gen_lin](subspecf_gen_lin.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_target_gene.md b/mixs6/mimarks_c_target_gene.md deleted file mode 100644 index 77612bff..00000000 --- a/mixs6/mimarks_c_target_gene.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_c_target_gene - - - - -URI: [mixs.vocab:mimarks_c_target_gene](https://w3id.org/mixs/vocab/mimarks_c_target_gene) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [target_gene](target_gene.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) diff --git a/mixs6/mimarks_c_target_subfragment.md b/mixs6/mimarks_c_target_subfragment.md deleted file mode 100644 index 42caae68..00000000 --- a/mixs6/mimarks_c_target_subfragment.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_target_subfragment - - - - -URI: [mixs.vocab:mimarks_c_target_subfragment](https://w3id.org/mixs/vocab/mimarks_c_target_subfragment) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [target_subfragment](target_subfragment.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_trophic_level.md b/mixs6/mimarks_c_trophic_level.md deleted file mode 100644 index 0932b65e..00000000 --- a/mixs6/mimarks_c_trophic_level.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_trophic_level - - - - -URI: [mixs.vocab:mimarks_c_trophic_level](https://w3id.org/mixs/vocab/mimarks_c_trophic_level) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT - -## Parents - - * is_a: [trophic_level](trophic_level.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_c_url.md b/mixs6/mimarks_c_url.md deleted file mode 100644 index 8eab9102..00000000 --- a/mixs6/mimarks_c_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_c_url - - - - -URI: [mixs.vocab:mimarks_c_url](https://w3id.org/mixs/vocab/mimarks_c_url) - - -## Domain and Range - -[MimarksC](MimarksC.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMimarksC](AirMimarksC.md) - * [BuiltEnvironmentMimarksC](BuiltEnvironmentMimarksC.md) - * [Host-associatedMimarksC](Host-associatedMimarksC.md) - * [Human-associatedMimarksC](Human-associatedMimarksC.md) - * [Human-gutMimarksC](Human-gutMimarksC.md) - * [Human-oralMimarksC](Human-oralMimarksC.md) - * [Human-skinMimarksC](Human-skinMimarksC.md) - * [Human-vaginalMimarksC](Human-vaginalMimarksC.md) - * [HydrocarbonResources-coresMimarksC](HydrocarbonResources-coresMimarksC.md) - * [HydrocarbonResources-fluidsSwabsMimarksC](HydrocarbonResources-fluidsSwabsMimarksC.md) - * [MicrobialMatBiofilmMimarksC](MicrobialMatBiofilmMimarksC.md) - * [MimarksC](MimarksC.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksC](MiscellaneousNaturalOrArtificialEnvironmentMimarksC.md) - * [Plant-associatedMimarksC](Plant-associatedMimarksC.md) - * [SedimentMimarksC](SedimentMimarksC.md) - * [SoilMimarksC](SoilMimarksC.md) - * [WastewaterSludgeMimarksC](WastewaterSludgeMimarksC.md) - * [WaterMimarksC](WaterMimarksC.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_adapters.md b/mixs6/mimarks_s_adapters.md deleted file mode 100644 index 219598d3..00000000 --- a/mixs6/mimarks_s_adapters.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_adapters - - - - -URI: [mixs.vocab:mimarks_s_adapters](https://w3id.org/mixs/vocab/mimarks_s_adapters) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [adapters](adapters.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_assembly_software.md b/mixs6/mimarks_s_assembly_software.md deleted file mode 100644 index 7081c1f7..00000000 --- a/mixs6/mimarks_s_assembly_software.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_assembly_software - - - - -URI: [mixs.vocab:mimarks_s_assembly_software](https://w3id.org/mixs/vocab/mimarks_s_assembly_software) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [assembly_software](assembly_software.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_chimera_check.md b/mixs6/mimarks_s_chimera_check.md deleted file mode 100644 index c05d04a4..00000000 --- a/mixs6/mimarks_s_chimera_check.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_chimera_check - - - - -URI: [mixs.vocab:mimarks_s_chimera_check](https://w3id.org/mixs/vocab/mimarks_s_chimera_check) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [chimera_check](chimera_check.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_collection_date.md b/mixs6/mimarks_s_collection_date.md deleted file mode 100644 index e0b78bea..00000000 --- a/mixs6/mimarks_s_collection_date.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_collection_date - - - - -URI: [mixs.vocab:mimarks_s_collection_date](https://w3id.org/mixs/vocab/mimarks_s_collection_date) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [collection_date](collection_date.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_broad_scale.md b/mixs6/mimarks_s_env_broad_scale.md deleted file mode 100644 index fe42d3e2..00000000 --- a/mixs6/mimarks_s_env_broad_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_env_broad_scale - - - - -URI: [mixs.vocab:mimarks_s_env_broad_scale](https://w3id.org/mixs/vocab/mimarks_s_env_broad_scale) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_broad_scale](env_broad_scale.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_local_scale.md b/mixs6/mimarks_s_env_local_scale.md deleted file mode 100644 index 3d5fec36..00000000 --- a/mixs6/mimarks_s_env_local_scale.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_env_local_scale - - - - -URI: [mixs.vocab:mimarks_s_env_local_scale](https://w3id.org/mixs/vocab/mimarks_s_env_local_scale) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_local_scale](env_local_scale.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_medium.md b/mixs6/mimarks_s_env_medium.md deleted file mode 100644 index 4bb72bb9..00000000 --- a/mixs6/mimarks_s_env_medium.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_env_medium - - - - -URI: [mixs.vocab:mimarks_s_env_medium](https://w3id.org/mixs/vocab/mimarks_s_env_medium) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [env_medium](env_medium.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_env_package.md b/mixs6/mimarks_s_env_package.md deleted file mode 100644 index 4b44fb07..00000000 --- a/mixs6/mimarks_s_env_package.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_env_package - - - - -URI: [mixs.vocab:mimarks_s_env_package](https://w3id.org/mixs/vocab/mimarks_s_env_package) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT - -## Parents - - * is_a: [env_package](env_package.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_experimental_factor.md b/mixs6/mimarks_s_experimental_factor.md deleted file mode 100644 index 9dffb071..00000000 --- a/mixs6/mimarks_s_experimental_factor.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_experimental_factor - - - - -URI: [mixs.vocab:mimarks_s_experimental_factor](https://w3id.org/mixs/vocab/mimarks_s_experimental_factor) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [experimental_factor](experimental_factor.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_geo_loc_name.md b/mixs6/mimarks_s_geo_loc_name.md deleted file mode 100644 index 520ab78c..00000000 --- a/mixs6/mimarks_s_geo_loc_name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_geo_loc_name - - - - -URI: [mixs.vocab:mimarks_s_geo_loc_name](https://w3id.org/mixs/vocab/mimarks_s_geo_loc_name) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [geo_loc_name](geo_loc_name.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_investigation_type.md b/mixs6/mimarks_s_investigation_type.md deleted file mode 100644 index 64c64c3b..00000000 --- a/mixs6/mimarks_s_investigation_type.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_investigation_type - - - - -URI: [mixs.vocab:mimarks_s_investigation_type](https://w3id.org/mixs/vocab/mimarks_s_investigation_type) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ - -## Parents - - * is_a: [investigation_type](investigation_type.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_lat_lon.md b/mixs6/mimarks_s_lat_lon.md deleted file mode 100644 index f0a0748e..00000000 --- a/mixs6/mimarks_s_lat_lon.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: mimarks_s_lat_lon - - - - -URI: [mixs.vocab:mimarks_s_lat_lon](https://w3id.org/mixs/vocab/mimarks_s_lat_lon) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [lat_lon](lat_lon.md) - -## Children - - -## Used by - - * [MimarksS](MimarksS.md) diff --git a/mixs6/mimarks_s_lib_layout.md b/mixs6/mimarks_s_lib_layout.md deleted file mode 100644 index 80c06f0a..00000000 --- a/mixs6/mimarks_s_lib_layout.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_lib_layout - - - - -URI: [mixs.vocab:mimarks_s_lib_layout](https://w3id.org/mixs/vocab/mimarks_s_lib_layout) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT - -## Parents - - * is_a: [lib_layout](lib_layout.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_lib_reads_seqd.md b/mixs6/mimarks_s_lib_reads_seqd.md deleted file mode 100644 index 3a1e63bd..00000000 --- a/mixs6/mimarks_s_lib_reads_seqd.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_lib_reads_seqd - - - - -URI: [mixs.vocab:mimarks_s_lib_reads_seqd](https://w3id.org/mixs/vocab/mimarks_s_lib_reads_seqd) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_reads_seqd](lib_reads_seqd.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_lib_screen.md b/mixs6/mimarks_s_lib_screen.md deleted file mode 100644 index 2f19a0e1..00000000 --- a/mixs6/mimarks_s_lib_screen.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_lib_screen - - - - -URI: [mixs.vocab:mimarks_s_lib_screen](https://w3id.org/mixs/vocab/mimarks_s_lib_screen) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_screen](lib_screen.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_lib_size.md b/mixs6/mimarks_s_lib_size.md deleted file mode 100644 index 16dea143..00000000 --- a/mixs6/mimarks_s_lib_size.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_lib_size - - - - -URI: [mixs.vocab:mimarks_s_lib_size](https://w3id.org/mixs/vocab/mimarks_s_lib_size) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_size](lib_size.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_lib_vector.md b/mixs6/mimarks_s_lib_vector.md deleted file mode 100644 index d0889f3e..00000000 --- a/mixs6/mimarks_s_lib_vector.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_lib_vector - - - - -URI: [mixs.vocab:mimarks_s_lib_vector](https://w3id.org/mixs/vocab/mimarks_s_lib_vector) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [lib_vector](lib_vector.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_mid.md b/mixs6/mimarks_s_mid.md deleted file mode 100644 index bdde8ece..00000000 --- a/mixs6/mimarks_s_mid.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_mid - - - - -URI: [mixs.vocab:mimarks_s_mid](https://w3id.org/mixs/vocab/mimarks_s_mid) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [mid](mid.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_nucl_acid_amp.md b/mixs6/mimarks_s_nucl_acid_amp.md deleted file mode 100644 index 968f9206..00000000 --- a/mixs6/mimarks_s_nucl_acid_amp.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_nucl_acid_amp - - - - -URI: [mixs.vocab:mimarks_s_nucl_acid_amp](https://w3id.org/mixs/vocab/mimarks_s_nucl_acid_amp) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_amp](nucl_acid_amp.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_nucl_acid_ext.md b/mixs6/mimarks_s_nucl_acid_ext.md deleted file mode 100644 index 6988d9fb..00000000 --- a/mixs6/mimarks_s_nucl_acid_ext.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_nucl_acid_ext - - - - -URI: [mixs.vocab:mimarks_s_nucl_acid_ext](https://w3id.org/mixs/vocab/mimarks_s_nucl_acid_ext) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucl_acid_ext](nucl_acid_ext.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_pcr_cond.md b/mixs6/mimarks_s_pcr_cond.md deleted file mode 100644 index fa49eceb..00000000 --- a/mixs6/mimarks_s_pcr_cond.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_pcr_cond - - - - -URI: [mixs.vocab:mimarks_s_pcr_cond](https://w3id.org/mixs/vocab/mimarks_s_pcr_cond) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pcr_cond](pcr_cond.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_pcr_primers.md b/mixs6/mimarks_s_pcr_primers.md deleted file mode 100644 index c157768c..00000000 --- a/mixs6/mimarks_s_pcr_primers.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_pcr_primers - - - - -URI: [mixs.vocab:mimarks_s_pcr_primers](https://w3id.org/mixs/vocab/mimarks_s_pcr_primers) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [pcr_primers](pcr_primers.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_project_name.md b/mixs6/mimarks_s_project_name.md deleted file mode 100644 index ed56a308..00000000 --- a/mixs6/mimarks_s_project_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_project_name - - - - -URI: [mixs.vocab:mimarks_s_project_name](https://w3id.org/mixs/vocab/mimarks_s_project_name) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [project_name](project_name.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_rel_to_oxygen.md b/mixs6/mimarks_s_rel_to_oxygen.md deleted file mode 100644 index 0256ff8a..00000000 --- a/mixs6/mimarks_s_rel_to_oxygen.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_rel_to_oxygen - - - - -URI: [mixs.vocab:mimarks_s_rel_to_oxygen](https://w3id.org/mixs/vocab/mimarks_s_rel_to_oxygen) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT - -## Parents - - * is_a: [rel_to_oxygen](rel_to_oxygen.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_samp_collect_device.md b/mixs6/mimarks_s_samp_collect_device.md deleted file mode 100644 index 9c7a0ed6..00000000 --- a/mixs6/mimarks_s_samp_collect_device.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_samp_collect_device - - - - -URI: [mixs.vocab:mimarks_s_samp_collect_device](https://w3id.org/mixs/vocab/mimarks_s_samp_collect_device) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_collect_device](samp_collect_device.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_samp_mat_process.md b/mixs6/mimarks_s_samp_mat_process.md deleted file mode 100644 index cb17af05..00000000 --- a/mixs6/mimarks_s_samp_mat_process.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_samp_mat_process - - - - -URI: [mixs.vocab:mimarks_s_samp_mat_process](https://w3id.org/mixs/vocab/mimarks_s_samp_mat_process) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [samp_mat_process](samp_mat_process.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_samp_size.md b/mixs6/mimarks_s_samp_size.md deleted file mode 100644 index 7b11e673..00000000 --- a/mixs6/mimarks_s_samp_size.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_samp_size - - - - -URI: [mixs.vocab:mimarks_s_samp_size](https://w3id.org/mixs/vocab/mimarks_s_samp_size) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [QuantityValue](QuantityValue.md) - -## Parents - - * is_a: [samp_size](samp_size.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_sample_name.md b/mixs6/mimarks_s_sample_name.md deleted file mode 100644 index 75b36885..00000000 --- a/mixs6/mimarks_s_sample_name.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_sample_name - - - - -URI: [mixs.vocab:mimarks_s_sample_name](https://w3id.org/mixs/vocab/mimarks_s_sample_name) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sample_name](sample_name.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_seq_meth.md b/mixs6/mimarks_s_seq_meth.md deleted file mode 100644 index ddc6e6f0..00000000 --- a/mixs6/mimarks_s_seq_meth.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_seq_meth - - - - -URI: [mixs.vocab:mimarks_s_seq_meth](https://w3id.org/mixs/vocab/mimarks_s_seq_meth) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ - -## Parents - - * is_a: [seq_meth](seq_meth.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_seq_quality_check.md b/mixs6/mimarks_s_seq_quality_check.md deleted file mode 100644 index 30657c3d..00000000 --- a/mixs6/mimarks_s_seq_quality_check.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_seq_quality_check - - - - -URI: [mixs.vocab:mimarks_s_seq_quality_check](https://w3id.org/mixs/vocab/mimarks_s_seq_quality_check) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [seq_quality_check](seq_quality_check.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_size_frac.md b/mixs6/mimarks_s_size_frac.md deleted file mode 100644 index fb33e692..00000000 --- a/mixs6/mimarks_s_size_frac.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_size_frac - - - - -URI: [mixs.vocab:mimarks_s_size_frac](https://w3id.org/mixs/vocab/mimarks_s_size_frac) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [size_frac](size_frac.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_sop.md b/mixs6/mimarks_s_sop.md deleted file mode 100644 index 8573e491..00000000 --- a/mixs6/mimarks_s_sop.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_sop - - - - -URI: [mixs.vocab:mimarks_s_sop](https://w3id.org/mixs/vocab/mimarks_s_sop) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [sop](sop.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_source_mat_id.md b/mixs6/mimarks_s_source_mat_id.md deleted file mode 100644 index 7b8dfbd2..00000000 --- a/mixs6/mimarks_s_source_mat_id.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_source_mat_id - - - - -URI: [mixs.vocab:mimarks_s_source_mat_id](https://w3id.org/mixs/vocab/mimarks_s_source_mat_id) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [source_mat_id](source_mat_id.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_submitted_to_insdc.md b/mixs6/mimarks_s_submitted_to_insdc.md deleted file mode 100644 index 214b9f04..00000000 --- a/mixs6/mimarks_s_submitted_to_insdc.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_submitted_to_insdc - - - - -URI: [mixs.vocab:mimarks_s_submitted_to_insdc](https://w3id.org/mixs/vocab/mimarks_s_submitted_to_insdc) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [submitted_to_insdc](submitted_to_insdc.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_target_gene.md b/mixs6/mimarks_s_target_gene.md deleted file mode 100644 index abd724f4..00000000 --- a/mixs6/mimarks_s_target_gene.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Slot: mimarks_s_target_gene - - - - -URI: [mixs.vocab:mimarks_s_target_gene](https://w3id.org/mixs/vocab/mimarks_s_target_gene) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> REQ [String](types/String.md) - -## Parents - - * is_a: [target_gene](target_gene.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) diff --git a/mixs6/mimarks_s_target_subfragment.md b/mixs6/mimarks_s_target_subfragment.md deleted file mode 100644 index 3b928359..00000000 --- a/mixs6/mimarks_s_target_subfragment.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_target_subfragment - - - - -URI: [mixs.vocab:mimarks_s_target_subfragment](https://w3id.org/mixs/vocab/mimarks_s_target_subfragment) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [target_subfragment](target_subfragment.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mimarks_s_url.md b/mixs6/mimarks_s_url.md deleted file mode 100644 index d4157a81..00000000 --- a/mixs6/mimarks_s_url.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Slot: mimarks_s_url - - - - -URI: [mixs.vocab:mimarks_s_url](https://w3id.org/mixs/vocab/mimarks_s_url) - - -## Domain and Range - -[MimarksS](MimarksS.md) -> OPT [String](types/String.md) - -## Parents - - * is_a: [url](url.md) - -## Children - - -## Used by - - * [AirMimarksS](AirMimarksS.md) - * [BuiltEnvironmentMimarksS](BuiltEnvironmentMimarksS.md) - * [Host-associatedMimarksS](Host-associatedMimarksS.md) - * [Human-associatedMimarksS](Human-associatedMimarksS.md) - * [Human-gutMimarksS](Human-gutMimarksS.md) - * [Human-oralMimarksS](Human-oralMimarksS.md) - * [Human-skinMimarksS](Human-skinMimarksS.md) - * [Human-vaginalMimarksS](Human-vaginalMimarksS.md) - * [HydrocarbonResources-coresMimarksS](HydrocarbonResources-coresMimarksS.md) - * [HydrocarbonResources-fluidsSwabsMimarksS](HydrocarbonResources-fluidsSwabsMimarksS.md) - * [MicrobialMatBiofilmMimarksS](MicrobialMatBiofilmMimarksS.md) - * [MimarksS](MimarksS.md) - * [MiscellaneousNaturalOrArtificialEnvironmentMimarksS](MiscellaneousNaturalOrArtificialEnvironmentMimarksS.md) - * [Plant-associatedMimarksS](Plant-associatedMimarksS.md) - * [SedimentMimarksS](SedimentMimarksS.md) - * [SoilMimarksS](SoilMimarksS.md) - * [WastewaterSludgeMimarksS](WastewaterSludgeMimarksS.md) - * [WaterMimarksS](WaterMimarksS.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | conditional mandatory | - diff --git a/mixs6/mineral_nutr_regm.md b/mixs6/mineral_nutr_regm.md index 606e7540..d3469384 100644 --- a/mixs6/mineral_nutr_regm.md +++ b/mixs6/mineral_nutr_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: mineral nutrient name;mineral nutrient amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/misag_collection_date.md b/mixs6/misag_collection_date.md index 0d310c2f..d0b7a5ed 100644 --- a/mixs6/misag_collection_date.md +++ b/mixs6/misag_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MISAG_collection_date](https://w3id.org/mixs/vocab/MISAG_collec ## Domain and Range -[MISAG](MISAG.md) -> REQ [String](types/String.md) +[MISAG](MISAG.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/misag_sample_name.md b/mixs6/misag_sample_name.md index de41f168..15c9fa8d 100644 --- a/mixs6/misag_sample_name.md +++ b/mixs6/misag_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MISAG_sample_name](https://w3id.org/mixs/vocab/MISAG_sample_nam ## Domain and Range -[MISAG](MISAG.md) -> OPT [String](types/String.md) +[MISAG](MISAG.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/misc_param.md b/mixs6/misc_param.md index dcaed98d..b1fff5ea 100644 --- a/mixs6/misc_param.md +++ b/mixs6/misc_param.md @@ -220,9 +220,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | miscellaneous parameter | | **Mappings:** | | MIXS:0000752 | | **Comments:** | | Expected value: parameter name;measurement value | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | | **Examples:** | | Example(value='Bicarbonate ion concentration;2075 micromole per kilogram', description=None) | diff --git a/mixs6/miuvig_collection_date.md b/mixs6/miuvig_collection_date.md index a8744090..8558aa5c 100644 --- a/mixs6/miuvig_collection_date.md +++ b/mixs6/miuvig_collection_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIUVIG_collection_date](https://w3id.org/mixs/vocab/MIUVIG_coll ## Domain and Range -[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) +[MIUVIG](MIUVIG.md) -> REQ [Date](types/Date.md) ## Parents diff --git a/mixs6/miuvig_sample_name.md b/mixs6/miuvig_sample_name.md index b1f4ac41..03935225 100644 --- a/mixs6/miuvig_sample_name.md +++ b/mixs6/miuvig_sample_name.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:MIUVIG_sample_name](https://w3id.org/mixs/vocab/MIUVIG_sample_n ## Domain and Range -[MIUVIG](MIUVIG.md) -> OPT [String](types/String.md) +[MIUVIG](MIUVIG.md) -> REQ [String](types/String.md) ## Parents diff --git a/mixs6/n_alkanes.md b/mixs6/n_alkanes.md index 9808f2bc..d5b83e79 100644 --- a/mixs6/n_alkanes.md +++ b/mixs6/n_alkanes.md @@ -66,7 +66,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: n-alkane name;measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='n-hexadecane;100 milligram per liter', description=None) | diff --git a/mixs6/nitrate.md b/mixs6/nitrate.md index 95ce10f2..c9687ad8 100644 --- a/mixs6/nitrate.md +++ b/mixs6/nitrate.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 61 | +| | | Position: 61.0 | | | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='65 micromole per liter', description=None) | diff --git a/mixs6/nitrite.md b/mixs6/nitrite.md index 973719d7..1b4b40a9 100644 --- a/mixs6/nitrite.md +++ b/mixs6/nitrite.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 62 | +| | | Position: 62.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.5 micromole per liter', description=None) | diff --git a/mixs6/nitro.md b/mixs6/nitro.md index 0f77f2a4..6044ee12 100644 --- a/mixs6/nitro.md +++ b/mixs6/nitro.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='4.2 micromole per liter', description=None) | diff --git a/mixs6/non_mineral_nutr_regm.md b/mixs6/non_mineral_nutr_regm.md index c328660e..7242f472 100644 --- a/mixs6/non_mineral_nutr_regm.md +++ b/mixs6/non_mineral_nutr_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/nose_mouth_teeth_throat_disord.md b/mixs6/nose_mouth_teeth_throat_disord.md index 2b3adc0b..d4a72fa2 100644 --- a/mixs6/nose_mouth_teeth_throat_disord.md +++ b/mixs6/nose_mouth_teeth_throat_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | nose/mouth/teeth/throat disorder | | **Mappings:** | | MIXS:0000283 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: human-oral | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/nose_throat_disord.md b/mixs6/nose_throat_disord.md index 994c51a1..0254863e 100644 --- a/mixs6/nose_throat_disord.md +++ b/mixs6/nose_throat_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | lung/nose-throat disorder | | **Mappings:** | | MIXS:0000270 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 31 | +| | | Position: 31.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/nucl_acid_amp.md b/mixs6/nucl_acid_amp.md index b0d9531a..4d3c9b1d 100644 --- a/mixs6/nucl_acid_amp.md +++ b/mixs6/nucl_acid_amp.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | nucleic acid amplification | | **Comments:** | | Expected value: PMID, DOI or URL | -| | | Preferred unit: | | | | Position: 38.0 | | **Examples:** | | Example(value='https://phylogenomics.me/protocols/16s-pcr-protocol/', description=None) | diff --git a/mixs6/nucl_acid_ext.md b/mixs6/nucl_acid_ext.md index 00180d9c..7bb2add5 100644 --- a/mixs6/nucl_acid_ext.md +++ b/mixs6/nucl_acid_ext.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | nucleic acid extraction | | **Comments:** | | Expected value: PMID, DOI or URL | -| | | Preferred unit: | | | | Position: 37.0 | | **Examples:** | | Example(value='https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf', description=None) | diff --git a/mixs6/nucleic_acid_sequence_source_field.md b/mixs6/nucleic_acid_sequence_source_field.md index 72cb32c1..733b61ed 100644 --- a/mixs6/nucleic_acid_sequence_source_field.md +++ b/mixs6/nucleic_acid_sequence_source_field.md @@ -29,9 +29,10 @@ None -> OPT [String](types/String.md) * [propagation](propagation.md) * [ref_biomaterial](ref_biomaterial.md) * [rel_to_oxygen](rel_to_oxygen.md) - * [samp_collect_device](samp_collect_device.md) * [samp_mat_process](samp_mat_process.md) * [samp_size](samp_size.md) + * [sample_collect_device](sample_collect_device.md) + * [sample_collect_method](sample_collect_method.md) * [size_frac](size_frac.md) * [source_mat_id](source_mat_id.md) * [source_uvig](source_uvig.md) diff --git a/mixs6/num_replicons.md b/mixs6/num_replicons.md index 4331e28f..fe07231a 100644 --- a/mixs6/num_replicons.md +++ b/mixs6/num_replicons.md @@ -31,7 +31,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | number of replicons | | **Comments:** | | Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments | -| | | Preferred unit: | | | | Position: 16.0 | | **Examples:** | | Example(value='2', description=None) | diff --git a/mixs6/number_contig.md b/mixs6/number_contig.md index f1cf1324..e68c4a77 100644 --- a/mixs6/number_contig.md +++ b/mixs6/number_contig.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | number of contigs | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Position: 58.0 | | **Examples:** | | Example(value='40', description=None) | diff --git a/mixs6/number_pets.md b/mixs6/number_pets.md index 8bfe99d4..ca1b800d 100644 --- a/mixs6/number_pets.md +++ b/mixs6/number_pets.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | number of pets | | **Mappings:** | | MIXS:0000231 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 93 | +| | | Position: 93.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/number_plants.md b/mixs6/number_plants.md index e83bda15..c2ba253f 100644 --- a/mixs6/number_plants.md +++ b/mixs6/number_plants.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | number of houseplants | | **Mappings:** | | MIXS:0000230 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 92 | +| | | Position: 92.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/number_resident.md b/mixs6/number_resident.md index dcd222b8..c2a93503 100644 --- a/mixs6/number_resident.md +++ b/mixs6/number_resident.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | number of residents | | **Mappings:** | | MIXS:0000232 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 94 | +| | | Position: 94.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/occup_density_samp.md b/mixs6/occup_density_samp.md index d6b4e88c..7aedac03 100644 --- a/mixs6/occup_density_samp.md +++ b/mixs6/occup_density_samp.md @@ -40,9 +40,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | occupant density at sampling | | **Mappings:** | | MIXS:0000217 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 26 | +| | | Position: 26.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/occup_document.md b/mixs6/occup_document.md index 6fb56e74..f3b7cbc3 100644 --- a/mixs6/occup_document.md +++ b/mixs6/occup_document.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | occupancy documentation | | **Mappings:** | | MIXS:0000816 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 95 | +| | | Position: 95.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='estimate', description=None) | diff --git a/mixs6/occup_samp.md b/mixs6/occup_samp.md index 94c16be0..165af97d 100644 --- a/mixs6/occup_samp.md +++ b/mixs6/occup_samp.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | occupancy at sampling | | **Mappings:** | | MIXS:0000772 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 25 | +| | | Position: 25.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='10', description=None) | diff --git a/mixs6/org_carb.md b/mixs6/org_carb.md index 3ddc21ea..746ff236 100644 --- a/mixs6/org_carb.md +++ b/mixs6/org_carb.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='1.5 microgram per liter', description=None) | diff --git a/mixs6/org_matter.md b/mixs6/org_matter.md index f9ecd874..0211396a 100644 --- a/mixs6/org_matter.md +++ b/mixs6/org_matter.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='1.75 milligram per cubic meter', description=None) | diff --git a/mixs6/org_nitro.md b/mixs6/org_nitro.md index 8e786400..56f72346 100644 --- a/mixs6/org_nitro.md +++ b/mixs6/org_nitro.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='4 micromole per liter', description=None) | diff --git a/mixs6/org_particles.md b/mixs6/org_particles.md index c1febbcd..9968feb6 100644 --- a/mixs6/org_particles.md +++ b/mixs6/org_particles.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: particle name;measurement value | | | | Preferred unit: gram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/organism_count.md b/mixs6/organism_count.md index 411f4277..2bb12d1d 100644 --- a/mixs6/organism_count.md +++ b/mixs6/organism_count.md @@ -222,7 +222,7 @@ None -> OPT | **Comments:** | | Expected value: organism name;measurement value;enumeration | | | | Preferred unit: number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 16 packages: air, built environment, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='total prokaryotes;3.5e7 cells per milliliter;qPCR', description=None) | diff --git a/mixs6/organism_count_qpcr_info.md b/mixs6/organism_count_qpcr_info.md index 930d3f80..178d8b09 100644 --- a/mixs6/organism_count_qpcr_info.md +++ b/mixs6/organism_count_qpcr_info.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles | | | | Preferred unit: number of cells per gram (or ml or cm^2) | | | | Occurrence: 1 | -| | | Position: 53 | +| | | Position: 53.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/owc_tvdss.md b/mixs6/owc_tvdss.md index 1f464f29..6431ba91 100644 --- a/mixs6/owc_tvdss.md +++ b/mixs6/owc_tvdss.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 15 | +| | | Position: 15.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/oxy_stat_samp.md b/mixs6/oxy_stat_samp.md index f7c12893..5a830385 100644 --- a/mixs6/oxy_stat_samp.md +++ b/mixs6/oxy_stat_samp.md @@ -208,9 +208,8 @@ None -> OPT | **Aliases:** | | oxygenation status of sample | | **Mappings:** | | MIXS:0000753 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='aerobic', description=None) | diff --git a/mixs6/oxygen.md b/mixs6/oxygen.md index bd5ca5fd..22ec1b7f 100644 --- a/mixs6/oxygen.md +++ b/mixs6/oxygen.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='600 parts per million', description=None) | diff --git a/mixs6/part_org_carb.md b/mixs6/part_org_carb.md index c828044a..69051815 100644 --- a/mixs6/part_org_carb.md +++ b/mixs6/part_org_carb.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='1.92 micromole per liter', description=None) | diff --git a/mixs6/part_org_nitro.md b/mixs6/part_org_nitro.md index cde8f82a..8289c1cf 100644 --- a/mixs6/part_org_nitro.md +++ b/mixs6/part_org_nitro.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='0.3 micromole per liter', description=None) | diff --git a/mixs6/particle_class.md b/mixs6/particle_class.md index ce3b5732..f47332ca 100644 --- a/mixs6/particle_class.md +++ b/mixs6/particle_class.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: particle name;measurement value | | | | Preferred unit: micrometer | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: sediment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/pathogenicity.md b/mixs6/pathogenicity.md index 8b6748c0..5c8cf35d 100644 --- a/mixs6/pathogenicity.md +++ b/mixs6/pathogenicity.md @@ -32,7 +32,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | known pathogenicity | | **Comments:** | | Expected value: names of organisms that the entity is pathogenic to | -| | | Preferred unit: | | | | Position: 21.0 | | **Examples:** | | Example(value='human, animal, plant, fungi, bacteria', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/65 | diff --git a/mixs6/pcr_cond.md b/mixs6/pcr_cond.md index 89b637b6..f19ef250 100644 --- a/mixs6/pcr_cond.md +++ b/mixs6/pcr_cond.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | pcr conditions | | **Comments:** | | Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles | -| | | Preferred unit: | | | | Position: 49.0 | | **Examples:** | | Example(value='initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35', description=None) | diff --git a/mixs6/pcr_primers.md b/mixs6/pcr_primers.md index e3806479..c6ba6049 100644 --- a/mixs6/pcr_primers.md +++ b/mixs6/pcr_primers.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | pcr primers | | **Comments:** | | Expected value: FWD: forward primer sequence;REV:reverse primer sequence | -| | | Preferred unit: | | | | Position: 46.0 | | **Examples:** | | Example(value='FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT', description=None) | diff --git a/mixs6/permeability.md b/mixs6/permeability.md index a5b76ced..6e2e1d11 100644 --- a/mixs6/permeability.md +++ b/mixs6/permeability.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value range | | | | Preferred unit: mD | | | | Occurrence: 1 | -| | | Position: 10 | +| | | Position: 10.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/perturbation.md b/mixs6/perturbation.md index 23cec6be..b94f6f07 100644 --- a/mixs6/perturbation.md +++ b/mixs6/perturbation.md @@ -184,9 +184,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | perturbation | | **Mappings:** | | MIXS:0000754 | | **Comments:** | | Expected value: perturbation type name;perturbation interval and duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 13 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M', description=None) | diff --git a/mixs6/pesticide_regm.md b/mixs6/pesticide_regm.md index 88a03381..df0e89a6 100644 --- a/mixs6/pesticide_regm.md +++ b/mixs6/pesticide_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: pesticide name;pesticide amount;treatment interval and duration | | | | Preferred unit: gram, mole per liter, milligram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/pet_farm_animal.md b/mixs6/pet_farm_animal.md index ce73318a..71efb9cf 100644 --- a/mixs6/pet_farm_animal.md +++ b/mixs6/pet_farm_animal.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | presence of pets or farm animals | | **Mappings:** | | MIXS:0000267 | | **Comments:** | | Expected value: presence status;type of animal or pet | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 25 | +| | | Position: 25.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes; 5 cats', description=None) | diff --git a/mixs6/petroleum_hydrocarb.md b/mixs6/petroleum_hydrocarb.md index 308274a9..1cf4434f 100644 --- a/mixs6/petroleum_hydrocarb.md +++ b/mixs6/petroleum_hydrocarb.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.05 micromole per liter', description=None) | diff --git a/mixs6/ph.md b/mixs6/ph.md index 20b75298..2127ffc6 100644 --- a/mixs6/ph.md +++ b/mixs6/ph.md @@ -124,9 +124,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | pH | | **Mappings:** | | MIXS:0001001 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 54 | +| | | Position: 54.0 | | | | This field is used in: 8 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, soil, wastewater_sludge, water | | **Examples:** | | Example(value='7.2', description=None) | diff --git a/mixs6/ph_meth.md b/mixs6/ph_meth.md index 565af776..f82ad2c2 100644 --- a/mixs6/ph_meth.md +++ b/mixs6/ph_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | pH method | | **Mappings:** | | MIXS:0001106 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 38 | +| | | Position: 38.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/ph_regm.md b/mixs6/ph_regm.md index d6b8be04..cbc96ba3 100644 --- a/mixs6/ph_regm.md +++ b/mixs6/ph_regm.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | pH regimen | | **Mappings:** | | MIXS:0001056 | | **Comments:** | | Expected value: measurement value;treatment interval and duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/phaeopigments.md b/mixs6/phaeopigments.md index 31c2ae2b..e2be2905 100644 --- a/mixs6/phaeopigments.md +++ b/mixs6/phaeopigments.md @@ -66,7 +66,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: phaeopigment name;measurement value | | | | Preferred unit: milligram per cubic meter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='2.5 milligram per cubic meter', description=None) | diff --git a/mixs6/phosphate.md b/mixs6/phosphate.md index fbf309a6..915153b0 100644 --- a/mixs6/phosphate.md +++ b/mixs6/phosphate.md @@ -90,7 +90,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 5 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='0.7 micromole per liter', description=None) | diff --git a/mixs6/phosplipid_fatt_acid.md b/mixs6/phosplipid_fatt_acid.md index 95d796aa..c269d966 100644 --- a/mixs6/phosplipid_fatt_acid.md +++ b/mixs6/phosplipid_fatt_acid.md @@ -78,7 +78,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: phospholipid fatty acid name;measurement value | | | | Preferred unit: mole per gram, mole per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='2.98 milligram per liter', description=None) | diff --git a/mixs6/photon_flux.md b/mixs6/photon_flux.md index 2a6b1729..62411795 100644 --- a/mixs6/photon_flux.md +++ b/mixs6/photon_flux.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: number of photons per second per unit area | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='3.926 micromole photons per second per square meter', description=None) | diff --git a/mixs6/plant_growth_med.md b/mixs6/plant_growth_med.md index 95729514..5f78515a 100644 --- a/mixs6/plant_growth_med.md +++ b/mixs6/plant_growth_med.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | plant growth medium | | **Mappings:** | | MIXS:0001057 | | **Comments:** | | Expected value: EO or enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='hydroponic plant culture media [EO:0007067]', description=None) | diff --git a/mixs6/plant_product.md b/mixs6/plant_product.md index 90ad01e0..ba48c408 100644 --- a/mixs6/plant_product.md +++ b/mixs6/plant_product.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | plant product | | **Mappings:** | | MIXS:0001058 | | **Comments:** | | Expected value: product name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='xylem sap [PO:0025539]', description=None) | diff --git a/mixs6/plant_sex.md b/mixs6/plant_sex.md index af3f4182..cce0f760 100644 --- a/mixs6/plant_sex.md +++ b/mixs6/plant_sex.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | plant sex | | **Mappings:** | | MIXS:0001059 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='Hermaphroditic', description=None) | diff --git a/mixs6/plant_struc.md b/mixs6/plant_struc.md index d40d7b2e..4e325177 100644 --- a/mixs6/plant_struc.md +++ b/mixs6/plant_struc.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | plant structure | | **Mappings:** | | MIXS:0001060 | | **Comments:** | | Expected value: PO | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='epidermis [PO:0005679]', description=None) | diff --git a/mixs6/ploidy.md b/mixs6/ploidy.md index 6fa85340..68873a72 100644 --- a/mixs6/ploidy.md +++ b/mixs6/ploidy.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | ploidy | | **Comments:** | | Expected value: PATO | -| | | Preferred unit: | | | | Position: 15.0 | | **Examples:** | | Example(value='allopolyploidy [PATO:0001379]', description=None) | diff --git a/mixs6/pollutants.md b/mixs6/pollutants.md index 420ae44b..98ad04c7 100644 --- a/mixs6/pollutants.md +++ b/mixs6/pollutants.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: pollutant name;measurement value | | | | Preferred unit: gram, mole per liter, milligram per liter, microgram per cubic meter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='lead;0.15 microgram per cubic meter', description=None) | diff --git a/mixs6/pool_dna_extracts.md b/mixs6/pool_dna_extracts.md index ba6196af..019fd2aa 100644 --- a/mixs6/pool_dna_extracts.md +++ b/mixs6/pool_dna_extracts.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | pooling of DNA extracts (if done) | | **Mappings:** | | MIXS:0000325 | | **Comments:** | | Expected value: pooling status;number of pooled extracts | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 18 | +| | | Position: 18.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='yes;5', description=None) | diff --git a/mixs6/porosity.md b/mixs6/porosity.md index 8834ba44..c24b6804 100644 --- a/mixs6/porosity.md +++ b/mixs6/porosity.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value or range | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 11 | +| | | Position: 11.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, sediment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/potassium.md b/mixs6/potassium.md index f709fb5f..a7e01886 100644 --- a/mixs6/potassium.md +++ b/mixs6/potassium.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 68 | +| | | Position: 68.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='463 milligram per liter', description=None) | diff --git a/mixs6/pour_point.md b/mixs6/pour_point.md index d6f9b157..b469a8f2 100644 --- a/mixs6/pour_point.md +++ b/mixs6/pour_point.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 88 | +| | | Position: 88.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/pre_treatment.md b/mixs6/pre_treatment.md index afaad096..54970036 100644 --- a/mixs6/pre_treatment.md +++ b/mixs6/pre_treatment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | pre-treatment | | **Mappings:** | | MIXS:0000348 | | **Comments:** | | Expected value: pre-treatment type | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/pred_genome_struc.md b/mixs6/pred_genome_struc.md index 5f0c4c06..bb7c3239 100644 --- a/mixs6/pred_genome_struc.md +++ b/mixs6/pred_genome_struc.md @@ -29,7 +29,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | predicted genome structure | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 85.0 | | **Examples:** | | Example(value='non-segmented', description=None) | diff --git a/mixs6/pred_genome_type.md b/mixs6/pred_genome_type.md index 2ea16948..336a1634 100644 --- a/mixs6/pred_genome_type.md +++ b/mixs6/pred_genome_type.md @@ -29,7 +29,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | predicted genome type | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 84.0 | | **Examples:** | | Example(value='dsDNA', description=None) | diff --git a/mixs6/pregnancy.md b/mixs6/pregnancy.md index b148c082..e43f2ff7 100644 --- a/mixs6/pregnancy.md +++ b/mixs6/pregnancy.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:pregnancy](https://w3id.org/mixs/vocab/pregnancy) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | pregnancy | | **Mappings:** | | MIXS:0000966 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/pres_animal.md b/mixs6/pres_animal.md index 1dd6f1e0..42079c46 100644 --- a/mixs6/pres_animal.md +++ b/mixs6/pres_animal.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | presence of pets, animals, or insects | | **Mappings:** | | MIXS:0000819 | | **Comments:** | | Expected value: enumeration;count | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 99 | +| | | Position: 99.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='cat;5', description=None) | diff --git a/mixs6/pressure.md b/mixs6/pressure.md index 52c21352..e2cc2d67 100644 --- a/mixs6/pressure.md +++ b/mixs6/pressure.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: atmosphere | | | | Occurrence: 1 | -| | | Position: 41 | +| | | Position: 41.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='50 atmosphere', description=None) | diff --git a/mixs6/previous_land_use.md b/mixs6/previous_land_use.md index b91b670f..e3b9785b 100644 --- a/mixs6/previous_land_use.md +++ b/mixs6/previous_land_use.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/previous land use | | **Mappings:** | | MIXS:0000315 | | **Comments:** | | Expected value: land use name;date | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 4 | +| | | Position: 4.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/previous_land_use_meth.md b/mixs6/previous_land_use_meth.md index d4ec556e..118a739e 100644 --- a/mixs6/previous_land_use_meth.md +++ b/mixs6/previous_land_use_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | history/previous land use method | | **Mappings:** | | MIXS:0000316 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/primary_prod.md b/mixs6/primary_prod.md index dcbdf807..a03e2452 100644 --- a/mixs6/primary_prod.md +++ b/mixs6/primary_prod.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per cubic meter per day, gram per square meter per day | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='100 milligram per cubic meter per day', description=None) | diff --git a/mixs6/primary_treatment.md b/mixs6/primary_treatment.md index d3fc4261..3405cdf7 100644 --- a/mixs6/primary_treatment.md +++ b/mixs6/primary_treatment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | primary treatment | | **Mappings:** | | MIXS:0000349 | | **Comments:** | | Expected value: primary treatment type | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/prod_rate.md b/mixs6/prod_rate.md index 0afab620..5b721354 100644 --- a/mixs6/prod_rate.md +++ b/mixs6/prod_rate.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: cubic meter per day | | | | Occurrence: 1 | -| | | Position: 24 | +| | | Position: 24.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/prod_start_date.md b/mixs6/prod_start_date.md index ea26e784..4b8f32a5 100644 --- a/mixs6/prod_start_date.md +++ b/mixs6/prod_start_date.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:prod_start_date](https://w3id.org/mixs/vocab/prod_start_date) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT [Date](types/Date.md) ## Parents @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | production start date | | **Mappings:** | | MIXS:0001008 | | **Comments:** | | Expected value: timestamp | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 23 | +| | | Position: 23.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='2018-05-11', description=None) | diff --git a/mixs6/profile_position.md b/mixs6/profile_position.md index d092e510..4791bf93 100644 --- a/mixs6/profile_position.md +++ b/mixs6/profile_position.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | profile position | | **Mappings:** | | MIXS:0001084 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 33 | +| | | Position: 33.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='summit', description=None) | diff --git a/mixs6/project_name.md b/mixs6/project_name.md index b09dcb56..14a810dd 100644 --- a/mixs6/project_name.md +++ b/mixs6/project_name.md @@ -38,8 +38,7 @@ None -> OPT [String](types/String.md) | | | | | --- | --- | --- | | **Aliases:** | | project name | -| **Comments:** | | Expected value: | -| | | Preferred unit: | -| | | Position: 3.0 | +| **Comments:** | | Position: 3.0 | +| | | This field is used in all packages | | **Examples:** | | Example(value='Forest soil metagenome', description=None) | diff --git a/mixs6/propagation.md b/mixs6/propagation.md index 6c5918da..6792bfb7 100644 --- a/mixs6/propagation.md +++ b/mixs6/propagation.md @@ -31,7 +31,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | propagation | | **Comments:** | | Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual | -| | | Preferred unit: | | | | Position: 27.0 | | **Examples:** | | Example(value='lytic', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/88 | diff --git a/mixs6/pulmonary_disord.md b/mixs6/pulmonary_disord.md index ff8a8cd7..1a8a19be 100644 --- a/mixs6/pulmonary_disord.md +++ b/mixs6/pulmonary_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | lung/pulmonary disorder | | **Mappings:** | | MIXS:0000269 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 30 | +| | | Position: 30.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/quad_pos.md b/mixs6/quad_pos.md index 81a77ced..f18d908d 100644 --- a/mixs6/quad_pos.md +++ b/mixs6/quad_pos.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | quadrant position | | **Mappings:** | | MIXS:0000820 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 100 | +| | | Position: 100.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='West side', description=None) | diff --git a/mixs6/radiation_regm.md b/mixs6/radiation_regm.md index 7b7d4567..6ff5351e 100644 --- a/mixs6/radiation_regm.md +++ b/mixs6/radiation_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: radiation type name;radiation amount;treatment interval and duration | | | | Preferred unit: rad, gray | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/rainfall_regm.md b/mixs6/rainfall_regm.md index 0379b700..68dcaaac 100644 --- a/mixs6/rainfall_regm.md +++ b/mixs6/rainfall_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;treatment interval and duration | | | | Preferred unit: millimeter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/reactor_type.md b/mixs6/reactor_type.md index 5f00dd4e..ecbb3dc5 100644 --- a/mixs6/reactor_type.md +++ b/mixs6/reactor_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | reactor type | | **Mappings:** | | MIXS:0000350 | | **Comments:** | | Expected value: reactor type name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/reassembly_bin.md b/mixs6/reassembly_bin.md index c94a38bd..2d11a282 100644 --- a/mixs6/reassembly_bin.md +++ b/mixs6/reassembly_bin.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | reassembly post binning | | **Comments:** | | Expected value: boolean | -| | | Preferred unit: | | | | Position: 81.0 | | **Examples:** | | Example(value='no', description=None) | diff --git a/mixs6/redox_potential.md b/mixs6/redox_potential.md index 36615afe..d6f5b81b 100644 --- a/mixs6/redox_potential.md +++ b/mixs6/redox_potential.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millivolt | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='300 millivolt', description=None) | diff --git a/mixs6/ref_biomaterial.md b/mixs6/ref_biomaterial.md index 1c8ebcb2..dfdce5b5 100644 --- a/mixs6/ref_biomaterial.md +++ b/mixs6/ref_biomaterial.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | reference for biomaterial | | **Comments:** | | Expected value: PMID, DOI or URL | -| | | Preferred unit: | | | | Position: 19.0 | | **Examples:** | | Example(value='doi:10.1016/j.syapm.2018.01.009', description=None) | diff --git a/mixs6/ref_db.md b/mixs6/ref_db.md index a7830813..cb7bccd7 100644 --- a/mixs6/ref_db.md +++ b/mixs6/ref_db.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | reference database(s) | | **Comments:** | | Expected value: names, versions, and references of databases | -| | | Preferred unit: | | | | Position: 60.0 | | **Examples:** | | Example(value='pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975', description=None) | diff --git a/mixs6/rel_air_humidity.md b/mixs6/rel_air_humidity.md index ef7307f2..5669b061 100644 --- a/mixs6/rel_air_humidity.md +++ b/mixs6/rel_air_humidity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='80%', description=None) | diff --git a/mixs6/rel_humidity_out.md b/mixs6/rel_humidity_out.md index 6d715107..8257dc63 100644 --- a/mixs6/rel_humidity_out.md +++ b/mixs6/rel_humidity_out.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram of air, kilogram of air | | | | Occurrence: 1 | -| | | Position: 98 | +| | | Position: 98.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='12 per kilogram of air', description=None) | diff --git a/mixs6/rel_samp_loc.md b/mixs6/rel_samp_loc.md index a5d7f3e5..bf4a0cea 100644 --- a/mixs6/rel_samp_loc.md +++ b/mixs6/rel_samp_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | relative sampling location | | **Mappings:** | | MIXS:0000821 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 101 | +| | | Position: 101.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='center of car', description=None) | diff --git a/mixs6/rel_to_oxygen.md b/mixs6/rel_to_oxygen.md index 8af98c6c..3d70b856 100644 --- a/mixs6/rel_to_oxygen.md +++ b/mixs6/rel_to_oxygen.md @@ -34,7 +34,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | relationship to oxygen | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 29.0 | | **Examples:** | | Example(value='aerobe', description=None) | diff --git a/mixs6/reservoir.md b/mixs6/reservoir.md index 1a2754ba..55b512e1 100644 --- a/mixs6/reservoir.md +++ b/mixs6/reservoir.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | reservoir name | | **Mappings:** | | MIXS:0000303 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/resins_pc.md b/mixs6/resins_pc.md index 48d36240..10368d39 100644 --- a/mixs6/resins_pc.md +++ b/mixs6/resins_pc.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name;measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 91 | +| | | Position: 91.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/resp_part_matter.md b/mixs6/resp_part_matter.md index 18ab9c0f..5ea24cf9 100644 --- a/mixs6/resp_part_matter.md +++ b/mixs6/resp_part_matter.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: particulate matter name;measurement value | | | | Preferred unit: microgram per cubic meter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='PM2.5;10 microgram per cubic meter', description=None) | diff --git a/mixs6/room_air_exch_rate.md b/mixs6/room_air_exch_rate.md index 21cbce51..3526c730 100644 --- a/mixs6/room_air_exch_rate.md +++ b/mixs6/room_air_exch_rate.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: liter per hour | | | | Occurrence: 1 | -| | | Position: 102 | +| | | Position: 102.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_architec_element.md b/mixs6/room_architec_element.md index 8fc56935..2afa9c45 100644 --- a/mixs6/room_architec_element.md +++ b/mixs6/room_architec_element.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | room architectural elements | | **Mappings:** | | MIXS:0000233 | | **Comments:** | | Expected value: free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 103 | +| | | Position: 103.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_condt.md b/mixs6/room_condt.md index 2a1393f6..418604e9 100644 --- a/mixs6/room_condt.md +++ b/mixs6/room_condt.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | room condition | | **Mappings:** | | MIXS:0000822 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 104 | +| | | Position: 104.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='new', description=None) | diff --git a/mixs6/room_connected.md b/mixs6/room_connected.md index f39788e4..e38a332b 100644 --- a/mixs6/room_connected.md +++ b/mixs6/room_connected.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | rooms connected by a doorway | | **Mappings:** | | MIXS:0000826 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 116 | +| | | Position: 116.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='office', description=None) | diff --git a/mixs6/room_count.md b/mixs6/room_count.md index 3cdb20f8..c830e33c 100644 --- a/mixs6/room_count.md +++ b/mixs6/room_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | room count | | **Mappings:** | | MIXS:0000234 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 105 | +| | | Position: 105.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_dim.md b/mixs6/room_dim.md index 1cba763b..60499d0e 100644 --- a/mixs6/room_dim.md +++ b/mixs6/room_dim.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 106 | +| | | Position: 106.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_door_dist.md b/mixs6/room_door_dist.md index 206ca8cc..2c4fa128 100644 --- a/mixs6/room_door_dist.md +++ b/mixs6/room_door_dist.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 107 | +| | | Position: 107.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_door_share.md b/mixs6/room_door_share.md index 22b0da5d..8698c60f 100644 --- a/mixs6/room_door_share.md +++ b/mixs6/room_door_share.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | rooms that share a door with sampling room | | **Mappings:** | | MIXS:0000242 | | **Comments:** | | Expected value: room name;room number | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 118 | +| | | Position: 118.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_hallway.md b/mixs6/room_hallway.md index 60fc8f2f..4695667b 100644 --- a/mixs6/room_hallway.md +++ b/mixs6/room_hallway.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | rooms that are on the same hallway | | **Mappings:** | | MIXS:0000238 | | **Comments:** | | Expected value: room name;room number | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 117 | +| | | Position: 117.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_loc.md b/mixs6/room_loc.md index 720b0887..9e06e0d7 100644 --- a/mixs6/room_loc.md +++ b/mixs6/room_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | room location in building | | **Mappings:** | | MIXS:0000823 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 108 | +| | | Position: 108.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='interior room', description=None) | diff --git a/mixs6/room_moist_damage_hist.md b/mixs6/room_moist_damage_hist.md index 1f7f12d9..1e061fb3 100644 --- a/mixs6/room_moist_damage_hist.md +++ b/mixs6/room_moist_damage_hist.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | room moisture damage or mold history | | **Mappings:** | | MIXS:0000235 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 109 | +| | | Position: 109.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_net_area.md b/mixs6/room_net_area.md index bce188ad..587b1a3b 100644 --- a/mixs6/room_net_area.md +++ b/mixs6/room_net_area.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square feet, square meter | | | | Occurrence: 1 | -| | | Position: 110 | +| | | Position: 110.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_occup.md b/mixs6/room_occup.md index 5ef9a1dc..4705acef 100644 --- a/mixs6/room_occup.md +++ b/mixs6/room_occup.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | room occupancy | | **Mappings:** | | MIXS:0000236 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 111 | +| | | Position: 111.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_samp_pos.md b/mixs6/room_samp_pos.md index 7003f8f1..d04a0d62 100644 --- a/mixs6/room_samp_pos.md +++ b/mixs6/room_samp_pos.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | room sampling position | | **Mappings:** | | MIXS:0000824 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 112 | +| | | Position: 112.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='south corner', description=None) | diff --git a/mixs6/room_type.md b/mixs6/room_type.md index ea4b27bf..b15925fd 100644 --- a/mixs6/room_type.md +++ b/mixs6/room_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | room type | | **Mappings:** | | MIXS:0000825 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 113 | +| | | Position: 113.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='bathroom', description=None) | diff --git a/mixs6/room_vol.md b/mixs6/room_vol.md index 6392d5da..31a0849d 100644 --- a/mixs6/room_vol.md +++ b/mixs6/room_vol.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: cubic feet, cubic meter | | | | Occurrence: 1 | -| | | Position: 114 | +| | | Position: 114.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_wall_share.md b/mixs6/room_wall_share.md index 68063d5a..bcaab353 100644 --- a/mixs6/room_wall_share.md +++ b/mixs6/room_wall_share.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | rooms that share a wall with sampling room | | **Mappings:** | | MIXS:0000243 | | **Comments:** | | Expected value: room name;room number | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 119 | +| | | Position: 119.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/room_window_count.md b/mixs6/room_window_count.md index 2a13261c..6cd875de 100644 --- a/mixs6/room_window_count.md +++ b/mixs6/room_window_count.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | room window count | | **Mappings:** | | MIXS:0000237 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 115 | +| | | Position: 115.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/root_cond.md b/mixs6/root_cond.md index 3165d47a..f2511bbb 100644 --- a/mixs6/root_cond.md +++ b/mixs6/root_cond.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | rooting conditions | | **Mappings:** | | MIXS:0001061 | | **Comments:** | | Expected value: PMID,DOI,url or free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='http://himedialabs.com/TD/PT158.pdf', description=None) | diff --git a/mixs6/root_med_carbon.md b/mixs6/root_med_carbon.md index fa4cba0c..b714e48d 100644 --- a/mixs6/root_med_carbon.md +++ b/mixs6/root_med_carbon.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: carbon source name;measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='sucrose', description=None) | diff --git a/mixs6/root_med_macronutr.md b/mixs6/root_med_macronutr.md index 1e1f5ba2..12b15365 100644 --- a/mixs6/root_med_macronutr.md +++ b/mixs6/root_med_macronutr.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: macronutrient name;measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='KH2PO4;170¬†milligram per liter', description=None) | diff --git a/mixs6/root_med_micronutr.md b/mixs6/root_med_micronutr.md index da50d0f6..f7e89093 100644 --- a/mixs6/root_med_micronutr.md +++ b/mixs6/root_med_micronutr.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: micronutrient name;measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='H3BO3;6.2¬†milligram per liter', description=None) | diff --git a/mixs6/root_med_ph.md b/mixs6/root_med_ph.md index b1bb72c4..9af9c472 100644 --- a/mixs6/root_med_ph.md +++ b/mixs6/root_med_ph.md @@ -40,9 +40,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | rooting medium pH | | **Mappings:** | | MIXS:0001062 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='7.5', description=None) | diff --git a/mixs6/root_med_regl.md b/mixs6/root_med_regl.md index 731214dc..0fc51c79 100644 --- a/mixs6/root_med_regl.md +++ b/mixs6/root_med_regl.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: regulator name;measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='abscisic acid;0.75 milligram per liter', description=None) | diff --git a/mixs6/root_med_solid.md b/mixs6/root_med_solid.md index f1b76d25..1194f84f 100644 --- a/mixs6/root_med_solid.md +++ b/mixs6/root_med_solid.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | rooting medium solidifier | | **Mappings:** | | MIXS:0001063 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='agar', description=None) | diff --git a/mixs6/root_med_suppl.md b/mixs6/root_med_suppl.md index d7c075b1..d1240766 100644 --- a/mixs6/root_med_suppl.md +++ b/mixs6/root_med_suppl.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: supplement name;measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='nicotinic acid;0.5 milligram per liter', description=None) | diff --git a/mixs6/salinity.md b/mixs6/salinity.md index bf562fb4..5e0bf704 100644 --- a/mixs6/salinity.md +++ b/mixs6/salinity.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: practical salinity unit, percentage | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='25 practical salinity unit', description=None) | diff --git a/mixs6/salinity_meth.md b/mixs6/salinity_meth.md index 80937d28..6ed377b3 100644 --- a/mixs6/salinity_meth.md +++ b/mixs6/salinity_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | extreme_unusual_properties/salinity method | | **Mappings:** | | MIXS:0000341 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 47 | +| | | Position: 47.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/salt_regm.md b/mixs6/salt_regm.md index 364b9e3a..fe5d387b 100644 --- a/mixs6/salt_regm.md +++ b/mixs6/salt_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: salt name;salt amount;treatment interval and duration | | | | Preferred unit: gram, microgram, mole per liter, gram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/samp_capt_status.md b/mixs6/samp_capt_status.md index 048e6c70..1adcfbbb 100644 --- a/mixs6/samp_capt_status.md +++ b/mixs6/samp_capt_status.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | sample capture status | | **Mappings:** | | MIXS:0000860 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='farm sample', description=None) | diff --git a/mixs6/samp_collect_device.md b/mixs6/samp_collect_device.md deleted file mode 100644 index 59a21dcd..00000000 --- a/mixs6/samp_collect_device.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Slot: samp_collect_device - - -The method or device employed for collecting the sample - -URI: [mixs.vocab:samp_collect_device](https://w3id.org/mixs/vocab/samp_collect_device) - - -## Domain and Range - -None -> OPT [String](types/String.md) - -## Parents - - * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) - -## Children - - * [ME➞samp_collect_device](ME_samp_collect_device.md) - * [MIGS bacteria➞samp_collect_device](MIGS_bacteria_samp_collect_device.md) - * [MIGS eukaryote➞samp_collect_device](MIGS_eukaryote_samp_collect_device.md) - * [MIGS org➞samp_collect_device](MIGS_org_samp_collect_device.md) - * [MIGS plant➞samp_collect_device](MIGS_plant_samp_collect_device.md) - * [MIGS virus➞samp_collect_device](MIGS_virus_samp_collect_device.md) - * [MIMAG➞samp_collect_device](MIMAG_samp_collect_device.md) - * [MIMARKS specimen➞samp_collect_device](MIMARKS_specimen_samp_collect_device.md) - * [MIMARKS survey➞samp_collect_device](MIMARKS_survey_samp_collect_device.md) - * [MISAG➞samp_collect_device](MISAG_samp_collect_device.md) - * [MIUVIG➞samp_collect_device](MIUVIG_samp_collect_device.md) - -## Used by - - * [Core](Core.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | sample collection device or method | -| **Comments:** | | Expected value: type name | -| | | Preferred unit: | -| | | Position: 31.0 | -| **Examples:** | | Example(value='environmental swab sampling, biopsy, niskin bottle, push core', description=None) | - diff --git a/mixs6/samp_collection_point.md b/mixs6/samp_collection_point.md index 2373015e..ffe2f799 100644 --- a/mixs6/samp_collection_point.md +++ b/mixs6/samp_collection_point.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | sample collection point | | **Mappings:** | | MIXS:0001015 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 39 | +| | | Position: 39.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='well', description=None) | diff --git a/mixs6/samp_dis_stage.md b/mixs6/samp_dis_stage.md index 4640e0c7..75757c62 100644 --- a/mixs6/samp_dis_stage.md +++ b/mixs6/samp_dis_stage.md @@ -9,7 +9,7 @@ URI: [mixs.vocab:samp_dis_stage](https://w3id.org/mixs/vocab/samp_dis_stage) ## Domain and Range -None -> OPT [String](types/String.md) +None -> OPT ## Parents @@ -51,10 +51,9 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | sample disease stage | | **Mappings:** | | MIXS:0000249 | -| **Comments:** | | Expected value: free text | -| | | Preferred unit: | +| **Comments:** | | Expected value: enumeration | | | | Occurrence: 1 | -| | | Position: 6 | +| | | Position: 6.0 | | | | This field is used in: 2 packages: host-associated, plant-associated | | **Examples:** | | Example(value='infection', description=None) | diff --git a/mixs6/samp_floor.md b/mixs6/samp_floor.md index b485db6e..932f5fdd 100644 --- a/mixs6/samp_floor.md +++ b/mixs6/samp_floor.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | sampling floor | | **Mappings:** | | MIXS:0000828 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 121 | +| | | Position: 121.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='4th floor', description=None) | diff --git a/mixs6/samp_loc_corr_rate.md b/mixs6/samp_loc_corr_rate.md index 2afdd3c6..ca96776c 100644 --- a/mixs6/samp_loc_corr_rate.md +++ b/mixs6/samp_loc_corr_rate.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value range | | | | Preferred unit: millimeter per year | | | | Occurrence: 1 | -| | | Position: 34 | +| | | Position: 34.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_mat_process.md b/mixs6/samp_mat_process.md index 20839dcd..4cb31948 100644 --- a/mixs6/samp_mat_process.md +++ b/mixs6/samp_mat_process.md @@ -2,7 +2,7 @@ # Slot: samp_mat_process -Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI +A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. URI: [mixs.vocab:samp_mat_process](https://w3id.org/mixs/vocab/samp_mat_process) @@ -38,8 +38,7 @@ None -> OPT [String](types/String.md) | | | | | --- | --- | --- | | **Aliases:** | | sample material processing | -| **Comments:** | | Expected value: text or OBI | -| | | Preferred unit: | +| **Comments:** | | Expected value: text | | | | Position: 32.0 | | **Examples:** | | Example(value='filtering of seawater, storing samples in ethanol', description=None) | diff --git a/mixs6/samp_md.md b/mixs6/samp_md.md index cf96da84..a8f00141 100644 --- a/mixs6/samp_md.md +++ b/mixs6/samp_md.md @@ -42,7 +42,7 @@ None -> OPT | **Comments:** | | Expected value: measurement value;enumeration | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 43 | +| | | Position: 43.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='1534 meter;MSL', description=None) | diff --git a/mixs6/samp_preserv.md b/mixs6/samp_preserv.md index d615e0f4..8efb600a 100644 --- a/mixs6/samp_preserv.md +++ b/mixs6/samp_preserv.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name;measurement value | | | | Preferred unit: milliliter | | | | Occurrence: 1 | -| | | Position: 46 | +| | | Position: 46.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_room_id.md b/mixs6/samp_room_id.md index 36741ba1..6b10107e 100644 --- a/mixs6/samp_room_id.md +++ b/mixs6/samp_room_id.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sampling room ID or name | | **Mappings:** | | MIXS:0000244 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 122 | +| | | Position: 122.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_salinity.md b/mixs6/samp_salinity.md index f34a059d..9f008837 100644 --- a/mixs6/samp_salinity.md +++ b/mixs6/samp_salinity.md @@ -162,7 +162,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, practical salinity unit, percentage | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 11 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, plant-associated, wastewater_sludge | | **Examples:** | | Example(value='1 milligram per liter', description=None) | diff --git a/mixs6/samp_sort_meth.md b/mixs6/samp_sort_meth.md index 6620affd..9d1ceb82 100644 --- a/mixs6/samp_sort_meth.md +++ b/mixs6/samp_sort_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sample size sorting method | | **Mappings:** | | MIXS:0000216 | | **Comments:** | | Expected value: description of method | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 22 | +| | | Position: 22.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_store_dur.md b/mixs6/samp_store_dur.md index c271c9e5..8fab1347 100644 --- a/mixs6/samp_store_dur.md +++ b/mixs6/samp_store_dur.md @@ -208,9 +208,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sample storage duration | | **Mappings:** | | MIXS:0000116 | | **Comments:** | | Expected value: duration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='P1Y6M', description=None) | diff --git a/mixs6/samp_store_loc.md b/mixs6/samp_store_loc.md index 5a72cfc6..ba8e2ffd 100644 --- a/mixs6/samp_store_loc.md +++ b/mixs6/samp_store_loc.md @@ -208,9 +208,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sample storage location | | **Mappings:** | | MIXS:0000755 | | **Comments:** | | Expected value: location name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='Freezer no:5', description=None) | diff --git a/mixs6/samp_store_temp.md b/mixs6/samp_store_temp.md index fb973fcd..b0fcafad 100644 --- a/mixs6/samp_store_temp.md +++ b/mixs6/samp_store_temp.md @@ -210,7 +210,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='-80 degree Celsius', description=None) | diff --git a/mixs6/samp_subtype.md b/mixs6/samp_subtype.md index 8fa07c34..c8b4167e 100644 --- a/mixs6/samp_subtype.md +++ b/mixs6/samp_subtype.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | sample subtype | | **Mappings:** | | MIXS:0000999 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 38 | +| | | Position: 38.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='biofilm', description=None) | diff --git a/mixs6/samp_time_out.md b/mixs6/samp_time_out.md index 978123de..b9c273e1 100644 --- a/mixs6/samp_time_out.md +++ b/mixs6/samp_time_out.md @@ -42,7 +42,7 @@ None -> OPT [Double](types/Double.md) | **Comments:** | | Expected value: time | | | | Preferred unit: hour | | | | Occurrence: 1 | -| | | Position: 123 | +| | | Position: 123.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_transport_cond.md b/mixs6/samp_transport_cond.md index 196bd163..6960df8a 100644 --- a/mixs6/samp_transport_cond.md +++ b/mixs6/samp_transport_cond.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;measurement value | | | | Preferred unit: days;degree Celsius | | | | Occurrence: 1 | -| | | Position: 47 | +| | | Position: 47.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='5 days;-20 degree Celsius', description=None) | diff --git a/mixs6/samp_tvdss.md b/mixs6/samp_tvdss.md index 63700453..630dff66 100644 --- a/mixs6/samp_tvdss.md +++ b/mixs6/samp_tvdss.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value or measurement value range | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 42 | +| | | Position: 42.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/samp_type.md b/mixs6/samp_type.md index 3e9c36c2..9a05167c 100644 --- a/mixs6/samp_type.md +++ b/mixs6/samp_type.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | sample type | | **Mappings:** | | MIXS:0000998 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 37 | +| | | Position: 37.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='solid deposit', description=None) | diff --git a/mixs6/samp_vol_we_dna_ext.md b/mixs6/samp_vol_we_dna_ext.md index 7ba4dd0c..8eb03232 100644 --- a/mixs6/samp_vol_we_dna_ext.md +++ b/mixs6/samp_vol_we_dna_ext.md @@ -222,7 +222,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millliter, gram, milligram, square centimeter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 16 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater_sludge, water | | **Examples:** | | Example(value='1500 milliliter', description=None) | diff --git a/mixs6/samp_weather.md b/mixs6/samp_weather.md index 70b4aa0b..95b8d701 100644 --- a/mixs6/samp_weather.md +++ b/mixs6/samp_weather.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | sampling day weather | | **Mappings:** | | MIXS:0000827 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 120 | +| | | Position: 120.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='foggy', description=None) | diff --git a/mixs6/samp_well_name.md b/mixs6/samp_well_name.md index dceffe3a..d175d559 100644 --- a/mixs6/samp_well_name.md +++ b/mixs6/samp_well_name.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sample well name | | **Mappings:** | | MIXS:0000296 | | **Comments:** | | Expected value: name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 35 | +| | | Position: 35.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/sample_collect_device.md b/mixs6/sample_collect_device.md new file mode 100644 index 00000000..d98c0341 --- /dev/null +++ b/mixs6/sample_collect_device.md @@ -0,0 +1,44 @@ + +# Slot: sample_collect_device + + +The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). + +URI: [mixs.vocab:sample_collect_device](https://w3id.org/mixs/vocab/sample_collect_device) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞sample_collect_device](ME_sample_collect_device.md) + * [MIGS bacteria➞sample_collect_device](MIGS_bacteria_sample_collect_device.md) + * [MIGS eukaryote➞sample_collect_device](MIGS_eukaryote_sample_collect_device.md) + * [MIGS org➞sample_collect_device](MIGS_org_sample_collect_device.md) + * [MIGS plant➞sample_collect_device](MIGS_plant_sample_collect_device.md) + * [MIGS virus➞sample_collect_device](MIGS_virus_sample_collect_device.md) + * [MIMAG➞sample_collect_device](MIMAG_sample_collect_device.md) + * [MIMARKS specimen➞sample_collect_device](MIMARKS_specimen_sample_collect_device.md) + * [MIMARKS survey➞sample_collect_device](MIMARKS_survey_sample_collect_device.md) + * [MISAG➞sample_collect_device](MISAG_sample_collect_device.md) + * [MIUVIG➞sample_collect_device](MIUVIG_sample_collect_device.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection device | +| **Comments:** | | Expected value: device name | +| | | Position: 31.0 | +| **Examples:** | | Example(value='swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]', description=None) | + diff --git a/mixs6/sample_collect_method.md b/mixs6/sample_collect_method.md new file mode 100644 index 00000000..51343740 --- /dev/null +++ b/mixs6/sample_collect_method.md @@ -0,0 +1,43 @@ + +# Slot: sample_collect_method + + +The method employed for collecting the sample. + +URI: [mixs.vocab:sample_collect_method](https://w3id.org/mixs/vocab/sample_collect_method) + + +## Domain and Range + +None -> OPT [String](types/String.md) + +## Parents + + * is_a: [nucleic acid sequence source field](nucleic_acid_sequence_source_field.md) + +## Children + + * [ME➞sample_collect_method](ME_sample_collect_method.md) + * [MIGS bacteria➞sample_collect_method](MIGS_bacteria_sample_collect_method.md) + * [MIGS eukaryote➞sample_collect_method](MIGS_eukaryote_sample_collect_method.md) + * [MIGS org➞sample_collect_method](MIGS_org_sample_collect_method.md) + * [MIGS plant➞sample_collect_method](MIGS_plant_sample_collect_method.md) + * [MIGS virus➞sample_collect_method](MIGS_virus_sample_collect_method.md) + * [MIMAG➞sample_collect_method](MIMAG_sample_collect_method.md) + * [MIMARKS specimen➞sample_collect_method](MIMARKS_specimen_sample_collect_method.md) + * [MIMARKS survey➞sample_collect_method](MIMARKS_survey_sample_collect_method.md) + * [MISAG➞sample_collect_method](MISAG_sample_collect_method.md) + * [MIUVIG➞sample_collect_method](MIUVIG_sample_collect_method.md) + +## Used by + + * [Core](Core.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | sample collection method | +| **Comments:** | | Expected value: PMID,DOI,url , or text | +| **Examples:** | | Example(value='swabbing', description=None) | + diff --git a/mixs6/sample_name.md b/mixs6/sample_name.md index 32b6604f..5e47c653 100644 --- a/mixs6/sample_name.md +++ b/mixs6/sample_name.md @@ -13,7 +13,7 @@ None -> OPT [String](types/String.md) ## Parents - * is_a: [core field](core_field.md) + * is_a: [investigation field](investigation_field.md) ## Children @@ -38,9 +38,8 @@ None -> OPT [String](types/String.md) | | | | | --- | --- | --- | | **Aliases:** | | sample name | -| **Comments:** | | Expected value: | -| | | Preferred unit: | -| | | Position: | -| **Examples:** | | Example(value='', description=None) | +| **Comments:** | | Expected value: text | +| | | This field is used in all packages | +| **Examples:** | | Example(value='ISDsoil1', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/78 | diff --git a/mixs6/saturates_pc.md b/mixs6/saturates_pc.md index b1167a1b..c9b33519 100644 --- a/mixs6/saturates_pc.md +++ b/mixs6/saturates_pc.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: name;measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 89 | +| | | Position: 89.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/season.md b/mixs6/season.md index 112d24de..80adbba6 100644 --- a/mixs6/season.md +++ b/mixs6/season.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | season | | **Mappings:** | | MIXS:0000829 | | **Comments:** | | Expected value: NCIT:C94729 | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 124 | +| | | Position: 124.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='autumn [NCIT:C94733]', description=None) | diff --git a/mixs6/season_environment.md b/mixs6/season_environment.md index 57e167b2..de42190f 100644 --- a/mixs6/season_environment.md +++ b/mixs6/season_environment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | seasonal environment | | **Mappings:** | | MIXS:0001068 | | **Comments:** | | Expected value: seasonal environment name;treatment interval and duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/season_precpt.md b/mixs6/season_precpt.md index 3e4ceee4..1cd61607 100644 --- a/mixs6/season_precpt.md +++ b/mixs6/season_precpt.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: millimeter | | | | Occurrence: 1 | -| | | Position: 24 | +| | | Position: 24.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/season_temp.md b/mixs6/season_temp.md index fc126b77..0087e8db 100644 --- a/mixs6/season_temp.md +++ b/mixs6/season_temp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 22 | +| | | Position: 22.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='18 degree Celsius', description=None) | diff --git a/mixs6/season_use.md b/mixs6/season_use.md index 76a0ba97..e5f02cc7 100644 --- a/mixs6/season_use.md +++ b/mixs6/season_use.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | seasonal use | | **Mappings:** | | MIXS:0000830 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 125 | +| | | Position: 125.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='Winter', description=None) | diff --git a/mixs6/secondary_treatment.md b/mixs6/secondary_treatment.md index 1e3529ba..db1ffd28 100644 --- a/mixs6/secondary_treatment.md +++ b/mixs6/secondary_treatment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | secondary treatment | | **Mappings:** | | MIXS:0000351 | | **Comments:** | | Expected value: secondary treatment type | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/sediment_type.md b/mixs6/sediment_type.md index f7ef1fac..1df30c9a 100644 --- a/mixs6/sediment_type.md +++ b/mixs6/sediment_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | sediment type | | **Mappings:** | | MIXS:0001078 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: sediment | | **Examples:** | | Example(value='biogenous', description=None) | diff --git a/mixs6/seq_meth.md b/mixs6/seq_meth.md index 7be0dd84..eb5719fa 100644 --- a/mixs6/seq_meth.md +++ b/mixs6/seq_meth.md @@ -39,7 +39,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | sequencing method | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 50.0 | | **Examples:** | | Example(value='Illumina HiSeq 1500', description=None) | diff --git a/mixs6/seq_quality_check.md b/mixs6/seq_quality_check.md index f2c2bb8e..29247655 100644 --- a/mixs6/seq_quality_check.md +++ b/mixs6/seq_quality_check.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | sequence quality check | | **Comments:** | | Expected value: none or manually edited | -| | | Preferred unit: | | | | Position: 51.0 | | **Examples:** | | Example(value='none', description=None) | diff --git a/mixs6/sequencing_field.md b/mixs6/sequencing_field.md index a85367e3..0d6c4d13 100644 --- a/mixs6/sequencing_field.md +++ b/mixs6/sequencing_field.md @@ -72,7 +72,6 @@ None -> OPT [String](types/String.md) * [wga_amp_appr](wga_amp_appr.md) * [wga_amp_kit](wga_amp_kit.md) * [x_16s_recover](x_16s_recover.md) - * [x_16s_recover_software](x_16s_recover_software.md) ## Used by diff --git a/mixs6/sewage_type.md b/mixs6/sewage_type.md index 4fbaf3b3..ae42908c 100644 --- a/mixs6/sewage_type.md +++ b/mixs6/sewage_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sewage type | | **Mappings:** | | MIXS:0000215 | | **Comments:** | | Expected value: sewage type name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/sexual_act.md b/mixs6/sexual_act.md index cb551f0f..84b3719c 100644 --- a/mixs6/sexual_act.md +++ b/mixs6/sexual_act.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | sexual activity | | **Mappings:** | | MIXS:0000285 | | **Comments:** | | Expected value: partner sex;frequency | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/shading_device_cond.md b/mixs6/shading_device_cond.md index f7e00f98..256229ff 100644 --- a/mixs6/shading_device_cond.md +++ b/mixs6/shading_device_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | shading device condition | | **Mappings:** | | MIXS:0000831 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 126 | +| | | Position: 126.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='new', description=None) | diff --git a/mixs6/shading_device_loc.md b/mixs6/shading_device_loc.md index 775e4cb4..cae73c53 100644 --- a/mixs6/shading_device_loc.md +++ b/mixs6/shading_device_loc.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | shading device location | | **Mappings:** | | MIXS:0000832 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 127 | +| | | Position: 127.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='exterior', description=None) | diff --git a/mixs6/shading_device_mat.md b/mixs6/shading_device_mat.md index 9d5065b6..a2140f18 100644 --- a/mixs6/shading_device_mat.md +++ b/mixs6/shading_device_mat.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | shading device material | | **Mappings:** | | MIXS:0000245 | | **Comments:** | | Expected value: material name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 128 | +| | | Position: 128.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/shading_device_type.md b/mixs6/shading_device_type.md index 625cc43c..61d23db3 100644 --- a/mixs6/shading_device_type.md +++ b/mixs6/shading_device_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | shading device type | | **Mappings:** | | MIXS:0000835 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 130 | +| | | Position: 130.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='slatted aluminum awning', description=None) | diff --git a/mixs6/shading_device_water_mold.md b/mixs6/shading_device_water_mold.md index 3b041c4f..3a20178f 100644 --- a/mixs6/shading_device_water_mold.md +++ b/mixs6/shading_device_water_mold.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | shading device signs of water/mold | | **Mappings:** | | MIXS:0000834 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 129 | +| | | Position: 129.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='no presence of mold visible', description=None) | diff --git a/mixs6/sieving.md b/mixs6/sieving.md index 2796bbbe..42523bad 100644 --- a/mixs6/sieving.md +++ b/mixs6/sieving.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | composite design/sieving (if any) | | **Mappings:** | | MIXS:0000322 | | **Comments:** | | Expected value: design name and/or size;amount | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 14 | +| | | Position: 14.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/silicate.md b/mixs6/silicate.md index e6feef8e..2a3f5d66 100644 --- a/mixs6/silicate.md +++ b/mixs6/silicate.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='0.05 micromole per liter', description=None) | diff --git a/mixs6/sim_search_meth.md b/mixs6/sim_search_meth.md index 5301445d..944a98a2 100644 --- a/mixs6/sim_search_meth.md +++ b/mixs6/sim_search_meth.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | similarity search method | | **Comments:** | | Expected value: names and versions of software(s), parameters used | -| | | Preferred unit: | | | | Position: 61.0 | | **Examples:** | | Example(value='HMMER3;3.1b2;hmmsearch, cutoff of 50 on score', description=None) | diff --git a/mixs6/single_cell_lysis_appr.md b/mixs6/single_cell_lysis_appr.md index f7b73f8c..adb609ee 100644 --- a/mixs6/single_cell_lysis_appr.md +++ b/mixs6/single_cell_lysis_appr.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | single cell or viral particle lysis approach | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 75.0 | | **Examples:** | | Example(value='enzymatic', description=None) | diff --git a/mixs6/single_cell_lysis_prot.md b/mixs6/single_cell_lysis_prot.md index 118970f4..203ea700 100644 --- a/mixs6/single_cell_lysis_prot.md +++ b/mixs6/single_cell_lysis_prot.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | single cell or viral particle lysis kit protocol | | **Comments:** | | Expected value: kit, protocol name | -| | | Preferred unit: | | | | Position: 76.0 | | **Examples:** | | Example(value='ambion single cell lysis kit', description=None) | diff --git a/mixs6/size_frac.md b/mixs6/size_frac.md index a2b9dcb9..c82690df 100644 --- a/mixs6/size_frac.md +++ b/mixs6/size_frac.md @@ -33,7 +33,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | size fraction selected | | **Comments:** | | Expected value: filter size value range | -| | | Preferred unit: | | | | Position: 33.0 | | **Examples:** | | Example(value='0-0.22 micrometer', description=None) | diff --git a/mixs6/size_frac_low.md b/mixs6/size_frac_low.md index 00adda41..7f164dd9 100644 --- a/mixs6/size_frac_low.md +++ b/mixs6/size_frac_low.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: micrometer | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='0.2 micrometer', description=None) | diff --git a/mixs6/size_frac_up.md b/mixs6/size_frac_up.md index 3fce79c0..ed7dee09 100644 --- a/mixs6/size_frac_up.md +++ b/mixs6/size_frac_up.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: micrometer | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='20 micrometer', description=None) | diff --git a/mixs6/slope_aspect.md b/mixs6/slope_aspect.md index 5a4ae480..42625811 100644 --- a/mixs6/slope_aspect.md +++ b/mixs6/slope_aspect.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree | | | | Occurrence: 1 | -| | | Position: 32 | +| | | Position: 32.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/slope_gradient.md b/mixs6/slope_gradient.md index 9ba5f8ff..4833d6e2 100644 --- a/mixs6/slope_gradient.md +++ b/mixs6/slope_gradient.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 31 | +| | | Position: 31.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/sludge_retent_time.md b/mixs6/sludge_retent_time.md index 199985fb..b6375977 100644 --- a/mixs6/sludge_retent_time.md +++ b/mixs6/sludge_retent_time.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: hours | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/smoker.md b/mixs6/smoker.md index 272e6702..9923ff4d 100644 --- a/mixs6/smoker.md +++ b/mixs6/smoker.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | smoker | | **Mappings:** | | MIXS:0000262 | | **Comments:** | | Expected value: smoking status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 17 | +| | | Position: 17.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/sodium.md b/mixs6/sodium.md index 7424e3b3..d45d486c 100644 --- a/mixs6/sodium.md +++ b/mixs6/sodium.md @@ -114,7 +114,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 66 | +| | | Position: 66.0 | | | | This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='10.5 milligram per liter', description=None) | diff --git a/mixs6/soil_type.md b/mixs6/soil_type.md index 7f90cf82..cf2ac75d 100644 --- a/mixs6/soil_type.md +++ b/mixs6/soil_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | soil type | | **Mappings:** | | MIXS:0000332 | | **Comments:** | | Expected value: soil type name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 29 | +| | | Position: 29.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/soil_type_meth.md b/mixs6/soil_type_meth.md index 1aa0c6ea..03c95050 100644 --- a/mixs6/soil_type_meth.md +++ b/mixs6/soil_type_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | soil type method | | **Mappings:** | | MIXS:0000334 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 30 | +| | | Position: 30.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/solar_irradiance.md b/mixs6/solar_irradiance.md index d6312ed6..e6237175 100644 --- a/mixs6/solar_irradiance.md +++ b/mixs6/solar_irradiance.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: kilowatts per square meter per day, ergs per square centimeter per second | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='1.36 kilowatts per square meter per day', description=None) | diff --git a/mixs6/soluble_inorg_mat.md b/mixs6/soluble_inorg_mat.md index bd7abeaa..928a87cd 100644 --- a/mixs6/soluble_inorg_mat.md +++ b/mixs6/soluble_inorg_mat.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: soluble inorganic material name;measurement value | | | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/soluble_org_mat.md b/mixs6/soluble_org_mat.md index 1f01e446..25b97b61 100644 --- a/mixs6/soluble_org_mat.md +++ b/mixs6/soluble_org_mat.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: soluble organic material name;measurement value | | | | Preferred unit: gram, microgram, mole per liter, gram per liter, parts per million | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/soluble_react_phosp.md b/mixs6/soluble_react_phosp.md index e0b0a190..7ec85d5c 100644 --- a/mixs6/soluble_react_phosp.md +++ b/mixs6/soluble_react_phosp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='0.1 milligram per liter', description=None) | diff --git a/mixs6/sop.md b/mixs6/sop.md index c19dd16c..1d45b831 100644 --- a/mixs6/sop.md +++ b/mixs6/sop.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | relevant standard operating procedures | | **Comments:** | | Expected value: reference to SOP | -| | | Preferred unit: | | | | Position: 93.0 | | **Examples:** | | Example(value='http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/', description=None) | diff --git a/mixs6/sort_tech.md b/mixs6/sort_tech.md index 9741f208..471f0b2c 100644 --- a/mixs6/sort_tech.md +++ b/mixs6/sort_tech.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | sorting technology | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 74.0 | | **Examples:** | | Example(value='optical manipulation', description=None) | diff --git a/mixs6/source_mat_id.md b/mixs6/source_mat_id.md index 6b478f3d..a0a2fd0a 100644 --- a/mixs6/source_mat_id.md +++ b/mixs6/source_mat_id.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | source material identifiers | | **Comments:** | | Expected value: for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer | -| | | Preferred unit: | | | | Position: 20.0 | | **Examples:** | | Example(value='MPI012345', description=None) | diff --git a/mixs6/source_uvig.md b/mixs6/source_uvig.md index 3bedba26..e38df17b 100644 --- a/mixs6/source_uvig.md +++ b/mixs6/source_uvig.md @@ -29,7 +29,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | source of UViGs | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 35.0 | | **Examples:** | | Example(value='viral fraction metagenome (virome)', description=None) | diff --git a/mixs6/space_typ_state.md b/mixs6/space_typ_state.md index 29f2f90b..58aa901f 100644 --- a/mixs6/space_typ_state.md +++ b/mixs6/space_typ_state.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | space typical state | | **Mappings:** | | MIXS:0000770 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 23 | +| | | Position: 23.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='typically occupied', description=None) | diff --git a/mixs6/special_diet.md b/mixs6/special_diet.md index 2cce5583..455bd8ca 100644 --- a/mixs6/special_diet.md +++ b/mixs6/special_diet.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | special diet | | **Mappings:** | | MIXS:0000905 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 3 | +| | | Position: 3.0 | | | | This field is used uniquely in: human-gut | | **Examples:** | | Example(value='other:vegan', description=None) | diff --git a/mixs6/specific.md b/mixs6/specific.md index 06e4395b..4b7fcc89 100644 --- a/mixs6/specific.md +++ b/mixs6/specific.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | specifications | | **Mappings:** | | MIXS:0000836 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 132 | +| | | Position: 132.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='construction', description=None) | diff --git a/mixs6/specific_host.md b/mixs6/specific_host.md index 5d081f02..d5bc01f0 100644 --- a/mixs6/specific_host.md +++ b/mixs6/specific_host.md @@ -33,7 +33,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | specific host | | **Comments:** | | Expected value: host taxid, unknown, environmental | -| | | Preferred unit: | | | | Position: 23.0 | | **Examples:** | | Example(value='9606', description=None) | diff --git a/mixs6/specific_humidity.md b/mixs6/specific_humidity.md index baa932bc..d68077f4 100644 --- a/mixs6/specific_humidity.md +++ b/mixs6/specific_humidity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram of air, kilogram of air | | | | Occurrence: 1 | -| | | Position: 131 | +| | | Position: 131.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='15 per kilogram of air', description=None) | diff --git a/mixs6/sr_dep_env.md b/mixs6/sr_dep_env.md index 900b1f61..930220a0 100644 --- a/mixs6/sr_dep_env.md +++ b/mixs6/sr_dep_env.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | source rock depositional environment | | **Mappings:** | | MIXS:0000996 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 21 | +| | | Position: 21.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='Marine', description=None) | diff --git a/mixs6/sr_geol_age.md b/mixs6/sr_geol_age.md index 7018fac5..c0f152f2 100644 --- a/mixs6/sr_geol_age.md +++ b/mixs6/sr_geol_age.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | source rock geological age | | **Mappings:** | | MIXS:0000997 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 22 | +| | | Position: 22.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='Silurian', description=None) | diff --git a/mixs6/sr_kerog_type.md b/mixs6/sr_kerog_type.md index 0723754e..a8734b8f 100644 --- a/mixs6/sr_kerog_type.md +++ b/mixs6/sr_kerog_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | source rock kerogen type | | **Mappings:** | | MIXS:0000994 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 19 | +| | | Position: 19.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='Type IV', description=None) | diff --git a/mixs6/sr_lithology.md b/mixs6/sr_lithology.md index 110f5f4c..f8cccd26 100644 --- a/mixs6/sr_lithology.md +++ b/mixs6/sr_lithology.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | source rock lithology | | **Mappings:** | | MIXS:0000995 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 20 | +| | | Position: 20.0 | | | | This field is used uniquely in: hydrocarbon resources-cores | | **Examples:** | | Example(value='Coal', description=None) | diff --git a/mixs6/standing_water_regm.md b/mixs6/standing_water_regm.md index dc3f0f73..6021a42e 100644 --- a/mixs6/standing_water_regm.md +++ b/mixs6/standing_water_regm.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | standing water regimen | | **Mappings:** | | MIXS:0001069 | | **Comments:** | | Expected value: standing water type;treatment interval and duration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/store_cond.md b/mixs6/store_cond.md index d05a7fec..46c7368f 100644 --- a/mixs6/store_cond.md +++ b/mixs6/store_cond.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | storage conditions (fresh/frozen/other) | | **Mappings:** | | MIXS:0000327 | | **Comments:** | | Expected value: storage condition type;duration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 19 | +| | | Position: 19.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='-20 degree Celsius freezer;P2Y10D', description=None) | diff --git a/mixs6/study_complt_stat.md b/mixs6/study_complt_stat.md index 5e43b5aa..70416b0c 100644 --- a/mixs6/study_complt_stat.md +++ b/mixs6/study_complt_stat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | study completion status | | **Mappings:** | | MIXS:0000898 | | **Comments:** | | Expected value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow up (4)other-specify | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 29 | +| | | Position: 29.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='no;non-compliance', description=None) | diff --git a/mixs6/submitted_to_insdc.md b/mixs6/submitted_to_insdc.md index 0af177a4..179c0b35 100644 --- a/mixs6/submitted_to_insdc.md +++ b/mixs6/submitted_to_insdc.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | submitted to insdc | | **Comments:** | | Expected value: boolean | -| | | Preferred unit: | | | | Position: 1.0 | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/subspecf_gen_lin.md b/mixs6/subspecf_gen_lin.md index 9c5bed12..63f13ed7 100644 --- a/mixs6/subspecf_gen_lin.md +++ b/mixs6/subspecf_gen_lin.md @@ -34,7 +34,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | subspecific genetic lineage | | **Comments:** | | Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype | -| | | Preferred unit: | | | | Position: 14.0 | | **Examples:** | | Example(value='serovar:Newport', description=None) | diff --git a/mixs6/substructure_type.md b/mixs6/substructure_type.md index d9e921eb..14d5432a 100644 --- a/mixs6/substructure_type.md +++ b/mixs6/substructure_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | substructure type | | **Mappings:** | | MIXS:0000767 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 19 | +| | | Position: 19.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='basement', description=None) | diff --git a/mixs6/sulfate.md b/mixs6/sulfate.md index d9c88fcf..be49d46c 100644 --- a/mixs6/sulfate.md +++ b/mixs6/sulfate.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 58 | +| | | Position: 58.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='5 micromole per liter', description=None) | diff --git a/mixs6/sulfate_fw.md b/mixs6/sulfate_fw.md index d3f9a9f3..e8f152e5 100644 --- a/mixs6/sulfate_fw.md +++ b/mixs6/sulfate_fw.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 17 | +| | | Position: 17.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/sulfide.md b/mixs6/sulfide.md index f9b7c045..1fe3b74f 100644 --- a/mixs6/sulfide.md +++ b/mixs6/sulfide.md @@ -102,7 +102,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 59 | +| | | Position: 59.0 | | | | This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, sediment, water | | **Examples:** | | Example(value='2 micromole per liter', description=None) | diff --git a/mixs6/surf_air_cont.md b/mixs6/surf_air_cont.md index d159879b..c0108d93 100644 --- a/mixs6/surf_air_cont.md +++ b/mixs6/surf_air_cont.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | surface-air contaminant | | **Mappings:** | | MIXS:0000759 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='radon', description=None) | diff --git a/mixs6/surf_humidity.md b/mixs6/surf_humidity.md index 72af3ddb..9ba9e579 100644 --- a/mixs6/surf_humidity.md +++ b/mixs6/surf_humidity.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percentage | | | | Occurrence: 1 | -| | | Position: 5 | +| | | Position: 5.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='10%', description=None) | diff --git a/mixs6/surf_material.md b/mixs6/surf_material.md index f0a9765e..2b6cf9b9 100644 --- a/mixs6/surf_material.md +++ b/mixs6/surf_material.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | surface material | | **Mappings:** | | MIXS:0000758 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wood', description=None) | diff --git a/mixs6/surf_moisture.md b/mixs6/surf_moisture.md index d0f15547..bb1aa5b6 100644 --- a/mixs6/surf_moisture.md +++ b/mixs6/surf_moisture.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: parts per million, gram per cubic meter, gram per square meter | | | | Occurrence: 1 | -| | | Position: 10 | +| | | Position: 10.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='0.01 gram per square meter', description=None) | diff --git a/mixs6/surf_moisture_ph.md b/mixs6/surf_moisture_ph.md index f152361c..338cb57c 100644 --- a/mixs6/surf_moisture_ph.md +++ b/mixs6/surf_moisture_ph.md @@ -40,9 +40,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | surface moisture pH | | **Mappings:** | | MIXS:0000760 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 8 | +| | | Position: 8.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='7', description=None) | diff --git a/mixs6/surf_temp.md b/mixs6/surf_temp.md index 77e15c5c..96707552 100644 --- a/mixs6/surf_temp.md +++ b/mixs6/surf_temp.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 7 | +| | | Position: 7.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='15 degree Celsius', description=None) | diff --git a/mixs6/suspend_part_matter.md b/mixs6/suspend_part_matter.md index 6a1ccefc..a9acd74f 100644 --- a/mixs6/suspend_part_matter.md +++ b/mixs6/suspend_part_matter.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='0.5 milligram per liter', description=None) | diff --git a/mixs6/suspend_solids.md b/mixs6/suspend_solids.md index b9a2f92a..002b4cee 100644 --- a/mixs6/suspend_solids.md +++ b/mixs6/suspend_solids.md @@ -66,7 +66,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: suspended solid name;measurement value | | | | Preferred unit: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million | | | | Occurrence: m | -| | | Position: 76 | +| | | Position: 76.0 | | | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tan.md b/mixs6/tan.md index b6919f17..70559516 100644 --- a/mixs6/tan.md +++ b/mixs6/tan.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 86 | +| | | Position: 86.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/target_gene.md b/mixs6/target_gene.md index dc6ffb23..11c10f64 100644 --- a/mixs6/target_gene.md +++ b/mixs6/target_gene.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | target gene | | **Comments:** | | Expected value: gene name | -| | | Preferred unit: | | | | Position: 44.0 | | **Examples:** | | Example(value='16S rRNA, 18S rRNA, nif, amoA, rpo', description=None) | diff --git a/mixs6/target_subfragment.md b/mixs6/target_subfragment.md index c73ae294..79870f66 100644 --- a/mixs6/target_subfragment.md +++ b/mixs6/target_subfragment.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | target subfragment | | **Comments:** | | Expected value: gene fragment name | -| | | Preferred unit: | | | | Position: 45.0 | | **Examples:** | | Example(value='V6, V9, ITS', description=None) | diff --git a/mixs6/tax_class.md b/mixs6/tax_class.md index b1e17209..551f7374 100644 --- a/mixs6/tax_class.md +++ b/mixs6/tax_class.md @@ -37,7 +37,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | taxonomic classification | | **Comments:** | | Expected value: classification method, database name, and other parameters | -| | | Preferred unit: | | | | Position: 62.0 | | **Examples:** | | Example(value='vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)', description=None) | diff --git a/mixs6/tax_ident.md b/mixs6/tax_ident.md index 3acadeab..68c73e14 100644 --- a/mixs6/tax_ident.md +++ b/mixs6/tax_ident.md @@ -36,7 +36,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | taxonomic identity marker | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 53.0 | | **Examples:** | | Example(value='other: rpoB gene', description=None) | diff --git a/mixs6/temp.md b/mixs6/temp.md index 78abba69..062bda66 100644 --- a/mixs6/temp.md +++ b/mixs6/temp.md @@ -210,7 +210,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 15 packages: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, wastewater_sludge, water | | **Examples:** | | Example(value='25 degree Celsius', description=None) | diff --git a/mixs6/temp_out.md b/mixs6/temp_out.md index 6b0be9aa..a76b78f6 100644 --- a/mixs6/temp_out.md +++ b/mixs6/temp_out.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: degree Celsius | | | | Occurrence: 1 | -| | | Position: 133 | +| | | Position: 133.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='5 degree Celsius', description=None) | diff --git a/mixs6/tertiary_treatment.md b/mixs6/tertiary_treatment.md index 0ee67ab2..5803022c 100644 --- a/mixs6/tertiary_treatment.md +++ b/mixs6/tertiary_treatment.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | tertiary treatment | | **Mappings:** | | MIXS:0000352 | | **Comments:** | | Expected value: tertiary treatment type | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/texture.md b/mixs6/texture.md index e2e8a57c..afc767e8 100644 --- a/mixs6/texture.md +++ b/mixs6/texture.md @@ -40,9 +40,8 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Aliases:** | | texture | | **Mappings:** | | MIXS:0000335 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 35 | +| | | Position: 35.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/texture_meth.md b/mixs6/texture_meth.md index f4385b50..f741d2e0 100644 --- a/mixs6/texture_meth.md +++ b/mixs6/texture_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | texture method | | **Mappings:** | | MIXS:0000336 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 36 | +| | | Position: 36.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tidal_stage.md b/mixs6/tidal_stage.md index 2ef5392e..dd33cb20 100644 --- a/mixs6/tidal_stage.md +++ b/mixs6/tidal_stage.md @@ -52,9 +52,8 @@ None -> OPT | **Aliases:** | | tidal stage | | **Mappings:** | | MIXS:0000750 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: sediment, water | | **Examples:** | | Example(value='high tide', description=None) | diff --git a/mixs6/tillage.md b/mixs6/tillage.md index ad68fb6b..ae63e81d 100644 --- a/mixs6/tillage.md +++ b/mixs6/tillage.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | history/tillage | | **Mappings:** | | MIXS:0001081 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 8 | +| | | Position: 8.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='chisel', description=None) | diff --git a/mixs6/time_last_toothbrush.md b/mixs6/time_last_toothbrush.md index 4a51578e..7fa8a55f 100644 --- a/mixs6/time_last_toothbrush.md +++ b/mixs6/time_last_toothbrush.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | time since last toothbrushing | | **Mappings:** | | MIXS:0000924 | | **Comments:** | | Expected value: duration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: human-oral | | **Examples:** | | Example(value='P2H45M', description=None) | diff --git a/mixs6/time_since_last_wash.md b/mixs6/time_since_last_wash.md index 2eccd0a6..b37b4117 100644 --- a/mixs6/time_since_last_wash.md +++ b/mixs6/time_since_last_wash.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | time since last wash | | **Mappings:** | | MIXS:0000943 | | **Comments:** | | Expected value: duration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 2 | +| | | Position: 2.0 | | | | This field is used uniquely in: human-skin | | **Examples:** | | Example(value='P1D', description=None) | diff --git a/mixs6/tiss_cult_growth_med.md b/mixs6/tiss_cult_growth_med.md index 8d8b4f0c..16000de1 100644 --- a/mixs6/tiss_cult_growth_med.md +++ b/mixs6/tiss_cult_growth_med.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | tissue culture growth media | | **Mappings:** | | MIXS:0001070 | | **Comments:** | | Expected value: PMID,DOI,url or free text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='https://link.springer.com/content/pdf/10.1007/BF02796489.pdf', description=None) | diff --git a/mixs6/toluene.md b/mixs6/toluene.md index 6f7872d7..726de363 100644 --- a/mixs6/toluene.md +++ b/mixs6/toluene.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 82 | +| | | Position: 82.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_carb.md b/mixs6/tot_carb.md index 2f65eaeb..623233b5 100644 --- a/mixs6/tot_carb.md +++ b/mixs6/tot_carb.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: microbial mat_biofilm, sediment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_depth_water_col.md b/mixs6/tot_depth_water_col.md index 4e52d339..d720b0de 100644 --- a/mixs6/tot_depth_water_col.md +++ b/mixs6/tot_depth_water_col.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: sediment, water | | **Examples:** | | Example(value='500 meter', description=None) | diff --git a/mixs6/tot_diss_nitro.md b/mixs6/tot_diss_nitro.md index 73776c12..1026b816 100644 --- a/mixs6/tot_diss_nitro.md +++ b/mixs6/tot_diss_nitro.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='40 microgram per liter', description=None) | diff --git a/mixs6/tot_inorg_nitro.md b/mixs6/tot_inorg_nitro.md index d3363acf..829ff123 100644 --- a/mixs6/tot_inorg_nitro.md +++ b/mixs6/tot_inorg_nitro.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='40 microgram per liter', description=None) | diff --git a/mixs6/tot_iron.md b/mixs6/tot_iron.md index 8bb56327..1ef01b7c 100644 --- a/mixs6/tot_iron.md +++ b/mixs6/tot_iron.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, milligram per kilogram | | | | Occurrence: 1 | -| | | Position: 71 | +| | | Position: 71.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_nitro.md b/mixs6/tot_nitro.md index 185f88f2..0a4d244e 100644 --- a/mixs6/tot_nitro.md +++ b/mixs6/tot_nitro.md @@ -78,7 +78,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 64 | +| | | Position: 64.0 | | | | This field is used in: 4 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, wastewater_sludge, water | | **Examples:** | | Example(value='50 micromole per liter', description=None) | diff --git a/mixs6/tot_nitro_content.md b/mixs6/tot_nitro_content.md index d77995ba..28610c03 100644 --- a/mixs6/tot_nitro_content.md +++ b/mixs6/tot_nitro_content.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter, milligram per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_nitro_content_meth.md b/mixs6/tot_nitro_content_meth.md index ed4cf0ba..faa38921 100644 --- a/mixs6/tot_nitro_content_meth.md +++ b/mixs6/tot_nitro_content_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | total nitrogen content method | | **Mappings:** | | MIXS:0000338 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 42 | +| | | Position: 42.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_org_c_meth.md b/mixs6/tot_org_c_meth.md index 958a9978..152d1ab1 100644 --- a/mixs6/tot_org_c_meth.md +++ b/mixs6/tot_org_c_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | total organic carbon method | | **Mappings:** | | MIXS:0000337 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 40 | +| | | Position: 40.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_org_carb.md b/mixs6/tot_org_carb.md index c3731ea2..7d36f2dc 100644 --- a/mixs6/tot_org_carb.md +++ b/mixs6/tot_org_carb.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram Carbon per kilogram sample material | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_part_carb.md b/mixs6/tot_part_carb.md index 04dad259..1cbf6232 100644 --- a/mixs6/tot_part_carb.md +++ b/mixs6/tot_part_carb.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: water | | **Examples:** | | Example(value='35 micromole per liter', description=None) | diff --git a/mixs6/tot_phosp.md b/mixs6/tot_phosp.md index 508bc87b..559784c5 100644 --- a/mixs6/tot_phosp.md +++ b/mixs6/tot_phosp.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: micromole per liter, milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 75 | +| | | Position: 75.0 | | | | This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs, water | | **Examples:** | | Example(value='0.03 milligram per liter', description=None) | diff --git a/mixs6/tot_phosphate.md b/mixs6/tot_phosphate.md index 6a5a2efa..ea1dcdbd 100644 --- a/mixs6/tot_phosphate.md +++ b/mixs6/tot_phosphate.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: microgram per liter, micromole per liter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tot_sulfur.md b/mixs6/tot_sulfur.md index 6c69aaec..2f31fd1d 100644 --- a/mixs6/tot_sulfur.md +++ b/mixs6/tot_sulfur.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 60 | +| | | Position: 60.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/train_line.md b/mixs6/train_line.md index 963b9eed..a37c038e 100644 --- a/mixs6/train_line.md +++ b/mixs6/train_line.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | train line | | **Mappings:** | | MIXS:0000837 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 134 | +| | | Position: 134.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='red', description=None) | diff --git a/mixs6/train_stat_loc.md b/mixs6/train_stat_loc.md index 91b0eefe..e15e09c8 100644 --- a/mixs6/train_stat_loc.md +++ b/mixs6/train_stat_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | train station collection location | | **Mappings:** | | MIXS:0000838 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 135 | +| | | Position: 135.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='forest hills', description=None) | diff --git a/mixs6/train_stop_loc.md b/mixs6/train_stop_loc.md index 47505a00..f6ffbceb 100644 --- a/mixs6/train_stop_loc.md +++ b/mixs6/train_stop_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | train stop collection location | | **Mappings:** | | MIXS:0000839 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 136 | +| | | Position: 136.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='end', description=None) | diff --git a/mixs6/travel_out_six_month.md b/mixs6/travel_out_six_month.md index 44d419bd..7371391e 100644 --- a/mixs6/travel_out_six_month.md +++ b/mixs6/travel_out_six_month.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | travel outside the country in last six months | | **Mappings:** | | MIXS:0000268 | | **Comments:** | | Expected value: country name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 26 | +| | | Position: 26.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/trna_ext_software.md b/mixs6/trna_ext_software.md index 3fa8bd25..47678922 100644 --- a/mixs6/trna_ext_software.md +++ b/mixs6/trna_ext_software.md @@ -31,7 +31,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | tRNA extraction software | | **Comments:** | | Expected value: names and versions of software(s), parameters used | -| | | Preferred unit: | | | | Position: 66.0 | | **Examples:** | | Example(value='infernal;v2;default parameters', description=None) | diff --git a/mixs6/trnas.md b/mixs6/trnas.md index 19b856fc..4fcce512 100644 --- a/mixs6/trnas.md +++ b/mixs6/trnas.md @@ -31,7 +31,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | number of standard tRNAs extracted | | **Comments:** | | Expected value: value from 0-21 | -| | | Preferred unit: | | | | Position: 65.0 | | **Examples:** | | Example(value='18', description=None) | diff --git a/mixs6/trophic_level.md b/mixs6/trophic_level.md index 40a22648..e3f0d2a2 100644 --- a/mixs6/trophic_level.md +++ b/mixs6/trophic_level.md @@ -31,7 +31,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | trophic level | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 26.0 | | **Examples:** | | Example(value='heterotroph', description=None) | diff --git a/mixs6/turbidity.md b/mixs6/turbidity.md index 147ae0e9..dd7ad58e 100644 --- a/mixs6/turbidity.md +++ b/mixs6/turbidity.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: formazin turbidity unit, formazin nephelometric units | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, water | | **Examples:** | | Example(value='0.3 nephelometric turbidity units', description=None) | diff --git a/mixs6/tvdss_of_hcr_pressure.md b/mixs6/tvdss_of_hcr_pressure.md index 5ae80280..fc9558ce 100644 --- a/mixs6/tvdss_of_hcr_pressure.md +++ b/mixs6/tvdss_of_hcr_pressure.md @@ -2,7 +2,7 @@ # Slot: tvdss_of_hcr_pressure -True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). URI: [mixs.vocab:tvdss_of_hcr_pressure](https://w3id.org/mixs/vocab/tvdss_of_hcr_pressure) @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 9 | +| | | Position: 9.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/tvdss_of_hcr_temp.md b/mixs6/tvdss_of_hcr_temp.md index 7e1f7576..b7e281a5 100644 --- a/mixs6/tvdss_of_hcr_temp.md +++ b/mixs6/tvdss_of_hcr_temp.md @@ -2,7 +2,7 @@ # Slot: tvdss_of_hcr_temp -True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) +True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). URI: [mixs.vocab:tvdss_of_hcr_temp](https://w3id.org/mixs/vocab/tvdss_of_hcr_temp) @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter | | | | Occurrence: 1 | -| | | Position: 7 | +| | | Position: 7.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/twin_sibling.md b/mixs6/twin_sibling.md index c811dd55..0c37d3a4 100644 --- a/mixs6/twin_sibling.md +++ b/mixs6/twin_sibling.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | twin sibling presence | | **Mappings:** | | MIXS:0000326 | | **Comments:** | | Expected value: presence status | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 27 | +| | | Position: 27.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/typ_occup_density.md b/mixs6/typ_occup_density.md index 341eab2f..80f8991b 100644 --- a/mixs6/typ_occup_density.md +++ b/mixs6/typ_occup_density.md @@ -40,9 +40,8 @@ None -> OPT [Double](types/Double.md) | **Aliases:** | | typical occupant density | | **Mappings:** | | MIXS:0000771 | | **Comments:** | | Expected value: measurement value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 24 | +| | | Position: 24.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='25', description=None) | diff --git a/mixs6/urine_collect_meth.md b/mixs6/urine_collect_meth.md index 0f9527c6..fff2520f 100644 --- a/mixs6/urine_collect_meth.md +++ b/mixs6/urine_collect_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | urine/collection method | | **Mappings:** | | MIXS:0000899 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 43 | +| | | Position: 43.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='catheter', description=None) | diff --git a/mixs6/url.md b/mixs6/url.md index 2343a57b..fd52ae53 100644 --- a/mixs6/url.md +++ b/mixs6/url.md @@ -39,7 +39,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | relevant electronic resources | | **Comments:** | | Expected value: URL | -| | | Preferred unit: | | | | Position: 92.0 | | **Examples:** | | Example(value='http://www.earthmicrobiome.org/', description=None) | | **See also:** | | https://github.com/GenomicsStandardsConsortium/mixs/issues/67 | diff --git a/mixs6/urogenit_disord.md b/mixs6/urogenit_disord.md index 6d2a8c04..0b02efad 100644 --- a/mixs6/urogenit_disord.md +++ b/mixs6/urogenit_disord.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | urogenital disorder | | **Mappings:** | | MIXS:0000289 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 10 | +| | | Position: 10.0 | | | | This field is used uniquely in: human-vaginal | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/urogenit_tract_disor.md b/mixs6/urogenit_tract_disor.md index 78282de7..1c7f6693 100644 --- a/mixs6/urogenit_tract_disor.md +++ b/mixs6/urogenit_tract_disor.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | urine/urogenital tract disorder | | **Mappings:** | | MIXS:0000278 | | **Comments:** | | Expected value: disorder name | -| | | Preferred unit: | | | | Occurrence: m | -| | | Position: 41 | +| | | Position: 41.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/ventilation_rate.md b/mixs6/ventilation_rate.md index 8acfdf75..29e58a7f 100644 --- a/mixs6/ventilation_rate.md +++ b/mixs6/ventilation_rate.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: cubic meter per minute, liters per second | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='750 cubic meter per minute', description=None) | diff --git a/mixs6/ventilation_type.md b/mixs6/ventilation_type.md index bd95ac2b..049fb7e3 100644 --- a/mixs6/ventilation_type.md +++ b/mixs6/ventilation_type.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | ventilation type | | **Mappings:** | | MIXS:0000756 | | **Comments:** | | Expected value: ventilation type name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: air, built environment | | **Examples:** | | Example(value='Operable windows', description=None) | diff --git a/mixs6/vfa.md b/mixs6/vfa.md index a9693b86..48395a33 100644 --- a/mixs6/vfa.md +++ b/mixs6/vfa.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 80 | +| | | Position: 80.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/vfa_fw.md b/mixs6/vfa_fw.md index d09d63d7..6f235c99 100644 --- a/mixs6/vfa_fw.md +++ b/mixs6/vfa_fw.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter | | | | Occurrence: 1 | -| | | Position: 18 | +| | | Position: 18.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/vir_ident_software.md b/mixs6/vir_ident_software.md index e671405a..0319feee 100644 --- a/mixs6/vir_ident_software.md +++ b/mixs6/vir_ident_software.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | viral identification software | | **Comments:** | | Expected value: software name, version and relevant parameters | -| | | Preferred unit: | | | | Position: 83.0 | | **Examples:** | | Example(value='VirSorter; 1.0.4; Virome database, category 2', description=None) | diff --git a/mixs6/virus_enrich_appr.md b/mixs6/virus_enrich_appr.md index a329a501..4fcccf6f 100644 --- a/mixs6/virus_enrich_appr.md +++ b/mixs6/virus_enrich_appr.md @@ -30,7 +30,6 @@ None -> OPT | --- | --- | --- | | **Aliases:** | | virus enrichment approach | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 36.0 | | **Examples:** | | Example(value='filtration + FeCl Precipitation + ultracentrifugation + DNAse', description=None) | diff --git a/mixs6/vis_media.md b/mixs6/vis_media.md index 0ba412bb..e59beaf3 100644 --- a/mixs6/vis_media.md +++ b/mixs6/vis_media.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | visual media | | **Mappings:** | | MIXS:0000840 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 137 | +| | | Position: 137.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='3D scans', description=None) | diff --git a/mixs6/viscosity.md b/mixs6/viscosity.md index a2990aa2..934f78bf 100644 --- a/mixs6/viscosity.md +++ b/mixs6/viscosity.md @@ -54,7 +54,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;measurement value | | | | Preferred unit: cP at degree Celsius | | | | Occurrence: 1 | -| | | Position: 87 | +| | | Position: 87.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/volatile_org_comp.md b/mixs6/volatile_org_comp.md index 4727a549..85198752 100644 --- a/mixs6/volatile_org_comp.md +++ b/mixs6/volatile_org_comp.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: volatile organic compound name;measurement value | | | | Preferred unit: microgram per cubic meter, parts per million, nanogram per liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='formaldehyde;500 nanogram per liter', description=None) | diff --git a/mixs6/votu_class_appr.md b/mixs6/votu_class_appr.md index 28e37396..86008679 100644 --- a/mixs6/votu_class_appr.md +++ b/mixs6/votu_class_appr.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | vOTU classification approach | | **Comments:** | | Expected value: cutoffs and method used | -| | | Preferred unit: | | | | Position: 87.0 | | **Examples:** | | Example(value='95% ANI;85% AF; greedy incremental clustering', description=None) | diff --git a/mixs6/votu_db.md b/mixs6/votu_db.md index 2214a7aa..256cbe4b 100644 --- a/mixs6/votu_db.md +++ b/mixs6/votu_db.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | vOTU database | | **Comments:** | | Expected value: database and version | -| | | Preferred unit: | | | | Position: 89.0 | | **Examples:** | | Example(value='NCBI Viral RefSeq;83', description=None) | diff --git a/mixs6/votu_seq_comp_appr.md b/mixs6/votu_seq_comp_appr.md index a9722ddf..94d749c0 100644 --- a/mixs6/votu_seq_comp_appr.md +++ b/mixs6/votu_seq_comp_appr.md @@ -29,7 +29,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | vOTU sequence comparison approach | | **Comments:** | | Expected value: software name, version and relevant parameters | -| | | Preferred unit: | | | | Position: 88.0 | | **Examples:** | | Example(value='blastn;2.6.0+;e-value cutoff: 0.001', description=None) | diff --git a/mixs6/wall_area.md b/mixs6/wall_area.md index bbed36c8..772e032c 100644 --- a/mixs6/wall_area.md +++ b/mixs6/wall_area.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 138 | +| | | Position: 138.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/wall_const_type.md b/mixs6/wall_const_type.md index 6f1932ce..c71506fc 100644 --- a/mixs6/wall_const_type.md +++ b/mixs6/wall_const_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | wall construction type | | **Mappings:** | | MIXS:0000841 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 139 | +| | | Position: 139.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='fire resistive', description=None) | diff --git a/mixs6/wall_finish_mat.md b/mixs6/wall_finish_mat.md index 55660d4f..ee565ae8 100644 --- a/mixs6/wall_finish_mat.md +++ b/mixs6/wall_finish_mat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | wall finish material | | **Mappings:** | | MIXS:0000842 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 140 | +| | | Position: 140.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wood', description=None) | diff --git a/mixs6/wall_height.md b/mixs6/wall_height.md index 8454c5d2..70b2e2b1 100644 --- a/mixs6/wall_height.md +++ b/mixs6/wall_height.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: value | | | | Preferred unit: centimeter | | | | Occurrence: 1 | -| | | Position: 141 | +| | | Position: 141.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/wall_loc.md b/mixs6/wall_loc.md index f8be255b..9e377510 100644 --- a/mixs6/wall_loc.md +++ b/mixs6/wall_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | wall location | | **Mappings:** | | MIXS:0000843 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 142 | +| | | Position: 142.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='north', description=None) | diff --git a/mixs6/wall_surf_treatment.md b/mixs6/wall_surf_treatment.md index cec0595e..34ceb675 100644 --- a/mixs6/wall_surf_treatment.md +++ b/mixs6/wall_surf_treatment.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | wall surface treatment | | **Mappings:** | | MIXS:0000845 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 144 | +| | | Position: 144.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='paneling', description=None) | diff --git a/mixs6/wall_texture.md b/mixs6/wall_texture.md index 47707aab..64e84493 100644 --- a/mixs6/wall_texture.md +++ b/mixs6/wall_texture.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | wall texture | | **Mappings:** | | MIXS:0000846 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 145 | +| | | Position: 145.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='popcorn', description=None) | diff --git a/mixs6/wall_thermal_mass.md b/mixs6/wall_thermal_mass.md index 99c976d1..672c3172 100644 --- a/mixs6/wall_thermal_mass.md +++ b/mixs6/wall_thermal_mass.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: joule per degree Celsius | | | | Occurrence: 1 | -| | | Position: 146 | +| | | Position: 146.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/wall_water_mold.md b/mixs6/wall_water_mold.md index 2d16e352..fb0fc30c 100644 --- a/mixs6/wall_water_mold.md +++ b/mixs6/wall_water_mold.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | wall signs of water/mold | | **Mappings:** | | MIXS:0000844 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 143 | +| | | Position: 143.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='no presence of mold visible', description=None) | diff --git a/mixs6/wastewater_type.md b/mixs6/wastewater_type.md index 956a1c0a..12c14043 100644 --- a/mixs6/wastewater_type.md +++ b/mixs6/wastewater_type.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | wastewater type | | **Mappings:** | | MIXS:0000353 | | **Comments:** | | Expected value: wastewater type name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: wastewater_sludge | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_content.md b/mixs6/water_content.md index e17ebbff..c4de331d 100644 --- a/mixs6/water_content.md +++ b/mixs6/water_content.md @@ -66,7 +66,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: gram per gram or cubic centimeter per cubic centimeter | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 3 packages: microbial mat_biofilm, sediment, soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_content_soil_meth.md b/mixs6/water_content_soil_meth.md index 863b650f..f91b5e6f 100644 --- a/mixs6/water_content_soil_meth.md +++ b/mixs6/water_content_soil_meth.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | water content method | | **Mappings:** | | MIXS:0000323 | | **Comments:** | | Expected value: PMID,DOI or url | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 16 | +| | | Position: 16.0 | | | | This field is used uniquely in: soil | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_current.md b/mixs6/water_current.md index fa1f3f42..4543e82c 100644 --- a/mixs6/water_current.md +++ b/mixs6/water_current.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: cubic meter per second, knots | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used in: 2 packages: miscellaneous natural or artificial environment, water | | **Examples:** | | Example(value='10 cubic meter per second', description=None) | diff --git a/mixs6/water_cut.md b/mixs6/water_cut.md index 1121ced7..18d6537e 100644 --- a/mixs6/water_cut.md +++ b/mixs6/water_cut.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: percent | | | | Occurrence: 1 | -| | | Position: 26 | +| | | Position: 26.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_feat_size.md b/mixs6/water_feat_size.md index b10d0e42..3c063203 100644 --- a/mixs6/water_feat_size.md +++ b/mixs6/water_feat_size.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: square meter | | | | Occurrence: 1 | -| | | Position: 147 | +| | | Position: 147.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_feat_type.md b/mixs6/water_feat_type.md index ff83901a..adddf71a 100644 --- a/mixs6/water_feat_type.md +++ b/mixs6/water_feat_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | water feature type | | **Mappings:** | | MIXS:0000847 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 148 | +| | | Position: 148.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='stream', description=None) | diff --git a/mixs6/water_production_rate.md b/mixs6/water_production_rate.md index 2cb74c9f..818be5d8 100644 --- a/mixs6/water_production_rate.md +++ b/mixs6/water_production_rate.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: cubic meter per day | | | | Occurrence: 1 | -| | | Position: 25 | +| | | Position: 25.0 | | | | This field is used uniquely in: hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/water_temp_regm.md b/mixs6/water_temp_regm.md index fd7380bc..0c934aa4 100644 --- a/mixs6/water_temp_regm.md +++ b/mixs6/water_temp_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;treatment interval and duration | | | | Preferred unit: degree Celsius | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/watering_regm.md b/mixs6/watering_regm.md index c08950ca..09c4e1fd 100644 --- a/mixs6/watering_regm.md +++ b/mixs6/watering_regm.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value;treatment interval and duration | | | | Preferred unit: milliliter, liter | | | | Occurrence: m | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: plant-associated | | **Examples:** | | Example(value='1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M', description=None) | diff --git a/mixs6/weekday.md b/mixs6/weekday.md index ab9c321a..22c1807d 100644 --- a/mixs6/weekday.md +++ b/mixs6/weekday.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | weekday | | **Mappings:** | | MIXS:0000848 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 149 | +| | | Position: 149.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='Sunday', description=None) | diff --git a/mixs6/weight_loss_3_month.md b/mixs6/weight_loss_3_month.md index 6d9b7a1f..239aedd4 100644 --- a/mixs6/weight_loss_3_month.md +++ b/mixs6/weight_loss_3_month.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: weight loss specification;measurement value | | | | Preferred unit: kilogram, gram | | | | Occurrence: 1 | -| | | Position: 22 | +| | | Position: 22.0 | | | | This field is used uniquely in: human-associated | | **Examples:** | | Example(value='yes;5 kilogram', description=None) | diff --git a/mixs6/wga_amp_appr.md b/mixs6/wga_amp_appr.md index a4221ed0..966b8ee8 100644 --- a/mixs6/wga_amp_appr.md +++ b/mixs6/wga_amp_appr.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | WGA amplification approach | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Position: 77.0 | | **Examples:** | | Example(value='mda based', description=None) | diff --git a/mixs6/wga_amp_kit.md b/mixs6/wga_amp_kit.md index 0e884c5a..4ae3cadf 100644 --- a/mixs6/wga_amp_kit.md +++ b/mixs6/wga_amp_kit.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | WGA amplification kit | | **Comments:** | | Expected value: kit name | -| | | Preferred unit: | | | | Position: 78.0 | | **Examples:** | | Example(value='qiagen repli-g', description=None) | diff --git a/mixs6/win.md b/mixs6/win.md index c00146ce..8282b4ba 100644 --- a/mixs6/win.md +++ b/mixs6/win.md @@ -52,9 +52,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | well identification number | | **Mappings:** | | MIXS:0000297 | | **Comments:** | | Expected value: text | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 36 | +| | | Position: 36.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/wind_direction.md b/mixs6/wind_direction.md index df73e5dc..b6324fb3 100644 --- a/mixs6/wind_direction.md +++ b/mixs6/wind_direction.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | wind direction | | **Mappings:** | | MIXS:0000757 | | **Comments:** | | Expected value: wind direction name | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='Northwest', description=None) | diff --git a/mixs6/wind_speed.md b/mixs6/wind_speed.md index 581d846f..6b9eeaf3 100644 --- a/mixs6/wind_speed.md +++ b/mixs6/wind_speed.md @@ -42,7 +42,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: meter per second, kilometer per hour | | | | Occurrence: 1 | -| | | Position: 1 | +| | | Position: 1.0 | | | | This field is used uniquely in: air | | **Examples:** | | Example(value='21 kilometer per hour', description=None) | diff --git a/mixs6/window_cond.md b/mixs6/window_cond.md index 8a54cbfc..4e161162 100644 --- a/mixs6/window_cond.md +++ b/mixs6/window_cond.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window condition | | **Mappings:** | | MIXS:0000849 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 151 | +| | | Position: 151.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='rupture', description=None) | diff --git a/mixs6/window_cover.md b/mixs6/window_cover.md index 87696bf4..95ab1cf6 100644 --- a/mixs6/window_cover.md +++ b/mixs6/window_cover.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window covering | | **Mappings:** | | MIXS:0000850 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 152 | +| | | Position: 152.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='curtains', description=None) | diff --git a/mixs6/window_horiz_pos.md b/mixs6/window_horiz_pos.md index f7f0f8b3..ad970e67 100644 --- a/mixs6/window_horiz_pos.md +++ b/mixs6/window_horiz_pos.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window horizontal position | | **Mappings:** | | MIXS:0000851 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 153 | +| | | Position: 153.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='middle', description=None) | diff --git a/mixs6/window_loc.md b/mixs6/window_loc.md index fec4f34e..5ff2ffdf 100644 --- a/mixs6/window_loc.md +++ b/mixs6/window_loc.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window location | | **Mappings:** | | MIXS:0000852 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 154 | +| | | Position: 154.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='west', description=None) | diff --git a/mixs6/window_mat.md b/mixs6/window_mat.md index 814cd492..e381ba32 100644 --- a/mixs6/window_mat.md +++ b/mixs6/window_mat.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window material | | **Mappings:** | | MIXS:0000853 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 155 | +| | | Position: 155.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='wood', description=None) | diff --git a/mixs6/window_open_freq.md b/mixs6/window_open_freq.md index 83be87ac..46e7262e 100644 --- a/mixs6/window_open_freq.md +++ b/mixs6/window_open_freq.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | window open frequency | | **Mappings:** | | MIXS:0000246 | | **Comments:** | | Expected value: value | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 156 | +| | | Position: 156.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/window_size.md b/mixs6/window_size.md index 13703099..f0f12567 100644 --- a/mixs6/window_size.md +++ b/mixs6/window_size.md @@ -42,7 +42,7 @@ None -> OPT [String](types/String.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: inch, meter | | | | Occurrence: 1 | -| | | Position: 150 | +| | | Position: 150.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='', description=None) | diff --git a/mixs6/window_status.md b/mixs6/window_status.md index 0beb873a..223ab0f1 100644 --- a/mixs6/window_status.md +++ b/mixs6/window_status.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | window status | | **Mappings:** | | MIXS:0000855 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 158 | +| | | Position: 158.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='open', description=None) | diff --git a/mixs6/window_type.md b/mixs6/window_type.md index be177955..1c71a8fc 100644 --- a/mixs6/window_type.md +++ b/mixs6/window_type.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window type | | **Mappings:** | | MIXS:0000856 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 159 | +| | | Position: 159.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='fixed window', description=None) | diff --git a/mixs6/window_vert_pos.md b/mixs6/window_vert_pos.md index ee3c8bc2..b553ea42 100644 --- a/mixs6/window_vert_pos.md +++ b/mixs6/window_vert_pos.md @@ -40,9 +40,8 @@ None -> OPT | **Aliases:** | | window vertical position | | **Mappings:** | | MIXS:0000857 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 160 | +| | | Position: 160.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='middle', description=None) | diff --git a/mixs6/window_water_mold.md b/mixs6/window_water_mold.md index c3790cbf..3422efd7 100644 --- a/mixs6/window_water_mold.md +++ b/mixs6/window_water_mold.md @@ -40,9 +40,8 @@ None -> OPT [String](types/String.md) | **Aliases:** | | window signs of water/mold | | **Mappings:** | | MIXS:0000854 | | **Comments:** | | Expected value: enumeration | -| | | Preferred unit: | | | | Occurrence: 1 | -| | | Position: 157 | +| | | Position: 157.0 | | | | This field is used uniquely in: built environment | | **Examples:** | | Example(value='no presence of mold visible', description=None) | diff --git a/mixs6/x_16s_recover.md b/mixs6/x_16s_recover.md index 2f57696b..b05bbeab 100644 --- a/mixs6/x_16s_recover.md +++ b/mixs6/x_16s_recover.md @@ -30,7 +30,6 @@ None -> OPT [String](types/String.md) | --- | --- | --- | | **Aliases:** | | 16S recovered | | **Comments:** | | Expected value: boolean | -| | | Preferred unit: | | | | Position: 63.0 | | **Examples:** | | Example(value='yes', description=None) | diff --git a/mixs6/x_16s_recover_software.md b/mixs6/x_16s_recover_software.md deleted file mode 100644 index 38de87ba..00000000 --- a/mixs6/x_16s_recover_software.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: x_16s_recover_software - - -Tools used for 16S rRNA gene extraction - -URI: [mixs.vocab:x_16s_recover_software](https://w3id.org/mixs/vocab/x_16s_recover_software) - - -## Domain and Range - -None -> OPT [String](types/String.md) - -## Parents - - * is_a: [sequencing field](sequencing_field.md) - -## Children - - * [MIMAG➞x_16s_recover_software](MIMAG_x_16s_recover_software.md) - * [MISAG➞x_16s_recover_software](MISAG_x_16s_recover_software.md) - -## Used by - - * [Core](Core.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | 16S recovery software | -| **Comments:** | | Expected value: names and versions of software(s), parameters used | -| | | Preferred unit: | -| | | Position: 64.0 | -| **Examples:** | | Example(value='rambl;v2;default parameters', description=None) | - diff --git a/mixs6/xylene.md b/mixs6/xylene.md index a228244a..7ea49f47 100644 --- a/mixs6/xylene.md +++ b/mixs6/xylene.md @@ -54,7 +54,7 @@ None -> OPT [QuantityValue](QuantityValue.md) | **Comments:** | | Expected value: measurement value | | | | Preferred unit: milligram per liter, parts per million | | | | Occurrence: 1 | -| | | Position: 84 | +| | | Position: 84.0 | | | | This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon resources-fluids_swabs | | **Examples:** | | Example(value='', description=None) | diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index ece04895..780be34c 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -1,15657 +1,32 @@ -id: http://w3id.org/mixs6 -description: MIxS 6 linkml rendering +id: http://w3id.org/mixs +name: MIxS +description: Minimal Information about any Sequence Standard imports: - linkml:types +- checklists +- core +- air +- built_environment +- host_associated +- human_associated +- human_gut +- human_oral +- human_skin +- human_vaginal +- hydrocarbon_resources_cores +- hydrocarbon_resources_fluids_swabs +- microbial_mat_biofilm +- miscellaneous_natural_or_artificial_environment +- plant_associated +- sediment +- soil +- wastewater_sludge +- water prefixes: linkml: https://w3id.org/linkml/ mixs.vocab: https://w3id.org/mixs/vocab/ MIXS: https://w3id.org/mixs/terms/ default_prefix: mixs.vocab -slots: - core field: - description: basic fields - investigation field: - description: field describing aspect of the investigation/study to which the sample - belongs - nucleic acid sequence source field: {} - sequencing field: {} - mixs extension field: {} - environment field: - description: field describing environmental aspect of a sample - submitted_to_insdc: - is_a: investigation field - aliases: - - submitted to insdc - description: Depending on the study (large-scale e.g. done with next generation - sequencing technology, or small-scale) sequences have to be submitted to SRA - (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin - systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant - as a self-test field, therefore it is not necessary to include this field in - contextual data submitted to databases - range: string - examples: - - value: 'yes' - comments: - - 'Expected value: boolean' - - 'Preferred unit: ' - - 'Position: 1.0' - pattern: '{boolean}' - investigation_type: - is_a: investigation field - aliases: - - investigation type - description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS - compliant reports as standardized by Genomic Standards Consortium. This field - is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, - mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled - genome, or uncultivated viral genome - range: investigation_type_enum - examples: - - value: metagenome - comments: - - 'Expected value: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,mimarks-survey, - mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled - genome, or uncultivated viral genomes' - - 'Preferred unit: ' - - 'Position: 2.0' - pattern: '[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig]' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/60 - sample_name: - is_a: core field - aliases: - - 'sample name ' - description: 'Sample Name is a name that you choose for the sample. It can have - any format, but we suggest that you make it concise, unique and consistent within - your lab, and as informative as possible. Every Sample Name from a single Submitter - must be unique. ' - range: string - examples: - - value: '' - comments: - - 'Expected value: ' - - 'Preferred unit: ' - - 'Position: ' - pattern: '' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/78 - project_name: - is_a: investigation field - aliases: - - project name - description: Name of the project within which the sequencing was organized - range: string - examples: - - value: Forest soil metagenome - comments: - - 'Expected value: ' - - 'Preferred unit: ' - - 'Position: 3.0' - pattern: '{text}' - experimental_factor: - is_a: investigation field - aliases: - - experimental factor - description: Experimental factors are essentially the variable aspects of an experiment - design which can be used to describe an experiment, or set of experiments, in - an increasingly detailed manner. This field accepts ontology terms from Experimental - Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For - a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; - for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - range: string - examples: - - value: time series design [EFO:EFO_0001779] - comments: - - 'Expected value: text or EFO and/or OBI' - - 'Preferred unit: ' - - 'Position: 4.0' - pattern: '{termLabel} {[termID]}|{text}' - lat_lon: - is_a: environment field - aliases: - - geographic location (latitude and longitude) - description: The geographical origin of the sample as defined by latitude and - longitude. The values should be reported in decimal degrees and in WGS84 system - range: string - examples: - - value: 50.586825 6.408977 - comments: - - 'Expected value: decimal degrees' - - 'Preferred unit: ' - - 'Position: 5.0' - pattern: '{float} {float}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/62 - depth: - is_a: environment field - aliases: - - geographic location (depth) - description: Please refer to the definitions of depth in the environmental packages - range: string - examples: - - value: '' - comments: - - 'Expected value: -' - - 'Preferred unit: ' - - 'Position: 6.0' - - 'This field is used in: 8 packages: host-associated, microbial mat_biofilm, - miscellaneous natural or artificial environment, plant-associated, sediment, - soil, wastewater_sludge, water' - pattern: '-' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/63 - alt: - is_a: environment field - aliases: - - altitude - description: "Altitude is a term used to identify heights of objects such as airplanes,\ - \ space shuttles, rockets, atmospheric balloons and heights of places such as\ - \ atmospheric layers and clouds. It is used to measure the height of an object\ - \ which is above the earth\u201A\xC4\xF4s surface. In this context, the altitude\ - \ measurement is the vertical distance between the earth's surface above sea\ - \ level and the sampled position in the air" - range: quantity value - examples: - - value: 100 meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Position: ' - - 'This field is used in: 3 packages: air, host-associated, miscellaneous natural - or artificial environment' - elev: - is_a: environment field - aliases: - - elevation - description: Elevation of the sampling site is its height above a fixed reference - point, most commonly the mean sea level. Elevation is mainly used when referring - to points on the earth's surface, while altitude is used for points above the - surface, such as an aircraft in flight or a spacecraft in orbit - range: quantity value - examples: - - value: 100 meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Position: 7.0' - - 'This field is used in: 9 packages: air, host-associated, hydrocarbon resources-cores, - microbial mat_biofilm, miscellaneous natural or artificial environment, plant-associated, - sediment, soil, water' - geo_loc_name: - is_a: environment field - aliases: - - geographic location (country and/or sea,region) - description: The geographical origin of the sample as defined by the country or - sea name followed by specific region name. Country or sea names should be chosen - from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology - (v 1.512) (http://purl.bioontology.org/ontology/GAZ) - range: string - examples: - - value: Germany;North Rhine-Westphalia;Eifel National Park - comments: - - 'Expected value: country or sea name (INSDC or GAZ);region(GAZ);specific location - name' - - 'Preferred unit: ' - - 'Position: 8.0' - pattern: '{term};{term};{text}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/17 - collection_date: - is_a: environment field - aliases: - - collection date - description: 'The time of sampling, either as an instance (single point in time) - or interval. In case no exact time is available, the date/time can be right - truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; - 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' - range: string - examples: - - value: '2018-05-11T10:00:00+01:00' - comments: - - 'Expected value: date and time' - - 'Preferred unit: ' - - 'Position: 9.0' - pattern: '{timestamp}' - env_broad_scale: - is_a: environment field - aliases: - - broad-scale environmental context - description: "In this field, report which major environmental system your sample\ - \ or specimen came from. The systems identified should have a coarse spatial\ - \ grain, to provide the general environmental context of where the sampling\ - \ was done (e.g. were you in the desert or a rainforest?). We recommend using\ - \ subclasses of ENVO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\ - \ Format (one term): termLabel [termID], Format (multiple terms): termLabel\ - \ [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water\ - \ sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic\ - \ epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the\ - \ Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228].\ - \ If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" - range: string - examples: - - value: forest biome [ENVO:01000174] - comments: - - 'Expected value: Add terms that identify the major environment type(s) where - your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple - terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine - biome [ENVO:01000020]' - - 'Preferred unit: ' - - 'Position: 10.0' - pattern: '{termLabel} {[termID]}' - env_local_scale: - is_a: environment field - aliases: - - local environmental context - description: "In this field, report the entity or entities which are in your sample\ - \ or specimen\u2019s local vicinity and which you believe have significant causal\ - \ influences on your sample or specimen. Please use terms that are present in\ - \ ENVO and which are of smaller spatial grain than your entry for env_broad_scale.\ - \ Format (one term): termLabel [termID]; Format (multiple terms): termLabel\ - \ [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled\ - \ sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb\ - \ and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub\ - \ layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified\ - \ here: http://www.obofoundry.org/ontology/envo.html" - range: string - examples: - - value: litter layer [ENVO:01000338] - comments: - - 'Expected value: Add terms that identify environmental entities having causal - influences upon the entity at time of sampling, multiple terms can be separated - by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]' - - 'Preferred unit: ' - - 'Position: 11.0' - pattern: '{termLabel} {[termID]}' - env_medium: - is_a: environment field - aliases: - - environmental medium - description: "In this field, report which environmental material or materials\ - \ (pipe separated) immediately surrounded your sample or specimen prior to sampling,\ - \ using one or more subclasses of ENVO\u2019s environmental material class:\ - \ http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel\ - \ [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel\ - \ [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic\ - \ Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on\ - \ a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed,\ - \ request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html" - range: string - examples: - - value: soil [ENVO:00001998] - comments: - - 'Expected value: Add terms that identify the material displaced by the entity - at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. - Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine - mud [ENVO:00002160]' - - 'Preferred unit: ' - - 'Position: 12.0' - pattern: '{termLabel} {[termID]}' - env_package: - is_a: mixs extension field - aliases: - - environmental package - description: MIxS extension for reporting of measurements and observations obtained - from one or more of the environments where the sample was obtained. All environmental - packages listed here are further defined in separate subtables. By giving the - name of the environmental package, a selection of fields can be made from the - subtables and can be reported - range: env_package_enum - examples: - - value: soil - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 13.0' - pattern: '[air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon - resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc - environment|plant-associated|sediment|soil|wastewater/sludge|water]' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/64 - subspecf_gen_lin: - is_a: nucleic acid sequence source field - aliases: - - subspecific genetic lineage - description: This should provide further information about the genetic distinctness - of the sequenced organism by recording additional information e.g. serovar, - serotype, biotype, ecotype, or any relevant genetic typing schemes like Group - I plasmid. It can also contain alternative taxonomic information. It should - contain both the lineage name, and the lineage rank, i.e. biovar:abc123 - range: string - examples: - - value: serovar:Newport - comments: - - 'Expected value: genetic lineage below lowest rank of NCBI taxonomy, which is - subspecies, e.g. serovar, biotype, ecotype' - - 'Preferred unit: ' - - 'Position: 14.0' - pattern: '{rank name}:{text}' - ploidy: - is_a: nucleic acid sequence source field - aliases: - - ploidy - description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, - triploid, tetraploid). It has implications for the downstream study of duplicated - gene and regions of the genomes (and perhaps for difficulties in assembly). - For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic - Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer - to http://purl.bioontology.org/ontology/PATO - range: string - examples: - - value: allopolyploidy [PATO:0001379] - comments: - - 'Expected value: PATO' - - 'Preferred unit: ' - - 'Position: 15.0' - pattern: '{termLabel} {[termID]}' - num_replicons: - is_a: nucleic acid sequence source field - aliases: - - number of replicons - description: Reports the number of replicons in a nuclear genome of eukaryotes, - in the genome of a bacterium or archaea or the number of segments in a segmented - virus. Always applied to the haploid chromosome count of a eukaryote - range: string - examples: - - value: '2' - comments: - - 'Expected value: for eukaryotes and bacteria: chromosomes (haploid count); for - viruses: segments' - - 'Preferred unit: ' - - 'Position: 16.0' - pattern: '{integer}' - extrachrom_elements: - is_a: nucleic acid sequence source field - aliases: - - extrachromosomal elements - description: Do plasmids exist of significant phenotypic consequence (e.g. ones - that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids - (borrelia has 15+ plasmids) - range: string - examples: - - value: '5' - comments: - - 'Expected value: number of extrachromosmal elements' - - 'Preferred unit: ' - - 'Position: 17.0' - pattern: '{integer}' - estimated_size: - is_a: nucleic acid sequence source field - aliases: - - estimated size - description: The estimated size of the genome prior to sequencing. Of particular - importance in the sequencing of (eukaryotic) genome which could remain in draft - form for a long or unspecified period. - range: string - examples: - - value: 300000 bp - comments: - - 'Expected value: number of base pairs' - - 'Preferred unit: ' - - 'Position: 18.0' - pattern: '{integer} bp' - ref_biomaterial: - is_a: nucleic acid sequence source field - aliases: - - reference for biomaterial - description: Primary publication if isolated before genome publication; otherwise, - primary genome report - range: string - examples: - - value: doi:10.1016/j.syapm.2018.01.009 - comments: - - 'Expected value: PMID, DOI or URL' - - 'Preferred unit: ' - - 'Position: 19.0' - pattern: '{PMID}|{DOI}|{URL}' - source_mat_id: - is_a: nucleic acid sequence source field - aliases: - - source material identifiers - description: A unique identifier assigned to a material sample (as defined by - http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular - digital record of a material sample) used for extracting nucleic acids, and - subsequent sequencing. The identifier can refer either to the original material - collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, - /bio_material, or /culture_collection may or may not share the same value as - the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id - may both contain 'UAM:Herps:14' , referring to both the specimen voucher and - sampled tissue with the same identifier. However, the /culture_collection qualifier - may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id - would refer to an identifier from some derived culture from which the nucleic - acids were extracted (e.g. xatc123 or ark:/2154/R2). - range: string - examples: - - value: MPI012345 - comments: - - 'Expected value: for cultures of microorganisms: identifiers for two culture - collections; for other material a unique arbitrary identifer' - - 'Preferred unit: ' - - 'Position: 20.0' - pattern: '{text}' - pathogenicity: - is_a: nucleic acid sequence source field - aliases: - - known pathogenicity - description: To what is the entity pathogenic - range: string - examples: - - value: human, animal, plant, fungi, bacteria - comments: - - 'Expected value: names of organisms that the entity is pathogenic to' - - 'Preferred unit: ' - - 'Position: 21.0' - pattern: '{text}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/65 - biotic_relationship: - is_a: nucleic acid sequence source field - aliases: - - observed biotic relationship - description: Description of relationship(s) between the subject organism and other - organism(s) it is associated with. E.g., parasite on species X; mutualist with - species Y. The target organism is the subject of the relationship, and the other - organism(s) is the object - range: biotic_relationship_enum - examples: - - value: free living - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 22.0' - pattern: '[free living|parasitism|commensalism|symbiotic|mutualism]' - specific_host: - is_a: nucleic acid sequence source field - aliases: - - specific host - description: If there is a host involved, please provide its taxid (or environmental - if not actually isolated from the dead or alive host - i.e. a pathogen could - be isolated from a swipe of a bench etc) and report whether it is a laboratory - or natural host) - range: string - examples: - - value: '9606' - comments: - - 'Expected value: host taxid, unknown, environmental' - - 'Preferred unit: ' - - 'Position: 23.0' - pattern: '{NCBI taxid}|{text}' - host_spec_range: - is_a: nucleic acid sequence source field - aliases: - - host specificity or range - description: The NCBI taxonomy identifier of the specific host if it is known - range: string - examples: - - value: '9606' - comments: - - 'Expected value: NCBI taxid' - - 'Preferred unit: ' - - 'Position: 24.0' - pattern: '{integer}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/66 - health_disease_stat: - is_a: nucleic acid sequence source field - aliases: - - health or disease status of specific host at time of collection - description: Health or disease status of specific host at time of collection - range: health_disease_stat_enum - examples: - - value: dead - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 25.0' - pattern: '[healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing - condition|pathological|life threatening|congenital]' - trophic_level: - is_a: nucleic acid sequence source field - aliases: - - trophic level - description: Trophic levels are the feeding position in a food chain. Microbes - can be a range of producers (e.g. chemolithotroph) - range: trophic_level_enum - examples: - - value: heterotroph - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 26.0' - pattern: '[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]' - propagation: - is_a: nucleic acid sequence source field - aliases: - - propagation - description: 'This field is specific to different taxa. For phages: lytic/lysogenic, - for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there - is the strong opinion to name phage propagation obligately lytic or temperate, - therefore we also give this choice' - range: string - examples: - - value: lytic - comments: - - 'Expected value: for virus: lytic, lysogenic, temperate, obligately lytic; for - plasmid: incompatibility group; for eukaryote: asexual, sexual' - - 'Preferred unit: ' - - 'Position: 27.0' - pattern: '{text}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/88 - encoded_traits: - is_a: nucleic acid sequence source field - aliases: - - encoded traits - description: Should include key traits like antibiotic resistance or xenobiotic - degradation phenotypes for plasmids, converting genes for phage - range: string - examples: - - value: beta-lactamase class A - comments: - - 'Expected value: for plasmid: antibiotic resistance; for phage: converting genes' - - 'Preferred unit: ' - - 'Position: 28.0' - pattern: '{text}' - rel_to_oxygen: - is_a: nucleic acid sequence source field - aliases: - - relationship to oxygen - description: Is this organism an aerobe, anaerobe? Please note that aerobic and - anaerobic are valid descriptors for microbial environments - range: rel_to_oxygen_enum - examples: - - value: aerobe - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 29.0' - pattern: '[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate - aerobe|obligate anaerobe]' - isol_growth_condt: - is_a: nucleic acid sequence source field - aliases: - - isolation and growth condition - description: Publication reference in the form of pubmed ID (pmid), digital object - identifier (doi) or url for isolation and growth condition specifications of - the organism/material - range: string - examples: - - value: 'doi: 10.1016/j.syapm.2018.01.009' - comments: - - 'Expected value: PMID,DOI or URL' - - 'Preferred unit: ' - - 'Position: 30.0' - pattern: '{PMID}|{DOI}|{URL}' - samp_collect_device: - is_a: nucleic acid sequence source field - aliases: - - sample collection device or method - description: The method or device employed for collecting the sample - range: string - examples: - - value: environmental swab sampling, biopsy, niskin bottle, push core - comments: - - 'Expected value: type name' - - 'Preferred unit: ' - - 'Position: 31.0' - pattern: '{text}' - samp_mat_process: - is_a: nucleic acid sequence source field - aliases: - - sample material processing - description: Any processing applied to the sample during or after retrieving the - sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) - terms please see http://purl.bioontology.org/ontology/OBI - range: string - examples: - - value: filtering of seawater, storing samples in ethanol - comments: - - 'Expected value: text or OBI' - - 'Preferred unit: ' - - 'Position: 32.0' - pattern: '{text}|{termLabel} {[termID]}' - size_frac: - is_a: nucleic acid sequence source field - aliases: - - size fraction selected - description: Filtering pore size used in sample preparation - range: string - examples: - - value: 0-0.22 micrometer - comments: - - 'Expected value: filter size value range' - - 'Preferred unit: ' - - 'Position: 33.0' - pattern: '{float}-{float} {unit}' - samp_size: - is_a: nucleic acid sequence source field - aliases: - - amount or size of sample collected - description: Amount or size of sample (volume, mass or area) that was collected - range: quantity value - examples: - - value: 5 liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millliter, gram, milligram, liter' - - 'Position: 34.0' - source_uvig: - is_a: nucleic acid sequence source field - aliases: - - source of UViGs - description: Type of dataset from which the UViG was obtained - range: source_uvig_enum - examples: - - value: viral fraction metagenome (virome) - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 35.0' - pattern: '[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted - metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome - (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome - (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]' - virus_enrich_appr: - is_a: nucleic acid sequence source field - aliases: - - virus enrichment approach - description: List of approaches used to enrich the sample for viruses, if any - range: virus_enrich_appr_enum - examples: - - value: filtration + FeCl Precipitation + ultracentrifugation + DNAse - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 36.0' - pattern: '[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl - Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]' - nucl_acid_ext: - is_a: sequencing field - aliases: - - nucleic acid extraction - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the material separation to recover - the nucleic acid fraction from a sample - range: string - examples: - - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf - comments: - - 'Expected value: PMID, DOI or URL' - - 'Preferred unit: ' - - 'Position: 37.0' - pattern: '{PMID}|{DOI}|{URL}' - nucl_acid_amp: - is_a: sequencing field - aliases: - - nucleic acid amplification - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the enzymatic amplification (PCR, - TMA, NASBA) of specific nucleic acids - range: string - examples: - - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ - comments: - - 'Expected value: PMID, DOI or URL' - - 'Preferred unit: ' - - 'Position: 38.0' - pattern: '{PMID}|{DOI}|{URL}' - lib_size: - is_a: sequencing field - aliases: - - library size - description: Total number of clones in the library prepared for the project - range: string - examples: - - value: '50' - comments: - - 'Expected value: number of clones' - - 'Preferred unit: ' - - 'Position: 39.0' - pattern: '{integer}' - lib_reads_seqd: - is_a: sequencing field - aliases: - - library reads sequenced - description: Total number of clones sequenced from the library - range: string - examples: - - value: '20' - comments: - - 'Expected value: number of reads sequenced' - - 'Preferred unit: ' - - 'Position: 40.0' - pattern: '{integer}' - lib_layout: - is_a: sequencing field - aliases: - - library layout - description: Specify whether to expect single, paired, or other configuration - of reads - range: lib_layout_enum - examples: - - value: paired - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 41.0' - pattern: '[paired|single|vector|other]' - lib_vector: - is_a: sequencing field - aliases: - - library vector - description: Cloning vector type(s) used in construction of libraries - range: string - examples: - - value: Bacteriophage P1 - comments: - - 'Expected value: vector' - - 'Preferred unit: ' - - 'Position: 42.0' - pattern: '{text}' - lib_screen: - is_a: sequencing field - aliases: - - library screening strategy - description: Specific enrichment or screening methods applied before and/or after - creating libraries - range: string - examples: - - value: enriched, screened, normalized - comments: - - 'Expected value: screening strategy name' - - 'Preferred unit: ' - - 'Position: 43.0' - pattern: '{text}' - target_gene: - is_a: sequencing field - aliases: - - target gene - description: Targeted gene or locus name for marker gene studies - range: string - examples: - - value: 16S rRNA, 18S rRNA, nif, amoA, rpo - comments: - - 'Expected value: gene name' - - 'Preferred unit: ' - - 'Position: 44.0' - pattern: '{text}' - target_subfragment: - is_a: sequencing field - aliases: - - target subfragment - description: Name of subfragment of a gene or locus. Important to e.g. identify - special regions on marker genes like V6 on 16S rRNA - range: string - examples: - - value: V6, V9, ITS - comments: - - 'Expected value: gene fragment name' - - 'Preferred unit: ' - - 'Position: 45.0' - pattern: '{text}' - pcr_primers: - is_a: sequencing field - aliases: - - pcr primers - description: PCR primers that were used to amplify the sequence of the targeted - gene, locus or subfragment. This field should contain all the primers used for - a single PCR reaction if multiple forward or reverse primers are present in - a single PCR reaction. The primer sequence should be reported in uppercase letters - range: string - examples: - - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT - comments: - - 'Expected value: FWD: forward primer sequence;REV:reverse primer sequence' - - 'Preferred unit: ' - - 'Position: 46.0' - pattern: FWD:{dna};REV:{dna} - mid: - is_a: sequencing field - aliases: - - multiplex identifiers - description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are - used to specifically tag unique samples in a sequencing run. Sequence should - be reported in uppercase letters - range: string - examples: - - value: GTGAATAT - comments: - - 'Expected value: multiplex identifier sequence' - - 'Preferred unit: ' - - 'Position: 47.0' - pattern: '{dna}' - adapters: - is_a: sequencing field - aliases: - - adapters - description: Adapters provide priming sequences for both amplification and sequencing - of the sample-library fragments. Both adapters should be reported; in uppercase - letters - range: string - examples: - - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT - comments: - - 'Expected value: adapter A and B sequence' - - 'Preferred unit: ' - - 'Position: 48.0' - pattern: '{dna};{dna}' - pcr_cond: - is_a: sequencing field - aliases: - - pcr conditions - description: Description of reaction conditions and components of PCR in the form - of 'initial denaturation:94degC_1.5min; annealing=...' - range: string - examples: - - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 - comments: - - 'Expected value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles' - - 'Preferred unit: ' - - 'Position: 49.0' - pattern: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles - seq_meth: - is_a: sequencing field - aliases: - - sequencing method - description: Sequencing method used; e.g. Sanger, ABI-solid - range: seq_meth_enum - examples: - - value: Illumina HiSeq 1500 - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 50.0' - pattern: '[454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS - Junior|AB 310 Genetic Analyzer|AB 3130 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB - 3500 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB - 3730xL Genetic Analyzer|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB - 5500xl-W Genetic Analysis System|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD - System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD - PI System|BGISEQ-500|GridION|Illumina Genome Analyzer|Illumina Genome Analyzer - II|Illumina Genome Analyzer IIx|Illumina HiSeq 1000|Illumina HiSeq 1500|Illumina - HiSeq 2000|Illumina HiSeq 2500|Illumina HiSeq 3000|Illumina HiSeq 4000|Illumina - HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina - NextSeq 500|Illumina NextSeq 550|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent - S5|Ion Torrent S5 XL|MinION|PacBio RS|PacBio RS II|PromethION|Sequel]' - seq_quality_check: - is_a: sequencing field - aliases: - - sequence quality check - description: Indicate if the sequence has been called by automatic systems (none) - or undergone a manual editing procedure (e.g. by inspecting the raw data or - chromatograms). Applied only for sequences that are not submitted to SRA,ENA - or DRA - range: string - examples: - - value: none - comments: - - 'Expected value: none or manually edited' - - 'Preferred unit: ' - - 'Position: 51.0' - pattern: '[none|manually edited]' - chimera_check: - is_a: sequencing field - aliases: - - chimera check - description: A chimeric sequence, or chimera for short, is a sequence comprised - of two or more phylogenetically distinct parent sequences. Chimeras are usually - PCR artifacts thought to occur when a prematurely terminated amplicon reanneals - to a foreign DNA strand and is copied to completion in the following PCR cycles. - The point at which the chimeric sequence changes from one parent to the next - is called the breakpoint or conversion point - range: string - examples: - - value: uchime;v4.1;default parameters - comments: - - 'Expected value: name and version of software, parameters used' - - 'Preferred unit: ' - - 'Position: 52.0' - pattern: '{software};{version};{parameters}' - tax_ident: - is_a: sequencing field - aliases: - - taxonomic identity marker - description: The phylogenetic marker(s) used to assign an organism name to the - SAG or MAG - range: tax_ident_enum - examples: - - value: 'other: rpoB gene' - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 53.0' - pattern: '[16S rRNA gene|multi-marker approach|other]' - assembly_qual: - is_a: sequencing field - aliases: - - assembly quality - description: "The assembly quality category is based on sets of criteria outlined\ - \ for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,\ - \ contiguous sequence per replicon without gaps or ambiguities with a consensus\ - \ error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments\ - \ where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes\ - \ and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to\ - \ no review of assembly other than reporting of standard assembly statistics.\ - \ Low Quality Draft:Many fragments with little to no review of assembly other\ - \ than reporting of standard assembly statistics. Assembly statistics include,\ - \ but are not limited to total assembly size, number of contigs, contig N50/L50,\ - \ and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous\ - \ sequence per replicon without gaps or ambiguities, with extensive manual review\ - \ and editing to annotate putative gene functions and transcriptional units.\ - \ High-quality draft genome: One or multiple fragments, totaling \u2265 90%\ - \ of the expected genome or replicon sequence or predicted complete. Genome\ - \ fragment(s): One or multiple fragments, totalling < 90% of the expected genome\ - \ or replicon sequence, or for which no genome size could be estimated" - range: assembly_qual_enum - examples: - - value: High-quality draft genome - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 54.0' - pattern: '[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality - draft genome|Genome fragment(s)]' - assembly_name: - is_a: sequencing field - aliases: - - assembly name - description: Name/version of the assembly provided by the submitter that is used - in the genome browsers and in the community - range: string - examples: - - value: HuRef, JCVI_ISG_i3_1.0 - comments: - - 'Expected value: name and version of assembly' - - 'Preferred unit: ' - - 'Position: 55.0' - pattern: '{text} {text}' - assembly_software: - is_a: sequencing field - aliases: - - assembly software - description: Tool(s) used for assembly, including version number and parameters - range: string - examples: - - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise - comments: - - 'Expected value: name and version of software, parameters used' - - 'Preferred unit: ' - - 'Position: 56.0' - pattern: '{software};{version};{parameters}' - annot: - is_a: sequencing field - aliases: - - annotation - description: Tool used for annotation, or for cases where annotation was provided - by a community jamboree or model organism database rather than by a specific - submitter - range: string - examples: - - value: prokka - comments: - - 'Expected value: name of tool or pipeline used, or annotation source description' - - 'Preferred unit: ' - - 'Position: 57.0' - pattern: '{text}' - number_contig: - is_a: sequencing field - aliases: - - number of contigs - description: Total number of contigs in the cleaned/submitted assembly that makes - up a given genome, SAG, MAG, or UViG - range: string - examples: - - value: '40' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Position: 58.0' - pattern: '{integer}' - feat_pred: - is_a: sequencing field - aliases: - - feature prediction - description: Method used to predict UViGs features such as ORFs, integration site, - etc. - range: string - examples: - - value: Prodigal;2.6.3;default parameters - comments: - - 'Expected value: names and versions of software(s), parameters used' - - 'Preferred unit: ' - - 'Position: 59.0' - pattern: '{software};{version};{parameters}' - ref_db: - is_a: sequencing field - aliases: - - reference database(s) - description: List of database(s) used for ORF annotation, along with version number - and reference to website or publication - range: string - examples: - - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 - doi:10.1093/nar/gkw975 - comments: - - 'Expected value: names, versions, and references of databases' - - 'Preferred unit: ' - - 'Position: 60.0' - pattern: '{database};{version};{reference}' - sim_search_meth: - is_a: sequencing field - aliases: - - similarity search method - description: Tool used to compare ORFs with database, along with version and cutoffs - used - range: string - examples: - - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score - comments: - - 'Expected value: names and versions of software(s), parameters used' - - 'Preferred unit: ' - - 'Position: 61.0' - pattern: '{software};{version};{parameters}' - tax_class: - is_a: sequencing field - aliases: - - taxonomic classification - description: Method used for taxonomic classification, along with reference database - used, classification rank, and thresholds used to classify new genomes - range: string - examples: - - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, - default parameters) - comments: - - 'Expected value: classification method, database name, and other parameters' - - 'Preferred unit: ' - - 'Position: 62.0' - pattern: '{text}' - x_16s_recover: - is_a: sequencing field - aliases: - - 16S recovered - description: Can a 16S gene be recovered from the submitted SAG or MAG? - range: string - examples: - - value: 'yes' - comments: - - 'Expected value: boolean' - - 'Preferred unit: ' - - 'Position: 63.0' - pattern: '{boolean}' - x_16s_recover_software: - is_a: sequencing field - aliases: - - 16S recovery software - description: Tools used for 16S rRNA gene extraction - range: string - examples: - - value: rambl;v2;default parameters - comments: - - 'Expected value: names and versions of software(s), parameters used' - - 'Preferred unit: ' - - 'Position: 64.0' - pattern: '{software};{version};{parameters}' - trnas: - is_a: sequencing field - aliases: - - number of standard tRNAs extracted - description: The total number of tRNAs identified from the SAG or MAG - range: string - examples: - - value: '18' - comments: - - 'Expected value: value from 0-21' - - 'Preferred unit: ' - - 'Position: 65.0' - pattern: '{integer}' - trna_ext_software: - is_a: sequencing field - aliases: - - tRNA extraction software - description: Tools used for tRNA identification - range: string - examples: - - value: infernal;v2;default parameters - comments: - - 'Expected value: names and versions of software(s), parameters used' - - 'Preferred unit: ' - - 'Position: 66.0' - pattern: '{software};{version};{parameters}' - compl_score: - is_a: sequencing field - aliases: - - completeness score - description: 'Completeness score is typically based on either the fraction of - markers found as compared to a database or the percent of a genome found as - compared to a closely related reference genome. High Quality Draft: >90%, Medium - Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated - completeness scores' - range: compl_score_enum - examples: - - value: med;60% - comments: - - 'Expected value: quality;percent completeness' - - 'Preferred unit: ' - - 'Position: 67.0' - pattern: '[high|med|low];{percentage}' - compl_software: - is_a: sequencing field - aliases: - - completeness software - description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - range: string - examples: - - value: checkm - comments: - - 'Expected value: names and versions of software(s) used' - - 'Preferred unit: ' - - 'Position: 68.0' - pattern: '{software};{version}' - compl_appr: - is_a: sequencing field - aliases: - - completeness approach - description: The approach used to determine the completeness of a given SAG or - MAG, which would typically make use of a set of conserved marker genes or a - closely related reference genome. For UViG completeness, include reference genome - or group used, and contig feature suggesting a complete genome - range: compl_appr_enum - examples: - - value: 'other: UViG length compared to the average length of reference genomes - from the P22virus genus (NCBI RefSeq v83)' - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 69.0' - pattern: '[marker gene|reference based|other]' - contam_score: - is_a: sequencing field - aliases: - - contamination score - description: 'The contamination score is based on the fraction of single-copy - genes that are observed more than once in a query genome. The following scores - are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low - Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be - deposited into any of the public databases' - range: string - examples: - - value: 1% - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Position: 70.0' - pattern: '{float} percentage' - contam_screen_input: - is_a: sequencing field - aliases: - - contamination screening input - description: The type of sequence data used as input - range: string - examples: - - value: contigs - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 71.0' - pattern: '[reads| contigs]' - contam_screen_param: - is_a: sequencing field - aliases: - - contamination screening parameters - description: Specific parameters used in the decontamination sofware, such as - reference database, coverage, and kmers. Combinations of these parameters may - also be used, i.e. kmer and coverage, or reference database and kmer - range: contam_screen_param_enum - examples: - - value: kmer - comments: - - 'Expected value: enumeration;value or name' - - 'Preferred unit: ' - - 'Position: 72.0' - pattern: '[ref db|kmer|coverage|combination];{text|integer}' - decontam_software: - is_a: sequencing field - aliases: - - decontamination software - description: Tool(s) used in contamination screening - range: decontam_software_enum - examples: - - value: anvi'o - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 73.0' - pattern: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' - sort_tech: - is_a: sequencing field - aliases: - - sorting technology - description: Method used to sort/isolate cells or particles of interest - range: sort_tech_enum - examples: - - value: optical manipulation - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 74.0' - pattern: '[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]' - single_cell_lysis_appr: - is_a: sequencing field - aliases: - - single cell or viral particle lysis approach - description: Method used to free DNA from interior of the cell(s) or particle(s) - range: single_cell_lysis_appr_enum - examples: - - value: enzymatic - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 75.0' - pattern: '[chemical|enzymatic|physical|combination]' - single_cell_lysis_prot: - is_a: sequencing field - aliases: - - single cell or viral particle lysis kit protocol - description: Name of the kit or standard protocol used for cell(s) or particle(s) - lysis - range: string - examples: - - value: ambion single cell lysis kit - comments: - - 'Expected value: kit, protocol name' - - 'Preferred unit: ' - - 'Position: 76.0' - pattern: '{text}' - wga_amp_appr: - is_a: sequencing field - aliases: - - WGA amplification approach - description: Method used to amplify genomic DNA in preparation for sequencing - range: string - examples: - - value: mda based - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 77.0' - pattern: '[pcr based|mda based]' - wga_amp_kit: - is_a: sequencing field - aliases: - - WGA amplification kit - description: Kit used to amplify genomic DNA in preparation for sequencing - range: string - examples: - - value: qiagen repli-g - comments: - - 'Expected value: kit name' - - 'Preferred unit: ' - - 'Position: 78.0' - pattern: '{text}' - bin_param: - is_a: sequencing field - aliases: - - binning parameters - description: The parameters that have been applied during the extraction of genomes - from metagenomic datasets - range: bin_param_enum - examples: - - value: coverage and kmer - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 79.0' - pattern: '[homology search|kmer|coverage|codon usage|combination]' - bin_software: - is_a: sequencing field - aliases: - - binning software - description: Tool(s) used for the extraction of genomes from metagenomic datasets - range: bin_software_enum - examples: - - value: concoct and maxbin - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 80.0' - pattern: '[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]' - reassembly_bin: - is_a: sequencing field - aliases: - - reassembly post binning - description: Has an assembly been performed on a genome bin extracted from a metagenomic - assembly? - range: string - examples: - - value: 'no' - comments: - - 'Expected value: boolean' - - 'Preferred unit: ' - - 'Position: 81.0' - pattern: '{boolean}' - mag_cov_software: - is_a: sequencing field - aliases: - - MAG coverage software - description: Tool(s) used to determine the genome coverage if coverage is used - as a binning parameter in the extraction of genomes from metagenomic datasets - range: mag_cov_software_enum - examples: - - value: bbmap - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 82.0' - pattern: '[bwa|bbmap|bowtie|other]' - vir_ident_software: - is_a: sequencing field - aliases: - - viral identification software - description: Tool(s) used for the identification of UViG as a viral genome, software - or protocol name including version number, parameters, and cutoffs used - range: string - examples: - - value: VirSorter; 1.0.4; Virome database, category 2 - comments: - - 'Expected value: software name, version and relevant parameters' - - 'Preferred unit: ' - - 'Position: 83.0' - pattern: '{software};{version};{parameters}' - pred_genome_type: - is_a: sequencing field - aliases: - - predicted genome type - description: Type of genome predicted for the UViG - range: pred_genome_type_enum - examples: - - value: dsDNA - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 84.0' - pattern: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' - pred_genome_struc: - is_a: sequencing field - aliases: - - predicted genome structure - description: Expected structure of the viral genome - range: pred_genome_struc_enum - examples: - - value: non-segmented - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 85.0' - pattern: '[segmented|non-segmented|undetermined]' - detec_type: - is_a: sequencing field - aliases: - - detection type - description: Type of UViG detection - range: string - examples: - - value: independent sequence (UViG) - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 86.0' - pattern: '[independent sequence (UViG)|provirus (UpViG)]' - votu_class_appr: - is_a: sequencing field - aliases: - - vOTU classification approach - description: "Cutoffs and approach used when clustering new UViGs in \u201Cspecies-level\u201D\ - \ vOTUs. Note that results from standard 95% ANI / 85% AF clustering should\ - \ be provided alongside vOTUS defined from another set of thresholds, even if\ - \ the latter are the ones primarily used during the analysis" - range: string - examples: - - value: 95% ANI;85% AF; greedy incremental clustering - comments: - - 'Expected value: cutoffs and method used' - - 'Preferred unit: ' - - 'Position: 87.0' - pattern: '{ANI cutoff};{AF cutoff};{clustering method}' - votu_seq_comp_appr: - is_a: sequencing field - aliases: - - vOTU sequence comparison approach - description: Tool and thresholds used to compare sequences when computing "species-level" - vOTUs - range: string - examples: - - value: 'blastn;2.6.0+;e-value cutoff: 0.001' - comments: - - 'Expected value: software name, version and relevant parameters' - - 'Preferred unit: ' - - 'Position: 88.0' - pattern: '{software};{version};{parameters}' - votu_db: - is_a: sequencing field - aliases: - - vOTU database - description: Reference database (i.e. sequences not generated as part of the current - study) used to cluster new genomes in "species-level" vOTUs, if any - range: string - examples: - - value: NCBI Viral RefSeq;83 - comments: - - 'Expected value: database and version' - - 'Preferred unit: ' - - 'Position: 89.0' - pattern: '{database};{version}' - host_pred_appr: - is_a: sequencing field - aliases: - - host prediction approach - description: Tool or approach used for host prediction - range: host_pred_appr_enum - examples: - - value: CRISPR spacer match - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Position: 90.0' - pattern: '[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co-occurrence|combination|other]' - host_pred_est_acc: - is_a: sequencing field - aliases: - - host prediction estimated accuracy - description: For each tool or approach used for host prediction, estimated false - discovery rates should be included, either computed de novo or from the literature - range: string - examples: - - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host - genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' - comments: - - 'Expected value: false discovery rate' - - 'Preferred unit: ' - - 'Position: 91.0' - pattern: '{text}' - url: - is_a: sequencing field - aliases: - - relevant electronic resources - description: '' - range: string - examples: - - value: http://www.earthmicrobiome.org/ - comments: - - 'Expected value: URL' - - 'Preferred unit: ' - - 'Position: 92.0' - pattern: '{URL}' - see_also: https://github.com/GenomicsStandardsConsortium/mixs/issues/67 - sop: - is_a: sequencing field - aliases: - - relevant standard operating procedures - description: Standard operating procedures used in assembly and/or annotation - of genomes, metagenomes or environmental sequences - range: string - examples: - - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ - comments: - - 'Expected value: reference to SOP' - - 'Preferred unit: ' - - 'Position: 93.0' - pattern: '{PMID}|{DOI}|{URL}' - barometric_press: - is_a: environment field - aliases: - - barometric pressure - description: Force per unit area exerted against a surface by the weight of air - above that surface - range: quantity value - examples: - - value: 5 millibar - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millibar' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000096 - carb_dioxide: - is_a: environment field - aliases: - - carbon dioxide - description: Carbon dioxide (gas) amount or concentration at the time of sampling - range: quantity value - examples: - - value: 410 parts per million - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: air, built environment' - slot_uri: MIXS:0000097 - carb_monoxide: - is_a: environment field - aliases: - - carbon monoxide - description: Carbon monoxide (gas) amount or concentration at the time of sampling - range: quantity value - examples: - - value: 0.1 parts per million - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000098 - chem_administration: - is_a: environment field - aliases: - - chemical administration - description: List of chemical compounds administered to the host or site where - sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can - include multiple compounds. For chemical entities of biological interest ontology - (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - range: string - examples: - - value: agar [CHEBI:2509];2018-05-11T20:00Z - comments: - - 'Expected value: CHEBI;timestamp' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 13 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous - natural or artificial environment, plant-associated, sediment, wastewater_sludge, - water' - pattern: '{termLabel} {[termID]};{timestamp}' - slot_uri: MIXS:0000751 - humidity: - is_a: environment field - aliases: - - humidity - description: Amount of water vapour in the air, at the time of sampling - range: quantity value - examples: - - value: 25 gram per cubic meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram per cubic meter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000100 - methane: - is_a: environment field - aliases: - - methane - description: Methane (gas) amount or concentration at the time of sampling - range: quantity value - examples: - - value: 1800 parts per billion - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, parts per billion, parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: air, microbial mat_biofilm, sediment' - slot_uri: MIXS:0000101 - misc_param: - is_a: environment field - aliases: - - miscellaneous parameter - description: Any other measurement performed or parameter collected, that is not - listed here - range: string - examples: - - value: Bicarbonate ion concentration;2075 micromole per kilogram - comments: - - 'Expected value: parameter name;measurement value' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 16 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, soil, wastewater_sludge, - water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000752 - organism_count: - is_a: environment field - aliases: - - organism count - description: 'Total cell count of any organism (or group of organisms) per gram, - volume or area of sample, should include name of organism followed by count. - The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should - also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' - range: organism_count_enum - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - comments: - - 'Expected value: organism name;measurement value;enumeration' - - 'Preferred unit: number of cells per cubic meter, number of cells per milliliter, - number of cells per cubic centimeter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 16 packages: air, built environment, host-associated, - human-associated, human-gut, human-oral, human-skin, human-vaginal, hydrocarbon - resources-cores, hydrocarbon resources-fluids_swabs, microbial mat_biofilm, - miscellaneous natural or artificial environment, plant-associated, sediment, - wastewater_sludge, water' - pattern: '{text};{float} {unit};[qPCR|ATP|MPN|other]' - slot_uri: MIXS:0000103 - oxygen: - is_a: environment field - aliases: - - oxygen - description: Oxygen (gas) amount or concentration at the time of sampling - range: quantity value - examples: - - value: 600 parts per million - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000104 - oxy_stat_samp: - is_a: environment field - aliases: - - oxygenation status of sample - description: Oxygenation status of sample - range: oxy_stat_samp_enum - examples: - - value: aerobic - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 15 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, wastewater_sludge, water' - pattern: '[aerobic|anaerobic|other]' - slot_uri: MIXS:0000753 - perturbation: - is_a: environment field - aliases: - - perturbation - description: Type of perturbation, e.g. chemical administration, physical disturbance, - etc., coupled with perturbation regimen including how many times the perturbation - was repeated, how long each perturbation lasted, and the start and end time - of the entire perturbation period; can include multiple perturbation types - range: string - examples: - - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M - comments: - - 'Expected value: perturbation type name;perturbation interval and duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 13 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, microbial mat_biofilm, miscellaneous - natural or artificial environment, plant-associated, sediment, wastewater_sludge, - water' - pattern: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000754 - pollutants: - is_a: environment field - aliases: - - pollutants - description: Pollutant types and, amount or concentrations measured at the time - of sampling; can report multiple pollutants by entering numeric values preceded - by name of pollutant - range: string - examples: - - value: lead;0.15 microgram per cubic meter - comments: - - 'Expected value: pollutant name;measurement value' - - 'Preferred unit: gram, mole per liter, milligram per liter, microgram per cubic - meter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: air' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000107 - resp_part_matter: - is_a: environment field - aliases: - - respirable particulate matter - description: Concentration of substances that remain suspended in the air, and - comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can - report multiple PM's by entering numeric values preceded by name of PM - range: string - examples: - - value: PM2.5;10 microgram per cubic meter - comments: - - 'Expected value: particulate matter name;measurement value' - - 'Preferred unit: microgram per cubic meter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: air' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000108 - samp_salinity: - is_a: environment field - aliases: - - sample salinity - description: Salinity is the total concentration of all dissolved salts in a liquid - or solid (in the form of an extract obtained by centrifugation) sample. While - salinity can be measured by a complete chemical analysis, this method is difficult - and time consuming. More often, it is instead derived from the conductivity - measurement. This is known as practical salinity. These derivations compare - the specific conductance of the sample to a salinity standard such as seawater - range: quantity value - examples: - - value: 1 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, practical salinity unit, percentage' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 11 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, plant-associated, wastewater_sludge' - slot_uri: MIXS:0000109 - samp_store_dur: - is_a: environment field - aliases: - - sample storage duration - description: Duration for which the sample was stored - range: string - examples: - - value: P1Y6M - comments: - - 'Expected value: duration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 15 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, wastewater_sludge, water' - pattern: '{duration}' - slot_uri: MIXS:0000116 - samp_store_loc: - is_a: environment field - aliases: - - sample storage location - description: Location at which sample was stored, usually name of a specific freezer/room - range: string - examples: - - value: Freezer no:5 - comments: - - 'Expected value: location name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 15 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, wastewater_sludge, water' - pattern: '{text}' - slot_uri: MIXS:0000755 - samp_store_temp: - is_a: environment field - aliases: - - sample storage temperature - description: Temperature at which sample was stored, e.g. -80 degree Celsius - range: quantity value - examples: - - value: -80 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 15 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000110 - samp_vol_we_dna_ext: - is_a: environment field - aliases: - - sample volume or weight for DNA extraction - description: Volume (ml), weight (g) of processed sample, or surface area swabbed - from sample for DNA extraction - range: quantity value - examples: - - value: 1500 milliliter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millliter, gram, milligram, square centimeter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 16 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, soil, wastewater_sludge, - water' - slot_uri: MIXS:0000111 - solar_irradiance: - is_a: environment field - aliases: - - solar irradiance - description: The amount of solar energy that arrives at a specific area of a surface - during a specific time interval - range: quantity value - examples: - - value: 1.36 kilowatts per square meter per day - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilowatts per square meter per day, ergs per square centimeter - per second' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000112 - temp: - is_a: environment field - aliases: - - temperature - description: Temperature of the sample at the time of sampling - range: quantity value - examples: - - value: 25 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 15 packages: air, host-associated, human-associated, - human-gut, human-oral, human-skin, human-vaginal, hydrocarbon resources-cores, - hydrocarbon resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural - or artificial environment, plant-associated, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000113 - ventilation_rate: - is_a: environment field - aliases: - - ventilation rate - description: Ventilation rate of the system in the sampled premises - range: quantity value - examples: - - value: 750 cubic meter per minute - comments: - - 'Expected value: measurement value' - - 'Preferred unit: cubic meter per minute, liters per second' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000114 - ventilation_type: - is_a: environment field - aliases: - - ventilation type - description: Ventilation system used in the sampled premises - range: string - examples: - - value: Operable windows - comments: - - 'Expected value: ventilation type name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: air, built environment' - pattern: '{text}' - slot_uri: MIXS:0000756 - volatile_org_comp: - is_a: environment field - aliases: - - volatile organic compounds - description: Concentration of carbon-based chemicals that easily evaporate at - room temperature; can report multiple volatile organic compounds by entering - numeric values preceded by name of compound - range: string - examples: - - value: formaldehyde;500 nanogram per liter - comments: - - 'Expected value: volatile organic compound name;measurement value' - - 'Preferred unit: microgram per cubic meter, parts per million, nanogram per - liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: air' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000115 - wind_direction: - is_a: environment field - aliases: - - wind direction - description: Wind direction is the direction from which a wind originates - range: string - examples: - - value: Northwest - comments: - - 'Expected value: wind direction name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - pattern: '{text}' - slot_uri: MIXS:0000757 - wind_speed: - is_a: environment field - aliases: - - wind speed - description: Speed of wind measured at the time of sampling - range: quantity value - examples: - - value: 21 kilometer per hour - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter per second, kilometer per hour' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: air' - slot_uri: MIXS:0000118 - surf_material: - is_a: environment field - aliases: - - surface material - description: Surface materials at the point of sampling - range: surf_material_enum - examples: - - value: wood - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: built environment' - pattern: '[adobe|carpet|cinder blocks|concrete|hay bales|glass|metal|paint|plastic|stainless - steel|stone|stucco|tile|vinyl|wood]' - slot_uri: MIXS:0000758 - surf_air_cont: - is_a: environment field - aliases: - - surface-air contaminant - description: Contaminant identified on surface - range: surf_air_cont_enum - examples: - - value: radon - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 2' - - 'This field is used uniquely in: built environment' - pattern: '[dust|organic matter|particulate matter|volatile organic compounds|biological - contaminants|radon|nutrients|biocides]' - slot_uri: MIXS:0000759 - rel_air_humidity: - is_a: environment field - aliases: - - relative air humidity - description: Partial vapor and air pressure, density of the vapor and air, or - by the actual mass of the vapor and air - range: quantity value - examples: - - value: 80% - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000121 - abs_air_humidity: - is_a: environment field - aliases: - - absolute air humidity - description: Actual mass of water vapor - mh20 - present in the air water vapor - mixture - range: quantity value - examples: - - value: 9 gram per gram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram per gram, kilogram per kilogram, kilogram, pound' - - 'Occurrence: 1' - - 'Position: 4' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000122 - surf_humidity: - is_a: environment field - aliases: - - surface humidity - description: 'Surfaces: water activity as a function of air and material moisture' - range: quantity value - examples: - - value: 10% - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 5' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000123 - air_temp: - is_a: environment field - aliases: - - air temperature - description: Temperature of the air at the time of sampling - range: quantity value - examples: - - value: 20 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 6' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000124 - surf_temp: - is_a: environment field - aliases: - - surface temperature - description: Temperature of the surface at the time of sampling - range: quantity value - examples: - - value: 15 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 7' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000125 - surf_moisture_ph: - is_a: environment field - aliases: - - surface moisture pH - description: ph measurement of surface - range: double - examples: - - value: '7' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 8' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000760 - build_occup_type: - is_a: environment field - aliases: - - building occupancy type - description: The primary function for which a building or discrete part of a building - is intended to be used - range: build_occup_type_enum - examples: - - value: market - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 9' - - 'This field is used uniquely in: built environment' - pattern: '[office|market|restaurant|residence|school|residential|commercial|low - rise|high rise|wood framed|office|health care|school|airport|sports complex]' - slot_uri: MIXS:0000761 - surf_moisture: - is_a: environment field - aliases: - - surface moisture - description: Water held on a surface - range: quantity value - examples: - - value: 0.01 gram per square meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: parts per million, gram per cubic meter, gram per square meter' - - 'Occurrence: 1' - - 'Position: 10' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000128 - dew_point: - is_a: environment field - aliases: - - dew point - description: The temperature to which a given parcel of humid air must be cooled, - at constant barometric pressure, for water vapor to condense into water. - range: quantity value - examples: - - value: 22 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 11' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000129 - indoor_space: - is_a: environment field - aliases: - - indoor space - description: A distinguishable space within a structure, the purpose for which - discrete areas of a building is used - range: indoor_space_enum - examples: - - value: foyer - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 15' - - 'This field is used uniquely in: built environment' - pattern: '[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]' - slot_uri: MIXS:0000763 - indoor_surf: - is_a: environment field - aliases: - - indoor surface - description: Type of indoor surface - range: indoor_surf_enum - examples: - - value: wall - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 16' - - 'This field is used uniquely in: built environment' - pattern: '[cabinet|ceiling|counter top|door|shelving|vent cover|window|wall]' - slot_uri: MIXS:0000764 - filter_type: - is_a: environment field - aliases: - - filter type - description: A device which removes solid particulates or airborne molecular contaminants - range: filter_type_enum - examples: - - value: HEPA - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 17' - - 'This field is used uniquely in: built environment' - pattern: '[particulate air filter|chemical air filter|low-MERV pleated media|HEPA|electrostatic|gas-phase - or ultraviolet air treatments]' - slot_uri: MIXS:0000765 - heat_cool_type: - is_a: environment field - aliases: - - heating and cooling system type - description: Methods of conditioning or heating a room or building - range: heat_cool_type_enum - examples: - - value: heat pump - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 18' - - 'This field is used uniquely in: built environment' - pattern: '[radiant system|heat pump|forced air system|steam forced heat|wood stove]' - slot_uri: MIXS:0000766 - substructure_type: - is_a: environment field - aliases: - - substructure type - description: The substructure or under building is that largely hidden section - of the building which is built off the foundations to the ground floor level - range: substructure_type_enum - examples: - - value: basement - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 19' - - 'This field is used uniquely in: built environment' - pattern: '[crawlspace|slab on grade|basement]' - slot_uri: MIXS:0000767 - building_setting: - is_a: environment field - aliases: - - building setting - description: A location (geography) where a building is set - range: building_setting_enum - examples: - - value: rural - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 20' - - 'This field is used uniquely in: built environment' - pattern: '[urban|suburban|exurban|rural]' - slot_uri: MIXS:0000768 - light_type: - is_a: environment field - aliases: - - light type - description: Application of light to achieve some practical or aesthetic effect. - Lighting includes the use of both artificial light sources such as lamps and - light fixtures, as well as natural illumination by capturing daylight. Can also - include absence of light - range: light_type_enum - examples: - - value: desk lamp - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 21' - - 'This field is used uniquely in: built environment' - pattern: '[natural light|electric light|desk lamp|flourescent lights|natural light|none]' - slot_uri: MIXS:0000769 - samp_sort_meth: - is_a: environment field - aliases: - - sample size sorting method - description: Method by which samples are sorted; open face filter collecting total - suspended particles, prefilter to remove particles larger than X micrometers - in diameter, where common values of X would be 10 and 2.5 full size sorting - in a cascade impactor. - range: string - examples: - - value: '' - comments: - - 'Expected value: description of method' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 22' - - 'This field is used uniquely in: built environment' - pattern: '{text}' - slot_uri: MIXS:0000216 - space_typ_state: - is_a: environment field - aliases: - - space typical state - description: Customary or normal state of the space - range: string - examples: - - value: typically occupied - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 23' - - 'This field is used uniquely in: built environment' - pattern: '[typically occupied|typically unoccupied]' - slot_uri: MIXS:0000770 - typ_occup_density: - is_a: environment field - aliases: - - typical occupant density - description: Customary or normal density of occupants - range: double - examples: - - value: '25' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 24' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000771 - occup_samp: - is_a: environment field - aliases: - - occupancy at sampling - description: Number of occupants present at time of sample within the given space - range: string - examples: - - value: '10' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 25' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000772 - occup_density_samp: - is_a: environment field - aliases: - - occupant density at sampling - description: Average number of occupants at time of sampling per square footage - range: double - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 26' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000217 - address: - is_a: environment field - aliases: - - address - description: The street name and building number where the sampling occurred. - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 27' - - 'This field is used uniquely in: built environment' - pattern: '{integer}{text}' - slot_uri: MIXS:0000218 - adj_room: - is_a: environment field - aliases: - - adjacent rooms - description: List of rooms (room number, room name) immediately adjacent to the - sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: room name;room number' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 28' - - 'This field is used uniquely in: built environment' - pattern: '{text};{integer}' - slot_uri: MIXS:0000219 - aero_struc: - is_a: environment field - aliases: - - aerospace structure - description: Aerospace structures typically consist of thin plates with stiffeners - for the external surfaces, bulkheads and frames to support the shape and fasteners - such as welds, rivets, screws and bolts to hold the components together - range: string - examples: - - value: plane - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 29' - - 'This field is used uniquely in: built environment' - pattern: '[plane|glider]' - slot_uri: MIXS:0000773 - amount_light: - is_a: environment field - aliases: - - amount of light - description: The unit of illuminance and luminous emittance, measuring luminous - flux per unit area - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: lux, lumens per square meter' - - 'Occurrence: 1' - - 'Position: 30' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000140 - arch_struc: - is_a: environment field - aliases: - - architectural structure - description: An architectural structure is a human-made, free-standing, immobile - outdoor construction - range: arch_struc_enum - examples: - - value: shed - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 31' - - 'This field is used uniquely in: built environment' - pattern: '[building|shed|home]' - slot_uri: MIXS:0000774 - avg_occup: - is_a: environment field - aliases: - - average daily occupancy - description: Daily average occupancy of room - range: double - examples: - - value: '2' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 32' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000775 - avg_dew_point: - is_a: environment field - aliases: - - average dew point - description: The average of dew point measures taken at the beginning of every - hour over a 24 hour period on the sampling day - range: quantity value - examples: - - value: 25.5 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 33' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000141 - avg_temp: - is_a: environment field - aliases: - - average temperature - description: The average of temperatures taken at the beginning of every hour - over a 24 hour period on the sampling day - range: quantity value - examples: - - value: 12.5 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 34' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000142 - bathroom_count: - is_a: environment field - aliases: - - bathroom count - description: The number of bathrooms in the building - range: string - examples: - - value: '1' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 35' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000776 - bedroom_count: - is_a: environment field - aliases: - - bedroom count - description: The number of bedrooms in the building - range: string - examples: - - value: '2' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 36' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000777 - built_struc_age: - is_a: environment field - aliases: - - built structure age - description: The age of the built structure since construction - range: quantity value - examples: - - value: '15' - comments: - - 'Expected value: value' - - 'Preferred unit: year' - - 'Occurrence: 1' - - 'Position: 37' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000145 - built_struc_set: - is_a: environment field - aliases: - - built structure setting - description: The characterization of the location of the built structure as high - or low human density - range: string - examples: - - value: rural - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 38' - - 'This field is used uniquely in: built environment' - pattern: '[urban|rural]' - slot_uri: MIXS:0000778 - built_struc_type: - is_a: environment field - aliases: - - built structure type - description: A physical structure that is a body or assemblage of bodies in space - to form a system capable of supporting loads - range: string - examples: - - value: '' - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 39' - - 'This field is used uniquely in: built environment' - pattern: '{text}' - slot_uri: MIXS:0000721 - ceil_area: - is_a: environment field - aliases: - - ceiling area - description: The area of the ceiling space within the room - range: quantity value - examples: - - value: 25 square meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 40' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000148 - ceil_cond: - is_a: environment field - aliases: - - ceiling condition - description: The physical condition of the ceiling at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - range: ceil_cond_enum - examples: - - value: damaged - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 41' - - 'This field is used uniquely in: built environment' - pattern: '[new|visible wear|needs repair|damaged|rupture]' - slot_uri: MIXS:0000779 - ceil_finish_mat: - is_a: environment field - aliases: - - ceiling finish material - description: The type of material used to finish a ceiling - range: ceil_finish_mat_enum - examples: - - value: stucco - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 42' - - 'This field is used uniquely in: built environment' - pattern: '[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral - wool/calcium silicate|wood]' - slot_uri: MIXS:0000780 - ceil_water_mold: - is_a: environment field - aliases: - - ceiling signs of water/mold - description: Signs of the presence of mold or mildew on the ceiling - range: string - examples: - - value: presence of mold visible - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 43' - - 'This field is used uniquely in: built environment' - pattern: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000781 - ceil_struc: - is_a: environment field - aliases: - - ceiling structure - description: The construction format of the ceiling - range: string - examples: - - value: concrete - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 44' - - 'This field is used uniquely in: built environment' - pattern: '[wood frame|concrete]' - slot_uri: MIXS:0000782 - ceil_texture: - is_a: environment field - aliases: - - ceiling texture - description: The feel, appearance, or consistency of a ceiling surface - range: ceil_texture_enum - examples: - - value: popcorn - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 45' - - 'This field is used uniquely in: built environment' - pattern: '[crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange - peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' - slot_uri: MIXS:0000783 - ceil_thermal_mass: - is_a: environment field - aliases: - - ceiling thermal mass - description: The ability of the ceiling to provide inertia against temperature - fluctuations. Generally this means concrete that is exposed. A metal deck that - supports a concrete slab will act thermally as long as it is exposed to room - air flow - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: joule per degree Celsius' - - 'Occurrence: 1' - - 'Position: 46' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000143 - ceil_type: - is_a: environment field - aliases: - - ceiling type - description: The type of ceiling according to the ceiling's appearance or construction - range: ceil_type_enum - examples: - - value: coffered - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 47' - - 'This field is used uniquely in: built environment' - pattern: '[cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched]' - slot_uri: MIXS:0000784 - cool_syst_id: - is_a: environment field - aliases: - - cooling system identifier - description: The cooling system identifier - range: string - examples: - - value: '12345' - comments: - - 'Expected value: unique identifier' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 48' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000785 - date_last_rain: - is_a: environment field - aliases: - - date last rain - description: The date of the last time it rained - range: string - examples: - - value: 2018-05-11:T14:30Z - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 49' - - 'This field is used uniquely in: built environment' - pattern: '{timestamp}' - slot_uri: MIXS:0000786 - build_docs: - is_a: environment field - aliases: - - design, construction, and operation documents - description: The building design, construction and operation documents - range: build_docs_enum - examples: - - value: maintenance plans - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 50' - - 'This field is used uniquely in: built environment' - pattern: '[building information model|commissioning report|complaint logs|contract - administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop - drawings|submittals|ventilation system|windows]' - slot_uri: MIXS:0000787 - door_size: - is_a: environment field - aliases: - - door area or size - description: The size of the door - range: quantity value - examples: - - value: 2.5 square meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 51' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000158 - door_cond: - is_a: environment field - aliases: - - door condition - description: The phsical condition of the door - range: door_cond_enum - examples: - - value: new - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 52' - - 'This field is used uniquely in: built environment' - pattern: '[damaged|needs repair|new|rupture|visible wear]' - slot_uri: MIXS:0000788 - door_direct: - is_a: environment field - aliases: - - door direction of opening - description: The direction the door opens - range: door_direct_enum - examples: - - value: inward - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 53' - - 'This field is used uniquely in: built environment' - pattern: '[inward|outward|sideways]' - slot_uri: MIXS:0000789 - door_loc: - is_a: environment field - aliases: - - door location - description: The relative location of the door in the room - range: door_loc_enum - examples: - - value: north - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 54' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west]' - slot_uri: MIXS:0000790 - door_mat: - is_a: environment field - aliases: - - door material - description: The material the door is composed of - range: door_mat_enum - examples: - - value: wood - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 55' - - 'This field is used uniquely in: built environment' - pattern: '[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic - alloy|vinyl|wood|wood/plastic composite]' - slot_uri: MIXS:0000791 - door_move: - is_a: environment field - aliases: - - door movement - description: The type of movement of the door - range: door_move_enum - examples: - - value: swinging - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 56' - - 'This field is used uniquely in: built environment' - pattern: '[collapsible|folding|revolving|rolling shutter|sliding|swinging]' - slot_uri: MIXS:0000792 - door_water_mold: - is_a: environment field - aliases: - - door signs of water/mold - description: Signs of the presence of mold or mildew on a door - range: string - examples: - - value: presence of mold visible - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 57' - - 'This field is used uniquely in: built environment' - pattern: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000793 - door_type: - is_a: environment field - aliases: - - door type - description: The type of door material - range: door_type_enum - examples: - - value: wooden - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 58' - - 'This field is used uniquely in: built environment' - pattern: '[composite|metal|wooden]' - slot_uri: MIXS:0000794 - door_comp_type: - is_a: environment field - aliases: - - door type, composite - description: The composite type of the door - range: door_comp_type_enum - examples: - - value: revolving - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 59' - - 'This field is used uniquely in: built environment' - pattern: '[metal covered|revolving|sliding|telescopic]' - slot_uri: MIXS:0000795 - door_type_metal: - is_a: environment field - aliases: - - door type, metal - description: The type of metal door - range: door_type_metal_enum - examples: - - value: hollow - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 60' - - 'This field is used uniquely in: built environment' - pattern: '[collapsible|corrugated steel|hollow|rolling shutters|steel plate]' - slot_uri: MIXS:0000796 - door_type_wood: - is_a: environment field - aliases: - - door type, wood - description: The type of wood door - range: door_type_wood_enum - examples: - - value: battened - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 61' - - 'This field is used uniquely in: built environment' - pattern: '[bettened and ledged|battened|ledged and braced|battened|ledged and - framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire - gauged]' - slot_uri: MIXS:0000797 - drawings: - is_a: environment field - aliases: - - drawings - description: The buildings architectural drawings; if design is chosen, indicate - phase-conceptual, schematic, design development, and construction documents - range: drawings_enum - examples: - - value: sketch - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 62' - - 'This field is used uniquely in: built environment' - pattern: '[operation|as built|construction|bid|design|building navigation map|diagram|sketch]' - slot_uri: MIXS:0000798 - elevator: - is_a: environment field - aliases: - - elevator count - description: The number of elevators within the built structure - range: string - examples: - - value: '2' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 63' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000799 - escalator: - is_a: environment field - aliases: - - escalator count - description: The number of escalators within the built structure - range: string - examples: - - value: '4' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 64' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000800 - exp_duct: - is_a: environment field - aliases: - - exposed ductwork - description: The amount of exposed ductwork in the room - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 65' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000144 - exp_pipe: - is_a: environment field - aliases: - - exposed pipes - description: The number of exposed pipes in the room - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 66' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000220 - ext_door: - is_a: environment field - aliases: - - exterior door count - description: The number of exterior doors in the built structure - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 67' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000170 - fireplace_type: - is_a: environment field - aliases: - - fireplace type - description: A firebox with chimney - range: string - examples: - - value: wood burning - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 68' - - 'This field is used uniquely in: built environment' - pattern: '[gas burning|wood burning]' - slot_uri: MIXS:0000802 - floor_age: - is_a: environment field - aliases: - - floor age - description: The time period since installment of the carpet or flooring - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: years, weeks, days' - - 'Occurrence: 1' - - 'Position: 69' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000164 - floor_area: - is_a: environment field - aliases: - - floor area - description: The area of the floor space within the room - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 70' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000165 - floor_cond: - is_a: environment field - aliases: - - floor condition - description: The physical condition of the floor at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - range: floor_cond_enum - examples: - - value: new - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 71' - - 'This field is used uniquely in: built environment' - pattern: '[new|visible wear|needs repair|damaged|rupture]' - slot_uri: MIXS:0000803 - floor_count: - is_a: environment field - aliases: - - floor count - description: The number of floors in the building, including basements and mechanical - penthouse - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 72' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000225 - floor_finish_mat: - is_a: environment field - aliases: - - floor finish material - description: The floor covering type; the finished surface that is walked on - range: floor_finish_mat_enum - examples: - - value: carpet - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 73' - - 'This field is used uniquely in: built environment' - pattern: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl - composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify - unfinished|sealed|clear finish|paint]' - slot_uri: MIXS:0000804 - floor_water_mold: - is_a: environment field - aliases: - - floor signs of water/mold - description: Signs of the presence of mold or mildew in a room - range: floor_water_mold_enum - examples: - - value: ceiling discoloration - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 74' - - 'This field is used uniquely in: built environment' - pattern: '[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling - discoloration|peeling paint or wallpaper|bulging walls|condensation]' - slot_uri: MIXS:0000805 - floor_struc: - is_a: environment field - aliases: - - floor structure - description: Refers to the structural elements and subfloor upon which the finish - flooring is installed - range: floor_struc_enum - examples: - - value: concrete - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 75' - - 'This field is used uniquely in: built environment' - pattern: '[balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete]' - slot_uri: MIXS:0000806 - floor_thermal_mass: - is_a: environment field - aliases: - - floor thermal mass - description: The ability of the floor to provide inertia against temperature fluctuations - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: joule per degree Celsius' - - 'Occurrence: 1' - - 'Position: 76' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000166 - freq_clean: - is_a: environment field - aliases: - - frequency of cleaning - description: The number of times the building is cleaned per week - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 77' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000226 - freq_cook: - is_a: environment field - aliases: - - frequency of cooking - description: The number of times a meal is cooked per week - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 78' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000227 - furniture: - is_a: environment field - aliases: - - furniture - description: The types of furniture present in the sampled room - range: furniture_enum - examples: - - value: chair - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 79' - - 'This field is used uniquely in: built environment' - pattern: '[cabinet|chair|desks]' - slot_uri: MIXS:0000807 - gender_restroom: - is_a: environment field - aliases: - - gender of restroom - description: The gender type of the restroom - range: string - examples: - - value: male - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 80' - - 'This field is used uniquely in: built environment' - pattern: '[male|female]' - slot_uri: MIXS:0000808 - hall_count: - is_a: environment field - aliases: - - hallway/corridor count - description: The total count of hallways and cooridors in the built structure - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 81' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000228 - handidness: - is_a: environment field - aliases: - - handidness - description: The handidness of the individual sampled - range: handidness_enum - examples: - - value: right handedness - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 82' - - 'This field is used uniquely in: built environment' - pattern: '[ambidexterity|left handedness|mixed-handedness|right handedness]' - slot_uri: MIXS:0000809 - heat_deliv_loc: - is_a: environment field - aliases: - - heating delivery locations - description: The location of heat delivery within the room - range: heat_deliv_loc_enum - examples: - - value: north - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 83' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west]' - slot_uri: MIXS:0000810 - heat_system_deliv_meth: - is_a: environment field - aliases: - - heating system delivery method - description: The method by which the heat is delivered through the system - range: string - examples: - - value: radiant - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 84' - - 'This field is used uniquely in: built environment' - pattern: '[conductive|radiant]' - slot_uri: MIXS:0000812 - heat_system_id: - is_a: environment field - aliases: - - heating system identifier - description: The heating system identifier - range: string - examples: - - value: '' - comments: - - 'Expected value: unique identifier' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 85' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000833 - height_carper_fiber: - is_a: environment field - aliases: - - height carpet fiber mat - description: The average carpet fiber height in the indoor environment - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: centimeter' - - 'Occurrence: 1' - - 'Position: 86' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000167 - inside_lux: - is_a: environment field - aliases: - - inside lux light - description: The recorded value at sampling time (power density) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilowatt per square metre' - - 'Occurrence: 1' - - 'Position: 87' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000168 - int_wall_cond: - is_a: environment field - aliases: - - interior wall condition - description: The physical condition of the wall at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - range: int_wall_cond_enum - examples: - - value: damaged - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 88' - - 'This field is used uniquely in: built environment' - pattern: '[new|visible wear|needs repair|damaged|rupture]' - slot_uri: MIXS:0000813 - last_clean: - is_a: environment field - aliases: - - last time swept/mopped/vacuumed - description: The last time the floor was cleaned (swept, mopped, vacuumed) - range: string - examples: - - value: 2018-05-11:T14:30Z - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 89' - - 'This field is used uniquely in: built environment' - pattern: '{timestamp}' - slot_uri: MIXS:0000814 - max_occup: - is_a: environment field - aliases: - - maximum occupancy - description: The maximum amount of people allowed in the indoor environment - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 90' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000229 - mech_struc: - is_a: environment field - aliases: - - mechanical structure - description: 'mechanical structure: a moving structure' - range: mech_struc_enum - examples: - - value: elevator - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 91' - - 'This field is used uniquely in: built environment' - pattern: '[subway|coach|carriage|elevator|escalator|boat|train|car|bus]' - slot_uri: MIXS:0000815 - number_plants: - is_a: environment field - aliases: - - number of houseplants - description: The number of plant(s) in the sampling space - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 92' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000230 - number_pets: - is_a: environment field - aliases: - - number of pets - description: The number of pets residing in the sampled space - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 93' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000231 - number_resident: - is_a: environment field - aliases: - - number of residents - description: The number of individuals currently occupying in the sampling location - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 94' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000232 - occup_document: - is_a: environment field - aliases: - - occupancy documentation - description: The type of documentation of occupancy - range: occup_document_enum - examples: - - value: estimate - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 95' - - 'This field is used uniquely in: built environment' - pattern: '[automated count|estimate|manual count|videos]' - slot_uri: MIXS:0000816 - ext_wall_orient: - is_a: environment field - aliases: - - orientations of exterior wall - description: The orientation of the exterior wall - range: ext_wall_orient_enum - examples: - - value: northwest - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 96' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' - slot_uri: MIXS:0000817 - ext_window_orient: - is_a: environment field - aliases: - - orientations of exterior window - description: The compass direction the exterior window of the room is facing - range: ext_window_orient_enum - examples: - - value: southwest - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 97' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west|northeast|southeast|southwest|northwest]' - slot_uri: MIXS:0000818 - rel_humidity_out: - is_a: environment field - aliases: - - outside relative humidity - description: The recorded outside relative humidity value at the time of sampling - range: quantity value - examples: - - value: 12 per kilogram of air - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram of air, kilogram of air' - - 'Occurrence: 1' - - 'Position: 98' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000188 - pres_animal: - is_a: environment field - aliases: - - presence of pets, animals, or insects - description: The number and type of animals present in the sampling space - range: pres_animal_enum - examples: - - value: cat;5 - comments: - - 'Expected value: enumeration;count' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 99' - - 'This field is used uniquely in: built environment' - pattern: '[cat|dog|rodent|snake|other];{integer}' - slot_uri: MIXS:0000819 - quad_pos: - is_a: environment field - aliases: - - quadrant position - description: The quadrant position of the sampling room within the building - range: quad_pos_enum - examples: - - value: West side - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 100' - - 'This field is used uniquely in: built environment' - pattern: '[North side|West side|South side|East side]' - slot_uri: MIXS:0000820 - rel_samp_loc: - is_a: environment field - aliases: - - relative sampling location - description: The sampling location within the train car - range: rel_samp_loc_enum - examples: - - value: center of car - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 101' - - 'This field is used uniquely in: built environment' - pattern: '[edge of car|center of car|under a seat]' - slot_uri: MIXS:0000821 - room_air_exch_rate: - is_a: environment field - aliases: - - room air exchange rate - description: The rate at which outside air replaces indoor air in a given space - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: liter per hour' - - 'Occurrence: 1' - - 'Position: 102' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000169 - room_architec_element: - is_a: environment field - aliases: - - room architectural elements - description: The unique details and component parts that, together, form the architecture - of a distinguisahable space within a built structure - range: string - examples: - - value: '' - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 103' - - 'This field is used uniquely in: built environment' - pattern: '{text}' - slot_uri: MIXS:0000233 - room_condt: - is_a: environment field - aliases: - - room condition - description: The condition of the room at the time of sampling - range: room_condt_enum - examples: - - value: new - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 104' - - 'This field is used uniquely in: built environment' - pattern: '[new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew]' - slot_uri: MIXS:0000822 - room_count: - is_a: environment field - aliases: - - room count - description: The total count of rooms in the built structure including all room - types - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 105' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000234 - room_dim: - is_a: environment field - aliases: - - room dimensions - description: The length, width and height of sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 106' - - 'This field is used uniquely in: built environment' - pattern: '{integer} {unit} x {integer} {unit} x {integer} {unit}' - slot_uri: MIXS:0000192 - room_door_dist: - is_a: environment field - aliases: - - room door distance - description: Distance between doors (meters) in the hallway between the sampling - room and adjacent rooms - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 107' - - 'This field is used uniquely in: built environment' - pattern: '{integer} {unit}' - slot_uri: MIXS:0000193 - room_loc: - is_a: environment field - aliases: - - room location in building - description: The position of the room within the building - range: room_loc_enum - examples: - - value: interior room - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 108' - - 'This field is used uniquely in: built environment' - pattern: '[corner room|interior room|exterior wall]' - slot_uri: MIXS:0000823 - room_moist_damage_hist: - is_a: environment field - aliases: - - room moisture damage or mold history - description: The history of moisture damage or mold in the past 12 months. Number - of events of moisture damage or mold observed - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 109' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000235 - room_net_area: - is_a: environment field - aliases: - - room net area - description: The net floor area of sampling room. Net area excludes wall thicknesses - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square feet, square meter' - - 'Occurrence: 1' - - 'Position: 110' - - 'This field is used uniquely in: built environment' - pattern: '{integer} {unit}' - slot_uri: MIXS:0000194 - room_occup: - is_a: environment field - aliases: - - room occupancy - description: Count of room occupancy at time of sampling - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 111' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000236 - room_samp_pos: - is_a: environment field - aliases: - - room sampling position - description: The horizontal sampling position in the room relative to architectural - elements - range: room_samp_pos_enum - examples: - - value: south corner - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 112' - - 'This field is used uniquely in: built environment' - pattern: '[north corner|south corner|west corner|east corner|northeast corner|northwest - corner|southeast corner|southwest corner|center]' - slot_uri: MIXS:0000824 - room_type: - is_a: environment field - aliases: - - room type - description: The main purpose or activity of the sampling room. A room is any - distinguishable space within a structure - range: room_type_enum - examples: - - value: bathroom - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 113' - - 'This field is used uniquely in: built environment' - pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail - room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical - or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' - slot_uri: MIXS:0000825 - room_vol: - is_a: environment field - aliases: - - room volume - description: Volume of sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: cubic feet, cubic meter' - - 'Occurrence: 1' - - 'Position: 114' - - 'This field is used uniquely in: built environment' - pattern: '{integer} {unit}' - slot_uri: MIXS:0000195 - room_window_count: - is_a: environment field - aliases: - - room window count - description: Number of windows in the room - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 115' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000237 - room_connected: - is_a: environment field - aliases: - - rooms connected by a doorway - description: List of rooms connected to the sampling room by a doorway - range: room_connected_enum - examples: - - value: office - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 116' - - 'This field is used uniquely in: built environment' - pattern: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail - room|office|stairwell]' - slot_uri: MIXS:0000826 - room_hallway: - is_a: environment field - aliases: - - rooms that are on the same hallway - description: List of room(s) (room number, room name) located in the same hallway - as sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: room name;room number' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 117' - - 'This field is used uniquely in: built environment' - pattern: '{text};{integer}' - slot_uri: MIXS:0000238 - room_door_share: - is_a: environment field - aliases: - - rooms that share a door with sampling room - description: List of room(s) (room number, room name) sharing a door with the - sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: room name;room number' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 118' - - 'This field is used uniquely in: built environment' - pattern: '{text};{integer}' - slot_uri: MIXS:0000242 - room_wall_share: - is_a: environment field - aliases: - - rooms that share a wall with sampling room - description: List of room(s) (room number, room name) sharing a wall with the - sampling room - range: string - examples: - - value: '' - comments: - - 'Expected value: room name;room number' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 119' - - 'This field is used uniquely in: built environment' - pattern: '{text};{integer}' - slot_uri: MIXS:0000243 - samp_weather: - is_a: environment field - aliases: - - sampling day weather - description: The weather on the sampling day - range: samp_weather_enum - examples: - - value: foggy - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 120' - - 'This field is used uniquely in: built environment' - pattern: '[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]' - slot_uri: MIXS:0000827 - samp_floor: - is_a: environment field - aliases: - - sampling floor - description: The floor of the building, where the sampling room is located - range: samp_floor_enum - examples: - - value: 4th floor - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 121' - - 'This field is used uniquely in: built environment' - pattern: '[1st floor|2nd floor|{integer} floor|basement|lobby]' - slot_uri: MIXS:0000828 - samp_room_id: - is_a: environment field - aliases: - - sampling room ID or name - description: Sampling room number. This ID should be consistent with the designations - on the building floor plans - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 122' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000244 - samp_time_out: - is_a: environment field - aliases: - - sampling time outside - description: The recent and long term history of outside sampling - range: double - examples: - - value: '' - comments: - - 'Expected value: time' - - 'Preferred unit: hour' - - 'Occurrence: 1' - - 'Position: 123' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000196 - season: - is_a: environment field - aliases: - - season - description: The season when sampling occurred. Any of the four periods into which - the year is divided by the equinoxes and solstices. This field accepts terms - listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - range: string - examples: - - value: autumn [NCIT:C94733] - comments: - - 'Expected value: NCIT:C94729' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 124' - - 'This field is used uniquely in: built environment' - pattern: '{termLabel} {[termID]}' - slot_uri: MIXS:0000829 - season_use: - is_a: environment field - aliases: - - seasonal use - description: The seasons the space is occupied - range: season_use_enum - examples: - - value: Winter - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 125' - - 'This field is used uniquely in: built environment' - pattern: '[Spring|Summer|Fall|Winter]' - slot_uri: MIXS:0000830 - shading_device_cond: - is_a: environment field - aliases: - - shading device condition - description: The physical condition of the shading device at the time of sampling - range: shading_device_cond_enum - examples: - - value: new - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 126' - - 'This field is used uniquely in: built environment' - pattern: '[damaged|needs repair|new|rupture|visible wear]' - slot_uri: MIXS:0000831 - shading_device_loc: - is_a: environment field - aliases: - - shading device location - description: The location of the shading device in relation to the built structure - range: string - examples: - - value: exterior - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 127' - - 'This field is used uniquely in: built environment' - pattern: '[exterior|interior]' - slot_uri: MIXS:0000832 - shading_device_mat: - is_a: environment field - aliases: - - shading device material - description: The material the shading device is composed of - range: string - examples: - - value: '' - comments: - - 'Expected value: material name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 128' - - 'This field is used uniquely in: built environment' - pattern: '{text}' - slot_uri: MIXS:0000245 - shading_device_water_mold: - is_a: environment field - aliases: - - shading device signs of water/mold - description: Signs of the presence of mold or mildew on the shading device - range: string - examples: - - value: no presence of mold visible - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 129' - - 'This field is used uniquely in: built environment' - pattern: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000834 - shading_device_type: - is_a: environment field - aliases: - - shading device type - description: The type of shading device - range: shading_device_type_enum - examples: - - value: slatted aluminum awning - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 130' - - 'This field is used uniquely in: built environment' - pattern: '[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller - awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian - awning]' - slot_uri: MIXS:0000835 - specific_humidity: - is_a: environment field - aliases: - - specific humidity - description: The mass of water vapour in a unit mass of moist air, usually expressed - as grams of vapour per kilogram of air, or, in air conditioning, as grains per - pound. - range: quantity value - examples: - - value: 15 per kilogram of air - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram of air, kilogram of air' - - 'Occurrence: 1' - - 'Position: 131' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000214 - specific: - is_a: environment field - aliases: - - specifications - description: 'The building specifications. If design is chosen, indicate phase: - conceptual, schematic, design development, construction documents' - range: specific_enum - examples: - - value: construction - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 132' - - 'This field is used uniquely in: built environment' - pattern: '[operation|as built|construction|bid|design|photos]' - slot_uri: MIXS:0000836 - temp_out: - is_a: environment field - aliases: - - temperature outside house - description: The recorded temperature value at sampling time outside - range: quantity value - examples: - - value: 5 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 133' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000197 - train_line: - is_a: environment field - aliases: - - train line - description: The subway line name - range: train_line_enum - examples: - - value: red - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 134' - - 'This field is used uniquely in: built environment' - pattern: '[red|green|orange]' - slot_uri: MIXS:0000837 - train_stat_loc: - is_a: environment field - aliases: - - train station collection location - description: The train station collection location - range: train_stat_loc_enum - examples: - - value: forest hills - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 135' - - 'This field is used uniquely in: built environment' - pattern: '[south station above ground|south station underground|south station - amtrak|forest hills|riverside]' - slot_uri: MIXS:0000838 - train_stop_loc: - is_a: environment field - aliases: - - train stop collection location - description: The train stop collection location - range: train_stop_loc_enum - examples: - - value: end - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 136' - - 'This field is used uniquely in: built environment' - pattern: '[end|mid|downtown]' - slot_uri: MIXS:0000839 - vis_media: - is_a: environment field - aliases: - - visual media - description: The building visual media - range: vis_media_enum - examples: - - value: 3D scans - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 137' - - 'This field is used uniquely in: built environment' - pattern: '[photos|videos|commonly of the building|site context (adjacent buildings, - vegetation, terrain, streets)|interiors|equipment|3D scans]' - slot_uri: MIXS:0000840 - wall_area: - is_a: environment field - aliases: - - wall area - description: The total area of the sampled room's walls - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 138' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000198 - wall_const_type: - is_a: environment field - aliases: - - wall construction type - description: The building class of the wall defined by the composition of the - building elements and fire-resistance rating. - range: wall_const_type_enum - examples: - - value: fire resistive - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 139' - - 'This field is used uniquely in: built environment' - pattern: '[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified - fire resistive|fire resistive]' - slot_uri: MIXS:0000841 - wall_finish_mat: - is_a: environment field - aliases: - - wall finish material - description: The material utilized to finish the outer most layer of the wall - range: wall_finish_mat_enum - examples: - - value: wood - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 140' - - 'This field is used uniquely in: built environment' - pattern: '[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone - facing|acoustical treatment|wood|metal|masonry]' - slot_uri: MIXS:0000842 - wall_height: - is_a: environment field - aliases: - - wall height - description: The average height of the walls in the sampled room - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: centimeter' - - 'Occurrence: 1' - - 'Position: 141' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000221 - wall_loc: - is_a: environment field - aliases: - - wall location - description: The relative location of the wall within the room - range: wall_loc_enum - examples: - - value: north - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 142' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west]' - slot_uri: MIXS:0000843 - wall_water_mold: - is_a: environment field - aliases: - - wall signs of water/mold - description: Signs of the presence of mold or mildew on a wall - range: string - examples: - - value: no presence of mold visible - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 143' - - 'This field is used uniquely in: built environment' - pattern: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000844 - wall_surf_treatment: - is_a: environment field - aliases: - - wall surface treatment - description: The surface treatment of interior wall - range: wall_surf_treatment_enum - examples: - - value: paneling - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 144' - - 'This field is used uniquely in: built environment' - pattern: '[painted|wall paper|no treatment|paneling|stucco|fabric]' - slot_uri: MIXS:0000845 - wall_texture: - is_a: environment field - aliases: - - wall texture - description: The feel, appearance, or consistency of a wall surface - range: wall_texture_enum - examples: - - value: popcorn - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 145' - - 'This field is used uniquely in: built environment' - pattern: '[crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange - peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl]' - slot_uri: MIXS:0000846 - wall_thermal_mass: - is_a: environment field - aliases: - - wall thermal mass - description: The ability of the wall to provide inertia against temperature fluctuations. - Generally this means concrete or concrete block that is either exposed or covered - only with paint - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: joule per degree Celsius' - - 'Occurrence: 1' - - 'Position: 146' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000222 - water_feat_size: - is_a: environment field - aliases: - - water feature size - description: The size of the water feature - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: square meter' - - 'Occurrence: 1' - - 'Position: 147' - - 'This field is used uniquely in: built environment' - slot_uri: MIXS:0000223 - water_feat_type: - is_a: environment field - aliases: - - water feature type - description: The type of water feature present within the building being sampled - range: water_feat_type_enum - examples: - - value: stream - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 148' - - 'This field is used uniquely in: built environment' - pattern: '[fountain|pool|standing feature|stream|waterfall]' - slot_uri: MIXS:0000847 - weekday: - is_a: environment field - aliases: - - weekday - description: The day of the week when sampling occurred - range: weekday_enum - examples: - - value: Sunday - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 149' - - 'This field is used uniquely in: built environment' - pattern: '[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]' - slot_uri: MIXS:0000848 - window_size: - is_a: environment field - aliases: - - window area/size - description: The window's length and width - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: inch, meter' - - 'Occurrence: 1' - - 'Position: 150' - - 'This field is used uniquely in: built environment' - pattern: '{float} {unit} x {float} {unit}' - slot_uri: MIXS:0000224 - window_cond: - is_a: environment field - aliases: - - window condition - description: The physical condition of the window at the time of sampling - range: window_cond_enum - examples: - - value: rupture - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 151' - - 'This field is used uniquely in: built environment' - pattern: '[damaged|needs repair|new|rupture|visible wear]' - slot_uri: MIXS:0000849 - window_cover: - is_a: environment field - aliases: - - window covering - description: The type of window covering - range: window_cover_enum - examples: - - value: curtains - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 152' - - 'This field is used uniquely in: built environment' - pattern: '[blinds|curtains|none]' - slot_uri: MIXS:0000850 - window_horiz_pos: - is_a: environment field - aliases: - - window horizontal position - description: The horizontal position of the window on the wall - range: window_horiz_pos_enum - examples: - - value: middle - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 153' - - 'This field is used uniquely in: built environment' - pattern: '[left|middle|right]' - slot_uri: MIXS:0000851 - window_loc: - is_a: environment field - aliases: - - window location - description: The relative location of the window within the room - range: window_loc_enum - examples: - - value: west - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 154' - - 'This field is used uniquely in: built environment' - pattern: '[north|south|east|west]' - slot_uri: MIXS:0000852 - window_mat: - is_a: environment field - aliases: - - window material - description: The type of material used to finish a window - range: window_mat_enum - examples: - - value: wood - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 155' - - 'This field is used uniquely in: built environment' - pattern: '[clad|fiberglass|metal|vinyl|wood]' - slot_uri: MIXS:0000853 - window_open_freq: - is_a: environment field - aliases: - - window open frequency - description: The number of times windows are opened per week - range: string - examples: - - value: '' - comments: - - 'Expected value: value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 156' - - 'This field is used uniquely in: built environment' - pattern: '{integer}' - slot_uri: MIXS:0000246 - window_water_mold: - is_a: environment field - aliases: - - window signs of water/mold - description: Signs of the presence of mold or mildew on the window. - range: string - examples: - - value: no presence of mold visible - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 157' - - 'This field is used uniquely in: built environment' - pattern: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000854 - window_status: - is_a: environment field - aliases: - - window status - description: Defines whether the windows were open or closed during environmental - testing - range: string - examples: - - value: open - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 158' - - 'This field is used uniquely in: built environment' - pattern: '[closed|open]' - slot_uri: MIXS:0000855 - window_type: - is_a: environment field - aliases: - - window type - description: The type of windows - range: window_type_enum - examples: - - value: fixed window - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 159' - - 'This field is used uniquely in: built environment' - pattern: '[single-hung sash window|horizontal sash window|fixed window]' - slot_uri: MIXS:0000856 - window_vert_pos: - is_a: environment field - aliases: - - window vertical position - description: The vertical position of the window on the wall - range: window_vert_pos_enum - examples: - - value: middle - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 160' - - 'This field is used uniquely in: built environment' - pattern: '[bottom|middle|top|low|middle|high]' - slot_uri: MIXS:0000857 - ances_data: - is_a: environment field - aliases: - - ancestral data - description: Information about either pedigree or other ancestral information - description (e.g. parental variety in case of mutant or selection), e.g. A/3*B - (meaning [(A x B) x B] x B) - range: string - examples: - - value: A/3*B - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000247 - biol_stat: - is_a: environment field - aliases: - - biological status - description: The level of genome modification - range: biol_stat_enum - examples: - - value: natural - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal - selection|mutant]' - slot_uri: MIXS:0000858 - genetic_mod: - is_a: environment field - aliases: - - genetic modification - description: Genetic modifications of the genome of an organism, which may occur - naturally by spontaneous mutation, or be introduced by some experimental means, - e.g. specification of a transgene or the gene knocked-out or details of transient - transfection - range: string - examples: - - value: aox1A transgenic - comments: - - 'Expected value: PMID,DOI,url or free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0000859 - host_common_name: - is_a: environment field - aliases: - - host common name - description: Common name of the host, e.g. Human - range: string - examples: - - value: mussel - comments: - - 'Expected value: common name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 4' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000248 - samp_capt_status: - is_a: environment field - aliases: - - sample capture status - description: Reason for the sample - range: samp_capt_status_enum - examples: - - value: farm sample - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 5' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '[active surveillance in response to an outbreak|active surveillance - not initiated by an outbreak|farm sample|market sample|other]' - slot_uri: MIXS:0000860 - samp_dis_stage: - is_a: environment field - aliases: - - sample disease stage - description: Stage of the disease at the time of sample collection, e.g. inoculation, - penetration, infection, growth and reproduction, dissemination of pathogen. - range: string - examples: - - value: infection - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 6' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000249 - host_taxid: - is_a: environment field - aliases: - - host taxid - description: NCBI taxon id of the host, e.g. 9606 - range: string - examples: - - value: '7955' - comments: - - 'Expected value: NCBI taxon identifier' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 7' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{NCBI taxid}' - slot_uri: MIXS:0000250 - host_subject_id: - is_a: environment field - aliases: - - host subject id - description: 'A unique identifier by which each subject can be referred to, de-identified, - e.g. #131' - range: string - examples: - - value: MPI123 - comments: - - 'Expected value: unique identifier' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 8' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000861 - host_age: - is_a: environment field - aliases: - - host age - description: Age of host at the time of sampling; relevant scale depends on species - and study, e.g. Could be seconds for amoebae or centuries for trees - range: quantity value - examples: - - value: 10 days - comments: - - 'Expected value: value' - - 'Preferred unit: year, day, hour' - - 'Occurrence: 1' - - 'Position: 9' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - slot_uri: MIXS:0000255 - host_life_stage: - is_a: environment field - aliases: - - host life stage - description: Description of life stage of host - range: string - examples: - - value: adult - comments: - - 'Expected value: stage' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 10' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000251 - host_sex: - is_a: environment field - aliases: - - host sex - description: Physical sex of the host - range: host_sex_enum - examples: - - value: female - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 11' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '[male|female|neuter|hermaphrodite|not determined]' - slot_uri: MIXS:0000811 - host_disease_stat: - is_a: environment field - aliases: - - host disease status - description: List of diseases with which the host has been diagnosed; can include - multiple diagnoses. The value of the field depends on host; for humans the terms - should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, - non-human host diseases are free text - range: string - examples: - - value: rabies [DOID:11260] - comments: - - 'Expected value: disease name or DO' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 12' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - pattern: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000031 - host_body_habitat: - is_a: environment field - aliases: - - host body habitat - description: Original body habitat where the sample was obtained from - range: string - examples: - - value: nasopharynx - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 14' - - 'This field is used uniquely in: host-associated' - pattern: '{text}' - slot_uri: MIXS:0000866 - host_body_site: - is_a: environment field - aliases: - - host body site - description: Name of body site where the sample was obtained from, such as a specific - organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology - (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, - please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - range: string - examples: - - value: gill [UBERON:0002535] - comments: - - 'Expected value: FMA or UBERON' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 15' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{termLabel} {[termID]}' - slot_uri: MIXS:0000867 - host_body_product: - is_a: environment field - aliases: - - host body product - description: Substance produced by the body, e.g. Stool, mucus, where the sample - was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy - ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma - or https://www.ebi.ac.uk/ols/ontologies/uberon - range: string - examples: - - value: Portion of mucus [fma66938] - comments: - - 'Expected value: FMA or UBERON' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 16' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{termLabel} {[termID]}' - slot_uri: MIXS:0000888 - host_tot_mass: - is_a: environment field - aliases: - - host total mass - description: Total mass of the host at collection, the unit depends on host - range: quantity value - examples: - - value: 2500 gram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilogram, gram' - - 'Occurrence: 1' - - 'Position: 17' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - slot_uri: MIXS:0000263 - host_height: - is_a: environment field - aliases: - - host height - description: The height of subject - range: quantity value - examples: - - value: 0.1 meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: centimeter, millimeter, meter' - - 'Occurrence: 1' - - 'Position: 18' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - slot_uri: MIXS:0000264 - host_length: - is_a: environment field - aliases: - - host length - description: The length of subject - range: quantity value - examples: - - value: 1 meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: centimeter, millimeter, meter' - - 'Occurrence: 1' - - 'Position: 19' - - 'This field is used in: 2 packages: host-associated, plant-associated' - slot_uri: MIXS:0000256 - host_diet: - is_a: environment field - aliases: - - host diet - description: Type of diet depending on the host, for animals omnivore, herbivore - etc., for humans high-fat, meditteranean etc.; can include multiple diet types - range: string - examples: - - value: herbivore - comments: - - 'Expected value: diet type' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 20' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000869 - host_last_meal: - is_a: environment field - aliases: - - host last meal - description: Content of last meal and time since feeding; can include multiple - values - range: string - examples: - - value: corn feed;P2H - comments: - - 'Expected value: content;duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 21' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{text};{duration}' - slot_uri: MIXS:0000870 - host_growth_cond: - is_a: environment field - aliases: - - host growth conditions - description: Literature reference giving growth conditions of the host - range: string - examples: - - value: https://academic.oup.com/icesjms/article/68/2/349/617247 - comments: - - 'Expected value: PMID,DOI,url or free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 22' - - 'This field is used uniquely in: host-associated' - pattern: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0000871 - host_substrate: - is_a: environment field - aliases: - - host substrate - description: The growth substrate of the host - range: string - examples: - - value: rock - comments: - - 'Expected value: substrate name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 23' - - 'This field is used uniquely in: host-associated' - pattern: '{text}' - slot_uri: MIXS:0000252 - host_family_relationship: - is_a: environment field - aliases: - - host family relationship - description: Relationships to other hosts in the same study; can include multiple - relationships - range: string - examples: - - value: offspring;Mussel25 - comments: - - 'Expected value: relationship type;arbitrary identifier' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 24' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - pattern: '{text};{text}' - slot_uri: MIXS:0000872 - host_infra_specific_name: - is_a: environment field - aliases: - - host infra-specific name - description: Taxonomic information about the host below subspecies level - range: string - examples: - - value: borealis - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 25' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000253 - host_infra_specific_rank: - is_a: environment field - aliases: - - host infra-specific rank - description: Taxonomic rank information about the host below subspecies level, - such as variety, form, rank etc. - range: string - examples: - - value: subspecies - comments: - - 'Expected value: rank' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 26' - - 'This field is used in: 2 packages: host-associated, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000254 - host_genotype: - is_a: environment field - aliases: - - host genotype - description: Observed genotype - range: string - examples: - - value: C57BL/6 - comments: - - 'Expected value: genotype' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 27' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - pattern: '{text}' - slot_uri: MIXS:0000365 - host_phenotype: - is_a: environment field - aliases: - - host phenotype - description: Phenotype of human or other host. For phenotypic quality ontology - (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. - For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - range: string - examples: - - value: elongated [PATO:0001154] - comments: - - 'Expected value: PATO or HP' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 28' - - 'This field is used in: 7 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal, plant-associated' - pattern: '{termLabel} {[termID]}' - slot_uri: MIXS:0000874 - host_body_temp: - is_a: environment field - aliases: - - host body temperature - description: Core body temperature of the host when sample was collected - range: quantity value - examples: - - value: 15 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 29' - - 'This field is used in: 6 packages: host-associated, human-associated, human-gut, - human-oral, human-skin, human-vaginal' - slot_uri: MIXS:0000274 - host_dry_mass: - is_a: environment field - aliases: - - host dry mass - description: Measurement of dry mass - range: quantity value - examples: - - value: 500 gram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilogram, gram' - - 'Occurrence: 1' - - 'Position: 30' - - 'This field is used in: 2 packages: host-associated, plant-associated' - slot_uri: MIXS:0000257 - host_blood_press_diast: - is_a: environment field - aliases: - - host blood pressure diastolic - description: Resting diastolic blood pressure, measured as mm mercury - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millimeter mercury' - - 'Occurrence: 1' - - 'Position: 31' - - 'This field is used uniquely in: host-associated' - slot_uri: MIXS:0000258 - host_blood_press_syst: - is_a: environment field - aliases: - - host blood pressure systolic - description: Resting systolic blood pressure, measured as mm mercury - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millimeter mercury' - - 'Occurrence: 1' - - 'Position: 32' - - 'This field is used uniquely in: host-associated' - slot_uri: MIXS:0000259 - host_color: - is_a: environment field - aliases: - - host color - description: The color of host - range: string - examples: - - value: '' - comments: - - 'Expected value: color' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 33' - - 'This field is used uniquely in: host-associated' - pattern: '{text}' - slot_uri: MIXS:0000260 - host_shape: - is_a: environment field - aliases: - - host shape - description: Morphological shape of host - range: string - examples: - - value: round - comments: - - 'Expected value: shape' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 34' - - 'This field is used uniquely in: host-associated' - pattern: '{text}' - slot_uri: MIXS:0000261 - gravidity: - is_a: environment field - aliases: - - gravidity - description: Whether or not subject is gravid, and if yes date due or date post-conception, - specifying which is used - range: string - examples: - - value: yes;due date:2018-05-11 - comments: - - 'Expected value: gravidity status;timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 35' - - 'This field is used uniquely in: host-associated' - pattern: '{boolean};{timestamp}' - slot_uri: MIXS:0000875 - ihmc_medication_code: - is_a: environment field - aliases: - - IHMC medication code - description: Can include multiple medication codes - range: string - examples: - - value: '810' - comments: - - 'Expected value: IHMC code' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 5' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - pattern: '{integer}' - slot_uri: MIXS:0000884 - smoker: - is_a: environment field - aliases: - - smoker - description: Specification of smoking status - range: string - examples: - - value: 'yes' - comments: - - 'Expected value: smoking status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 17' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean}' - slot_uri: MIXS:0000262 - host_hiv_stat: - is_a: environment field - aliases: - - host HIV status - description: HIV status of subject, if yes HAART initiation status should also - be indicated as [YES or NO] - range: string - examples: - - value: yes;yes - comments: - - 'Expected value: HIV status;HAART initiation status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 18' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean};{boolean}' - slot_uri: MIXS:0000265 - drug_usage: - is_a: environment field - aliases: - - drug usage - description: Any drug used by subject and the frequency of usage; can include - multiple drugs used - range: drug_usage_enum - examples: - - value: Lipitor;2/day - comments: - - 'Expected value: drug name;frequency' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 19' - - 'This field is used uniquely in: human-associated' - pattern: '{text};{integer}/[year|month|week|day|hour]' - slot_uri: MIXS:0000894 - host_body_mass_index: - is_a: environment field - aliases: - - host body-mass index - description: Body mass index, calculated as weight/(height)squared - range: quantity value - examples: - - value: 22 kilogram per square meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilogram per square meter' - - 'Occurrence: 1' - - 'Position: 20' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - slot_uri: MIXS:0000317 - diet_last_six_month: - is_a: environment field - aliases: - - major diet change in last six months - description: Specification of major diet changes in the last six months, if yes - the change should be specified - range: string - examples: - - value: yes;vegetarian diet - comments: - - 'Expected value: diet change;current diet' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 21' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean};{text}' - slot_uri: MIXS:0000266 - weight_loss_3_month: - is_a: environment field - aliases: - - weight loss in last three months - description: Specification of weight loss in the last three months, if yes should - be further specified to include amount of weight loss - range: string - examples: - - value: yes;5 kilogram - comments: - - 'Expected value: weight loss specification;measurement value' - - 'Preferred unit: kilogram, gram' - - 'Occurrence: 1' - - 'Position: 22' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean};{float} {unit}' - slot_uri: MIXS:0000295 - ihmc_ethnicity: - is_a: environment field - aliases: - - IHMC ethnicity - description: Ethnicity of the subject - range: string - examples: - - value: caucasian - comments: - - 'Expected value: IHMC code or free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 23' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - pattern: '{integer}|{text}' - slot_uri: MIXS:0000895 - host_occupation: - is_a: environment field - aliases: - - host occupation - description: Most frequent job performed by subject - range: string - examples: - - value: veterinary - comments: - - 'Expected value: IHMC code' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 24' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - pattern: '{integer}' - slot_uri: MIXS:0000896 - pet_farm_animal: - is_a: environment field - aliases: - - presence of pets or farm animals - description: Specification of presence of pets or farm animals in the environment - of subject, if yes the animals should be specified; can include multiple animals - present - range: string - examples: - - value: yes; 5 cats - comments: - - 'Expected value: presence status;type of animal or pet' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 25' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean};{text}' - slot_uri: MIXS:0000267 - travel_out_six_month: - is_a: environment field - aliases: - - travel outside the country in last six months - description: Specification of the countries travelled in the last six months; - can include multiple travels - range: string - examples: - - value: '' - comments: - - 'Expected value: country name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 26' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000268 - twin_sibling: - is_a: environment field - aliases: - - twin sibling presence - description: Specification of twin sibling presence - range: string - examples: - - value: 'yes' - comments: - - 'Expected value: presence status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 27' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean}' - slot_uri: MIXS:0000326 - medic_hist_perform: - is_a: environment field - aliases: - - medical history performed - description: Whether full medical history was collected - range: string - examples: - - value: 'TRUE' - comments: - - 'Expected value: true or false' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 28' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - pattern: '{boolean}' - slot_uri: MIXS:0000897 - study_complt_stat: - is_a: environment field - aliases: - - study completion status - description: Specification of study completion status, if no the reason should - be specified - range: study_complt_stat_enum - examples: - - value: no;non-compliance - comments: - - 'Expected value: YES or NO due to (1)adverse event (2) non-compliance (3) lost - to follow up (4)other-specify' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 29' - - 'This field is used uniquely in: human-associated' - pattern: '{boolean};[adverse event|non-compliance|lost to follow up|other-specify]' - slot_uri: MIXS:0000898 - pulmonary_disord: - is_a: environment field - aliases: - - lung/pulmonary disorder - description: History of pulmonary disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - lung disease (https://disease-ontology.org/?id=DOID:850). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 30' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000269 - nose_throat_disord: - is_a: environment field - aliases: - - lung/nose-throat disorder - description: History of nose-throat disorders; can include multiple disorders, The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory - tract disease (https://disease-ontology.org/?id=DOID:974). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 31' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000270 - blood_blood_disord: - is_a: environment field - aliases: - - blood/blood disorder - description: History of blood disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 32' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000271 - host_pulse: - is_a: environment field - aliases: - - host pulse - description: Resting pulse, measured as beats per minute - range: quantity value - examples: - - value: 65 beats per minute - comments: - - 'Expected value: measurement value' - - 'Preferred unit: beats per minute' - - 'Occurrence: 1' - - 'Position: 35' - - 'This field is used in: 5 packages: human-associated, human-gut, human-oral, - human-skin, human-vaginal' - slot_uri: MIXS:0000333 - gestation_state: - is_a: environment field - aliases: - - amniotic fluid/gestation state - description: Specification of the gestation state - range: string - examples: - - value: '' - comments: - - 'Expected value: gestation state' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 36' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000272 - maternal_health_stat: - is_a: environment field - aliases: - - amniotic fluid/maternal health status - description: Specification of the maternal health status - range: string - examples: - - value: '' - comments: - - 'Expected value: health status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 37' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000273 - foetal_health_stat: - is_a: environment field - aliases: - - amniotic fluid/foetal health status - description: Specification of foetal health status, should also include abortion - range: string - examples: - - value: '' - comments: - - 'Expected value: health status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 38' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000275 - amniotic_fluid_color: - is_a: environment field - aliases: - - amniotic fluid/color - description: Specification of the color of the amniotic fluid sample - range: string - examples: - - value: '' - comments: - - 'Expected value: color' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 39' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000276 - urogenit_tract_disor: - is_a: environment field - aliases: - - urine/urogenital tract disorder - description: 'History of urogenital tract disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - urinary system disease (https://disease-ontology.org/?id=DOID:18). ' - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 41' - - 'This field is used uniquely in: human-associated' - pattern: '{text}' - slot_uri: MIXS:0000278 - urine_collect_meth: - is_a: environment field - aliases: - - urine/collection method - description: Specification of urine collection method - range: string - examples: - - value: catheter - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 43' - - 'This field is used uniquely in: human-associated' - pattern: '[clean catch|catheter]' - slot_uri: MIXS:0000899 - gastrointest_disord: - is_a: environment field - aliases: - - gastrointestinal tract disorder - description: History of gastrointestinal tract disorders; can include multiple - disorders. History of blood disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: human-gut' - pattern: '{text}' - slot_uri: MIXS:0000280 - liver_disord: - is_a: environment field - aliases: - - liver disorder - description: History of liver disorders; can include multiple disorders. The terms - should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - liver disease (https://disease-ontology.org/?id=DOID:409). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 2' - - 'This field is used uniquely in: human-gut' - pattern: '{text}' - slot_uri: MIXS:0000282 - special_diet: - is_a: environment field - aliases: - - special diet - description: Specification of special diet; can include multiple special diets - range: special_diet_enum - examples: - - value: other:vegan - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 3' - - 'This field is used uniquely in: human-gut' - pattern: '[low carb|reduced calorie|vegetarian|other(to be specified)]' - slot_uri: MIXS:0000905 - nose_mouth_teeth_throat_disord: - is_a: environment field - aliases: - - nose/mouth/teeth/throat disorder - description: History of nose/mouth/teeth/throat disorders; can include multiple - disorders. The terms should be chosen from the DO (Human Disease Ontology) at - http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), - mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), - or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: human-oral' - pattern: '{text}' - slot_uri: MIXS:0000283 - time_last_toothbrush: - is_a: environment field - aliases: - - time since last toothbrushing - description: Specification of the time since last toothbrushing - range: string - examples: - - value: P2H45M - comments: - - 'Expected value: duration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used uniquely in: human-oral' - pattern: '{duration}' - slot_uri: MIXS:0000924 - dermatology_disord: - is_a: environment field - aliases: - - dermatology disorder - description: History of dermatology disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - skin disease (https://disease-ontology.org/?id=DOID:37). - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: human-skin' - pattern: '{text}' - slot_uri: MIXS:0000284 - time_since_last_wash: - is_a: environment field - aliases: - - time since last wash - description: Specification of the time since last wash - range: string - examples: - - value: P1D - comments: - - 'Expected value: duration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used uniquely in: human-skin' - pattern: '{duration}' - slot_uri: MIXS:0000943 - dominant_hand: - is_a: environment field - aliases: - - dominant hand - description: Dominant hand of the subject - range: dominant_hand_enum - examples: - - value: right - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used uniquely in: human-skin' - pattern: '[left|right|ambidextrous]' - slot_uri: MIXS:0000944 - menarche: - is_a: environment field - aliases: - - menarche - description: Date of most recent menstruation - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: human-vaginal' - pattern: '{timestamp}' - slot_uri: MIXS:0000965 - sexual_act: - is_a: environment field - aliases: - - sexual activity - description: Current sexual partner and frequency of sex - range: string - examples: - - value: '' - comments: - - 'Expected value: partner sex;frequency' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used uniquely in: human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000285 - pregnancy: - is_a: environment field - aliases: - - pregnancy - description: Date due of pregnancy - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used uniquely in: human-vaginal' - pattern: '{timestamp}' - slot_uri: MIXS:0000966 - douche: - is_a: environment field - aliases: - - douche - description: Date of most recent douche - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 4' - - 'This field is used uniquely in: human-vaginal' - pattern: '{timestamp}' - slot_uri: MIXS:0000967 - birth_control: - is_a: environment field - aliases: - - birth control - description: Specification of birth control medication used - range: string - examples: - - value: '' - comments: - - 'Expected value: medication name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 5' - - 'This field is used uniquely in: human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000286 - menopause: - is_a: environment field - aliases: - - menopause - description: Date of onset of menopause - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 6' - - 'This field is used uniquely in: human-vaginal' - pattern: '{timestamp}' - slot_uri: MIXS:0000968 - hrt: - is_a: environment field - aliases: - - HRT - description: Whether subject had hormone replacement theraphy, and if yes start - date - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 7' - - 'This field is used uniquely in: human-vaginal' - pattern: '{timestamp}' - slot_uri: MIXS:0000969 - hysterectomy: - is_a: environment field - aliases: - - hysterectomy - description: Specification of whether hysterectomy was performed - range: string - examples: - - value: 'no' - comments: - - 'Expected value: hysterectomy status' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 8' - - 'This field is used uniquely in: human-vaginal' - pattern: '{boolean}' - slot_uri: MIXS:0000287 - gynecologic_disord: - is_a: environment field - aliases: - - gynecological disorder - description: History of gynecological disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - female reproductive system disease (https://disease-ontology.org/?id=DOID:229). - range: string - examples: - - value: '' - comments: - - 'Expected value: gynecological disorder' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 9' - - 'This field is used uniquely in: human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000288 - urogenit_disord: - is_a: environment field - aliases: - - urogenital disorder - description: 'History of urogenital disorders, can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary - system disease (https://disease-ontology.org/?id=DOID:18). ' - range: string - examples: - - value: '' - comments: - - 'Expected value: disorder name' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 10' - - 'This field is used uniquely in: human-vaginal' - pattern: '{text}' - slot_uri: MIXS:0000289 - hcr: - is_a: environment field - aliases: - - hydrocarbon resource type - description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR - defined as a natural environmental feature containing large amounts of hydrocarbons - at high concentrations potentially suitable for commercial exploitation. This - term should not be confused with the Hydrocarbon Occurrence term which also - includes hydrocarbon-rich environments with currently limited commercial interest - such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose - entry in "additional info" field - range: hcr_enum - examples: - - value: Oil Sand - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight - Gas Reservoir|other]' - slot_uri: MIXS:0000988 - hc_produced: - is_a: environment field - aliases: - - hydrocarbon type produced - description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, - etc). If "other" is specified, please propose entry in "additional info" field - range: hc_produced_enum - examples: - - value: Gas - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other]' - slot_uri: MIXS:0000989 - basin: - is_a: environment field - aliases: - - basin name - description: Name of the basin (e.g. Campos) - range: string - examples: - - value: '' - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000290 - field: - is_a: environment field - aliases: - - field name - description: Name of the hydrocarbon field (e.g. Albacora) - range: string - examples: - - value: '' - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 4' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000291 - reservoir: - is_a: environment field - aliases: - - reservoir name - description: Name of the reservoir (e.g. Carapebus) - range: string - examples: - - value: '' - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 5' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000303 - hcr_temp: - is_a: environment field - aliases: - - hydrocarbon resource original temperature - description: Original temperature of the hydrocarbon resource - range: string - examples: - - value: 150-295 degree Celsius - comments: - - 'Expected value: measurement value range' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 6' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{float} - {float} {unit}' - slot_uri: MIXS:0000393 - tvdss_of_hcr_temp: - is_a: environment field - aliases: - - depth (TVDSS) of hydrocarbon resource temperature - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original temperature was measured (e.g. 1345 m) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 7' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000394 - hcr_pressure: - is_a: environment field - aliases: - - hydrocarbon resource original pressure - description: Original pressure of the hydrocarbon resource - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value range' - - 'Preferred unit: atmosphere, kilopascal' - - 'Occurrence: 1' - - 'Position: 8' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{float} - {float} {unit}' - slot_uri: MIXS:0000395 - tvdss_of_hcr_pressure: - is_a: environment field - aliases: - - depth (TVDSS) of hydrocarbon resource pressure - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original pressure was measured (e.g. 1578 m ) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 9' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000397 - permeability: - is_a: environment field - aliases: - - permeability - description: 'Measure of the ability of a hydrocarbon resource to allow fluids - to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value range' - - 'Preferred unit: mD' - - 'Occurrence: 1' - - 'Position: 10' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '{integer} - {integer} {unit}' - slot_uri: MIXS:0000404 - porosity: - is_a: environment field - aliases: - - porosity - description: Porosity of deposited sediment is volume of voids divided by the - total volume of sample - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value or range' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 11' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, sediment' - pattern: '{float} - {float} {unit}' - slot_uri: MIXS:0000211 - lithology: - is_a: environment field - aliases: - - lithology - description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). - If "other" is specified, please propose entry in "additional info" field' - range: lithology_enum - examples: - - value: Volcanic - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 12' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]' - slot_uri: MIXS:0000990 - depos_env: - is_a: environment field - aliases: - - depositional environment - description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). - If "other" is specified, please propose entry in "additional info" field - range: depos_env_enum - examples: - - value: Continental - Alluvial - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 13' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|Continental - - Lacustrine|Transitional - Deltaic|Transitional - Tidal|Transitional - Lagoonal|Transitional - - Beach|Transitional - Lake|Marine - Shallow|Marine - Deep|Marine - Reef|Other - - Evaporite|Other - Glacial|Other - Volcanic|other]' - slot_uri: MIXS:0000992 - hcr_geol_age: - is_a: environment field - aliases: - - hydrocarbon resource geological age - description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - range: hcr_geol_age_enum - examples: - - value: Silurian - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 14' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' - slot_uri: MIXS:0000993 - owc_tvdss: - is_a: environment field - aliases: - - oil water contact depth - description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 15' - - 'This field is used uniquely in: hydrocarbon resources-cores' - slot_uri: MIXS:0000405 - hcr_fw_salinity: - is_a: environment field - aliases: - - formation water salinity - description: Original formation water salinity (prior to secondary recovery e.g. - Waterflooding) expressed as TDS - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 16' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000406 - sulfate_fw: - is_a: environment field - aliases: - - sulfate in formation water - description: Original sulfate concentration in the hydrocarbon resource - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 17' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000407 - vfa_fw: - is_a: environment field - aliases: - - vfa in formation water - description: Original volatile fatty acid concentration in the hydrocarbon resource - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 18' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000408 - sr_kerog_type: - is_a: environment field - aliases: - - source rock kerogen type - description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic - and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ - fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris - (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). - If "other" is specified, please propose entry in "additional info" field' - range: sr_kerog_type_enum - examples: - - value: Type IV - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 19' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '[Type I|Type II|Type III|Type IV|other]' - slot_uri: MIXS:0000994 - sr_lithology: - is_a: environment field - aliases: - - source rock lithology - description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - range: sr_lithology_enum - examples: - - value: Coal - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 20' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '[Clastic|Carbonate|Coal|Biosilicieous|other]' - slot_uri: MIXS:0000995 - sr_dep_env: - is_a: environment field - aliases: - - source rock depositional environment - description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - range: sr_dep_env_enum - examples: - - value: Marine - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 21' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]' - slot_uri: MIXS:0000996 - sr_geol_age: - is_a: environment field - aliases: - - source rock geological age - description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - range: sr_geol_age_enum - examples: - - value: Silurian - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 22' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]' - slot_uri: MIXS:0000997 - samp_well_name: - is_a: environment field - aliases: - - sample well name - description: Name of the well (e.g. BXA1123) where sample was taken - range: string - examples: - - value: '' - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 35' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000296 - win: - is_a: environment field - aliases: - - well identification number - description: 'A unique identifier of a well or wellbore. This is part of the Global - Framework for Well Identification initiative which is compiled by the Professional - Petroleum Data Management Association (PPDM) in an effort to improve well identification - systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' - range: string - examples: - - value: '' - comments: - - 'Expected value: text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 36' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000297 - samp_type: - is_a: environment field - aliases: - - sample type - description: Type of material (i.e. sample) collected. Includes types like core, - rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid - deposit, produced fluid, produced water, injected water, swabs, etc. If "other" - is specified, please propose entry in "additional info" field - range: samp_type_enum - examples: - - value: solid deposit - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 37' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid - deposit|produced fluid|produced water|injected water|water from treatment plant|fresh - water|sea water|drilling fluid|procedural blank|positive control|negative control|other]' - slot_uri: MIXS:0000998 - samp_subtype: - is_a: environment field - aliases: - - sample subtype - description: Name of sample sub-type. For example if "sample type" is "Produced - Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, - please propose entry in "additional info" field - range: samp_subtype_enum - examples: - - value: biofilm - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 38' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '[oil phase|water phase|biofilm|not applicable|other]' - slot_uri: MIXS:0000999 - pressure: - is_a: environment field - aliases: - - pressure - description: Pressure to which the sample is subject to, in atmospheres - range: quantity value - examples: - - value: 50 atmosphere - comments: - - 'Expected value: measurement value' - - 'Preferred unit: atmosphere' - - 'Occurrence: 1' - - 'Position: 41' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000412 - samp_tvdss: - is_a: environment field - aliases: - - sample true vertical depth subsea - description: Depth of the sample i.e. The vertical distance between the sea level - and the sampled position in the subsurface. Depth can be reported as an interval - for subsurface samples e.g. 1325.75-1362.25 m - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value or measurement value range' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 42' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '{float}-{float} {unit}' - slot_uri: MIXS:0000409 - samp_md: - is_a: environment field - aliases: - - sample measured depth - description: In non deviated well, measured depth is equal to the true vertical - depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated - wells, the MD is the length of trajectory of the borehole measured from the - same reference or datum. Common datums used are ground level (GL), drilling - rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). - If "other" is specified, please propose entry in "additional info" field - range: samp_md_enum - examples: - - value: 1534 meter;MSL - comments: - - 'Expected value: measurement value;enumeration' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 43' - - 'This field is used uniquely in: hydrocarbon resources-cores' - pattern: '{float} {unit};[GL|DF|RT|KB|MSL|other]' - slot_uri: MIXS:0000413 - samp_transport_cond: - is_a: environment field - aliases: - - sample transport conditions - description: "Sample transport duration (in days or hrs) and temperature the sample\ - \ was exposed to (e.g. 5.5 days; 20 \xAC\u221EC)" - range: string - examples: - - value: 5 days;-20 degree Celsius - comments: - - 'Expected value: measurement value;measurement value' - - 'Preferred unit: days;degree Celsius' - - 'Occurrence: 1' - - 'Position: 47' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000410 - organism_count_qpcr_info: - is_a: environment field - aliases: - - organism count qPCR information - description: 'If qpcr was used for the cell count, the target gene name, the primer - sequence and the cycling conditions should also be provided. (Example: 16S rrna; - FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; - annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; - 30 cycles)' - range: string - examples: - - value: '' - comments: - - 'Expected value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial - denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles' - - 'Preferred unit: number of cells per gram (or ml or cm^2)' - - 'Occurrence: 1' - - 'Position: 53' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles' - slot_uri: MIXS:0000099 - ph: - is_a: environment field - aliases: - - pH - description: Ph measurement of the sample, or liquid portion of sample, or aqueous - phase of the fluid - range: double - examples: - - value: '7.2' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 54' - - 'This field is used in: 8 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, soil, wastewater_sludge, water' - slot_uri: MIXS:0001001 - alkalinity: - is_a: environment field - aliases: - - alkalinity - description: Alkalinity, the ability of a solution to neutralize acids to the - equivalence point of carbonate or bicarbonate - range: quantity value - examples: - - value: 50 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milliequivalent per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 56' - - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000421 - alkalinity_method: - is_a: environment field - aliases: - - alkalinity method - description: Method used for alkalinity measurement - range: string - examples: - - value: titration - comments: - - 'Expected value: description of method' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 57' - - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, water' - pattern: '{text}' - slot_uri: MIXS:0000298 - sulfate: - is_a: environment field - aliases: - - sulfate - description: Concentration of sulfate in the sample - range: quantity value - examples: - - value: 5 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 58' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000423 - sulfide: - is_a: environment field - aliases: - - sulfide - description: Concentration of sulfide in the sample - range: quantity value - examples: - - value: 2 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 59' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000424 - tot_sulfur: - is_a: environment field - aliases: - - total sulfur - description: Concentration of total sulfur in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 60' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000419 - nitrate: - is_a: environment field - aliases: - - nitrate - description: Concentration of nitrate in the sample - range: quantity value - examples: - - value: 65 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 61' - - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000425 - nitrite: - is_a: environment field - aliases: - - nitrite - description: Concentration of nitrite in the sample - range: quantity value - examples: - - value: 0.5 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 62' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000426 - ammonium: - is_a: environment field - aliases: - - ammonium - description: Concentration of ammonium in the sample - range: quantity value - examples: - - value: 1.5 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 63' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000427 - tot_nitro: - is_a: environment field - aliases: - - total nitrogen concentration - description: 'Total nitrogen concentration of water samples, calculated by: total - nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured - without filtering, reported as nitrogen' - range: quantity value - examples: - - value: 50 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 64' - - 'This field is used in: 4 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, wastewater_sludge, water' - slot_uri: MIXS:0000102 - diss_iron: - is_a: environment field - aliases: - - dissolved iron - description: Concentration of dissolved iron in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 65' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000139 - sodium: - is_a: environment field - aliases: - - sodium - description: Sodium concentration in the sample - range: quantity value - examples: - - value: 10.5 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 66' - - 'This field is used in: 7 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000428 - chloride: - is_a: environment field - aliases: - - chloride - description: Concentration of chloride in the sample - range: quantity value - examples: - - value: 5000 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 67' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000429 - potassium: - is_a: environment field - aliases: - - potassium - description: Concentration of potassium in the sample - range: quantity value - examples: - - value: 463 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 68' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000430 - magnesium: - is_a: environment field - aliases: - - magnesium - description: Concentration of magnesium in the sample - range: quantity value - examples: - - value: 52.8 micromole per kilogram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: mole per liter, milligram per liter, parts per million, micromole - per kilogram' - - 'Occurrence: 1' - - 'Position: 69' - - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000431 - calcium: - is_a: environment field - aliases: - - calcium - description: Concentration of calcium in the sample - range: quantity value - examples: - - value: 0.2 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, micromole per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 70' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000432 - tot_iron: - is_a: environment field - aliases: - - total iron - description: Concentration of total iron in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, milligram per kilogram' - - 'Occurrence: 1' - - 'Position: 71' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000105 - diss_org_carb: - is_a: environment field - aliases: - - dissolved organic carbon - description: Concentration of dissolved organic carbon in the sample, liquid portion - of the sample, or aqueous phase of the fluid - range: quantity value - examples: - - value: 197 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 72' - - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000433 - diss_inorg_carb: - is_a: environment field - aliases: - - dissolved inorganic carbon - description: Dissolved inorganic carbon concentration in the sample, typically - measured after filtering the sample using a 0.45 micrometer filter - range: quantity value - examples: - - value: 2059 micromole per kilogram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 73' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000434 - diss_inorg_phosp: - is_a: environment field - aliases: - - dissolved inorganic phosphorus - description: Concentration of dissolved inorganic phosphorus in the sample - range: quantity value - examples: - - value: 56.5 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 74' - - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, water' - slot_uri: MIXS:0000106 - tot_phosp: - is_a: environment field - aliases: - - total phosphorus - description: 'Total phosphorus concentration in the sample, calculated by: total - phosphorus = total dissolved phosphorus + particulate phosphorus' - range: quantity value - examples: - - value: 0.03 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 75' - - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, water' - slot_uri: MIXS:0000117 - suspend_solids: - is_a: environment field - aliases: - - suspended solids - description: Concentration of substances including a wide variety of material, - such as silt, decaying plant and animal matter; can include multiple substances - range: string - examples: - - value: '' - comments: - - 'Expected value: suspended solid name;measurement value' - - 'Preferred unit: gram, microgram, milligram per liter, mole per liter, gram - per liter, part per million' - - 'Occurrence: m' - - 'Position: 76' - - 'This field is used in: 3 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000150 - density: - is_a: environment field - aliases: - - density - description: Density of the sample, which is its mass per unit volume (aka volumetric - mass density) - range: quantity value - examples: - - value: 1000 kilogram per cubic meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram per cubic meter, gram per cubic centimeter' - - 'Occurrence: 1' - - 'Position: 77' - - 'This field is used in: 5 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, miscellaneous natural or artificial environment, sediment, - water' - slot_uri: MIXS:0000435 - diss_carb_dioxide: - is_a: environment field - aliases: - - dissolved carbon dioxide - description: Concentration of dissolved carbon dioxide in the sample or liquid - portion of the sample - range: quantity value - examples: - - value: 5 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 78' - - 'This field is used in: 6 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs, microbial mat_biofilm, miscellaneous natural or artificial - environment, sediment, water' - slot_uri: MIXS:0000436 - diss_oxygen_fluid: - is_a: environment field - aliases: - - dissolved oxygen in fluids - description: Concentration of dissolved oxygen in the oil field produced fluids - as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per kilogram, milligram per liter' - - 'Occurrence: 1' - - 'Position: 79' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000438 - vfa: - is_a: environment field - aliases: - - volatile fatty acids - description: Concentration of Volatile Fatty Acids in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 80' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000152 - benzene: - is_a: environment field - aliases: - - benzene - description: Concentration of benzene in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 81' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000153 - toluene: - is_a: environment field - aliases: - - toluene - description: Concentration of toluene in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 82' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000154 - ethylbenzene: - is_a: environment field - aliases: - - ethylbenzene - description: Concentration of ethylbenzene in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 83' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000155 - xylene: - is_a: environment field - aliases: - - xylene - description: Concentration of xylene in the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 84' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000156 - api: - is_a: environment field - aliases: - - API gravity - description: "API gravity is a measure of how heavy or light a petroleum liquid\ - \ is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\ - \ 31.1\xAC\u221E API)" - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degrees API' - - 'Occurrence: 1' - - 'Position: 85' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000157 - tan: - is_a: environment field - aliases: - - total acid number - description: "Total Acid Number\xAC\u2020(TAN) is a measurement of acidity that\ - \ is determined by the amount of\xAC\u2020potassium hydroxide\xAC\u2020in milligrams\ - \ that is needed to neutralize the acids in one gram of oil.\xAC\u2020It is\ - \ an important quality measurement of\xAC\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 86' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000120 - viscosity: - is_a: environment field - aliases: - - viscosity - description: "A measure of oil's resistance\xAC\u2020to gradual deformation by\xAC\ - \u2020shear stress\xAC\u2020or\xAC\u2020tensile stress (e.g. 3.5 cp; 100 \xAC\ - \u221EC)" - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value;measurement value' - - 'Preferred unit: cP at degree Celsius' - - 'Occurrence: 1' - - 'Position: 87' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000126 - pour_point: - is_a: environment field - aliases: - - pour point - description: "Temperature at which a liquid becomes semi solid and loses its flow\ - \ characteristics. In crude oil a high\xAC\u2020pour point\xAC\u2020is generally\ - \ associated with a high paraffin content, typically found in crude deriving\ - \ from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 88' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - slot_uri: MIXS:0000127 - saturates_pc: - is_a: environment field - aliases: - - saturates wt% - description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ - \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ - \ polarizability and polarity. There are three main methods to obtain SARA results.\ - \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ - \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - range: string - examples: - - value: '' - comments: - - 'Expected value: name;measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 89' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000131 - aromatics_pc: - is_a: environment field - aliases: - - aromatics wt% - description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ - \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ - \ polarizability and polarity. There are three main methods to obtain SARA results.\ - \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ - \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - range: string - examples: - - value: '' - comments: - - 'Expected value: name;measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 90' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000133 - resins_pc: - is_a: environment field - aliases: - - resins wt% - description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ - \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ - \ polarizability and polarity. There are three main methods to obtain SARA results.\ - \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ - \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - range: string - examples: - - value: '' - comments: - - 'Expected value: name;measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 91' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000134 - asphaltenes_pc: - is_a: environment field - aliases: - - asphaltenes wt% - description: "Saturate, Aromatic, Resin and Asphaltene\xAC\u2020(SARA) is an analysis\ - \ method that divides\xAC\u2020crude oil\xAC\u2020components according to their\ - \ polarizability and polarity. There are three main methods to obtain SARA results.\ - \ The most popular one is known as the Iatroscan TLC-FID and is referred to\ - \ as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - range: string - examples: - - value: '' - comments: - - 'Expected value: name;measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 92' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000135 - additional_info: - is_a: environment field - aliases: - - additional info - description: Information that doesn't fit anywhere else. Can also be used to propose - new entries for fields with controlled vocabulary - range: string - examples: - - value: '' - comments: - - 'Expected value: text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 94' - - 'This field is used in: 2 packages: hydrocarbon resources-cores, hydrocarbon - resources-fluids_swabs' - pattern: '{text}' - slot_uri: MIXS:0000300 - prod_start_date: - is_a: environment field - aliases: - - production start date - description: Date of field's first production - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 23' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{timestamp}' - slot_uri: MIXS:0001008 - prod_rate: - is_a: environment field - aliases: - - production rate - description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: cubic meter per day' - - 'Occurrence: 1' - - 'Position: 24' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - slot_uri: MIXS:0000452 - water_production_rate: - is_a: environment field - aliases: - - water production rate - description: Water production rates per well (e.g. 987 m3 / day) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: cubic meter per day' - - 'Occurrence: 1' - - 'Position: 25' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - slot_uri: MIXS:0000453 - water_cut: - is_a: environment field - aliases: - - water cut - description: Current amount of water (%) in a produced fluid stream; or the average - of the combined streams - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 26' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - slot_uri: MIXS:0000454 - iwf: - is_a: environment field - aliases: - - injection water fraction - description: Proportion of the produced fluids derived from injected water at - the time of sampling. (e.g. 87%) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percent' - - 'Occurrence: 1' - - 'Position: 27' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - slot_uri: MIXS:0000455 - add_recov_method: - is_a: environment field - aliases: - - secondary and tertiary recovery methods and start date - description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed - for increase of hydrocarbon recovery from resource and start date for each one - of them. If "other" is specified, please propose entry in "additional info" - field - range: add_recov_method_enum - examples: - - value: Polymer Addition;2018-06-21T14:30Z - comments: - - 'Expected value: enumeration;timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 28' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer - Addition|Surfactant Addition|Not Applicable|other];{timestamp}' - slot_uri: MIXS:0001009 - iw_bt_date_well: - is_a: environment field - aliases: - - injection water breakthrough date of specific well - description: Injection water breakthrough date per well following a secondary - and/or tertiary recovery - range: string - examples: - - value: '2018-05-11' - comments: - - 'Expected value: timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 29' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{timestamp}' - slot_uri: MIXS:0001010 - biocide: - is_a: environment field - aliases: - - biocide administration - description: List of biocides (commercial name of product and supplier) and date - of administration - range: string - examples: - - value: ALPHA 1427;Baker Hughes;2008-01-23 - comments: - - 'Expected value: name;name;timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 30' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{text};{text};{timestamp}' - slot_uri: MIXS:0001011 - biocide_admin_method: - is_a: environment field - aliases: - - biocide administration method - description: Method of biocide administration (dose, frequency, duration, time - elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 - days) - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value;frequency;duration;duration' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 31' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' - slot_uri: MIXS:0000456 - chem_treatment: - is_a: environment field - aliases: - - chemical treatment - description: List of chemical compounds administered upstream the sampling location - where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, - demulsifiers, and other production chemicals etc.). The commercial name of the - product and name of the supplier should be provided. The date of administration - should also be included - range: string - examples: - - value: ACCENT 1125;DOW;2010-11-17 - comments: - - 'Expected value: name;name;timestamp' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 32' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{text};{text};{timestamp}' - slot_uri: MIXS:0001012 - chem_treatment_method: - is_a: environment field - aliases: - - chemical treatment method - description: Method of chemical administration(dose, frequency, duration, time - elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 - hr; 0 days) - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value;frequency;duration;duration' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 33' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' - slot_uri: MIXS:0000457 - samp_loc_corr_rate: - is_a: environment field - aliases: - - corrosion rate at sample location - description: Metal corrosion rate is the speed of metal deterioration due to environmental - conditions. As environmental conditions change corrosion rates change accordingly. - Therefore, long term corrosion rates are generally more informative than short - term rates and for that reason they are preferred during reporting. In the case - of suspected MIC, corrosion rate measurements at the time of sampling might - provide insights into the involvement of certain microbial community members - in MIC as well as potential microbial interplays - range: string - examples: - - value: '' - comments: - - 'Expected value: measurement value range' - - 'Preferred unit: millimeter per year' - - 'Occurrence: 1' - - 'Position: 34' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{float} - {float} {unit}' - slot_uri: MIXS:0000136 - samp_collection_point: - is_a: environment field - aliases: - - sample collection point - description: Sampling point on the asset were sample was collected (e.g. Wellhead, - storage tank, separator, etc). If "other" is specified, please propose entry - in "additional info" field - range: samp_collection_point_enum - examples: - - value: well - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 39' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '[well|test well|drilling rig|wellhead|separator|storage tank|other]' - slot_uri: MIXS:0001015 - samp_preserv: - is_a: environment field - aliases: - - preservative added to sample - description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, - etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - range: string - examples: - - value: '' - comments: - - 'Expected value: name;measurement value' - - 'Preferred unit: milliliter' - - 'Occurrence: 1' - - 'Position: 46' - - 'This field is used uniquely in: hydrocarbon resources-fluids_swabs' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000463 - alkyl_diethers: - is_a: environment field - aliases: - - alkyl diethers - description: Concentration of alkyl diethers - range: quantity value - examples: - - value: 0.005 mole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: mole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000490 - aminopept_act: - is_a: environment field - aliases: - - aminopeptidase activity - description: Measurement of aminopeptidase activity - range: quantity value - examples: - - value: 0.269 mole per liter per hour - comments: - - 'Expected value: measurement value' - - 'Preferred unit: mole per liter per hour' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000172 - bacteria_carb_prod: - is_a: environment field - aliases: - - bacterial carbon production - description: Measurement of bacterial carbon production - range: quantity value - examples: - - value: 2.53 microgram per liter per hour - comments: - - 'Expected value: measurement value' - - 'Preferred unit: nanogram per hour' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000173 - biomass: - is_a: environment field - aliases: - - biomass - description: Amount of biomass; should include the name for the part of biomass - measured, e.g. Microbial, total. Can include multiple measurements - range: string - examples: - - value: total;20 gram - comments: - - 'Expected value: biomass type;measurement value' - - 'Preferred unit: ton, kilogram, gram' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000174 - bishomohopanol: - is_a: environment field - aliases: - - bishomohopanol - description: Concentration of bishomohopanol - range: quantity value - examples: - - value: 14 microgram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, microgram per gram' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000175 - bromide: - is_a: environment field - aliases: - - bromide - description: Concentration of bromide - range: quantity value - examples: - - value: 0.05 parts per million - comments: - - 'Expected value: measurement value' - - 'Preferred unit: parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000176 - carb_nitro_ratio: - is_a: environment field - aliases: - - carbon/nitrogen ratio - description: Ratio of amount or concentrations of carbon to nitrogen - range: quantity value - examples: - - value: '0.417361111' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000310 - chlorophyll: - is_a: environment field - aliases: - - chlorophyll - description: Concentration of chlorophyll - range: quantity value - examples: - - value: 5 milligram per cubic meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per cubic meter, microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000177 - diether_lipids: - is_a: environment field - aliases: - - diether lipids - description: Concentration of diether lipids; can include multiple types of diether - lipids - range: string - examples: - - value: 0.2 nanogram per liter - comments: - - 'Expected value: diether lipid name;measurement value' - - 'Preferred unit: nanogram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000178 - diss_hydrogen: - is_a: environment field - aliases: - - dissolved hydrogen - description: Concentration of dissolved hydrogen - range: quantity value - examples: - - value: 0.3 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000179 - diss_org_nitro: - is_a: environment field - aliases: - - dissolved organic nitrogen - description: Dissolved organic nitrogen concentration measured as; total dissolved - nitrogen - NH4 - NO3 - NO2 - range: quantity value - examples: - - value: 0.05 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000162 - diss_oxygen: - is_a: environment field - aliases: - - dissolved oxygen - description: Concentration of dissolved oxygen - range: quantity value - examples: - - value: 175 micromole per kilogram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per kilogram, milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000119 - glucosidase_act: - is_a: environment field - aliases: - - glucosidase activity - description: Measurement of glucosidase activity - range: quantity value - examples: - - value: 5 mol per liter per hour - comments: - - 'Expected value: measurement value' - - 'Preferred unit: mol per liter per hour' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000137 - mean_frict_vel: - is_a: environment field - aliases: - - mean friction velocity - description: Measurement of mean friction velocity - range: quantity value - examples: - - value: 0.5 meter per second - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter per second' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000498 - mean_peak_frict_vel: - is_a: environment field - aliases: - - mean peak friction velocity - description: Measurement of mean peak friction velocity - range: quantity value - examples: - - value: 1 meter per second - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter per second' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000502 - n_alkanes: - is_a: environment field - aliases: - - n-alkanes - description: Concentration of n-alkanes; can include multiple n-alkanes - range: string - examples: - - value: n-hexadecane;100 milligram per liter - comments: - - 'Expected value: n-alkane name;measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000503 - nitro: - is_a: environment field - aliases: - - nitrogen - description: Concentration of nitrogen (total) - range: quantity value - examples: - - value: 4.2 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000504 - org_carb: - is_a: environment field - aliases: - - organic carbon - description: Concentration of organic carbon - range: quantity value - examples: - - value: 1.5 microgram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000508 - org_matter: - is_a: environment field - aliases: - - organic matter - description: Concentration of organic matter - range: quantity value - examples: - - value: 1.75 milligram per cubic meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000204 - org_nitro: - is_a: environment field - aliases: - - organic nitrogen - description: Concentration of organic nitrogen - range: quantity value - examples: - - value: 4 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000205 - part_org_carb: - is_a: environment field - aliases: - - particulate organic carbon - description: Concentration of particulate organic carbon - range: quantity value - examples: - - value: 1.92 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000515 - petroleum_hydrocarb: - is_a: environment field - aliases: - - petroleum hydrocarbon - description: Concentration of petroleum hydrocarbon - range: quantity value - examples: - - value: 0.05 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000516 - phaeopigments: - is_a: environment field - aliases: - - phaeopigments - description: Concentration of phaeopigments; can include multiple phaeopigments - range: string - examples: - - value: 2.5 milligram per cubic meter - comments: - - 'Expected value: phaeopigment name;measurement value' - - 'Preferred unit: milligram per cubic meter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000180 - phosphate: - is_a: environment field - aliases: - - phosphate - description: Concentration of phosphate - range: quantity value - examples: - - value: 0.7 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 5 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, wastewater_sludge, water' - slot_uri: MIXS:0000505 - phosplipid_fatt_acid: - is_a: environment field - aliases: - - phospholipid fatty acid - description: Concentration of phospholipid fatty acids; can include multiple values - range: string - examples: - - value: 2.98 milligram per liter - comments: - - 'Expected value: phospholipid fatty acid name;measurement value' - - 'Preferred unit: mole per gram, mole per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000181 - redox_potential: - is_a: environment field - aliases: - - redox potential - description: Redox potential, measured relative to a hydrogen cell, indicating - oxidation or reduction potential - range: quantity value - examples: - - value: 300 millivolt - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millivolt' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000182 - salinity: - is_a: environment field - aliases: - - salinity - description: Salinity is the total concentration of all dissolved salts in a water - sample. While salinity can be measured by a complete chemical analysis, this - method is difficult and time consuming. More often, it is instead derived from - the conductivity measurement. This is known as practical salinity. These derivations - compare the specific conductance of the sample to a salinity standard such as - seawater - range: quantity value - examples: - - value: 25 practical salinity unit - comments: - - 'Expected value: measurement value' - - 'Preferred unit: practical salinity unit, percentage' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000183 - silicate: - is_a: environment field - aliases: - - silicate - description: Concentration of silicate - range: quantity value - examples: - - value: 0.05 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 4 packages: microbial mat_biofilm, miscellaneous natural - or artificial environment, sediment, water' - slot_uri: MIXS:0000184 - tot_carb: - is_a: environment field - aliases: - - total carbon - description: Total carbon content - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: microbial mat_biofilm, sediment' - slot_uri: MIXS:0000525 - tot_nitro_content: - is_a: environment field - aliases: - - total nitrogen content - description: Total nitrogen content of the sample - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter, milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' - slot_uri: MIXS:0000530 - tot_org_carb: - is_a: environment field - aliases: - - total organic carbon - description: 'Definition for soil: total organic carbon content of the soil, definition - otherwise: total organic carbon content' - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram Carbon per kilogram sample material' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' - slot_uri: MIXS:0000533 - turbidity: - is_a: environment field - aliases: - - turbidity - description: Measure of the amount of cloudiness or haziness in water caused by - individual particles - range: quantity value - examples: - - value: 0.3 nephelometric turbidity units - comments: - - 'Expected value: measurement value' - - 'Preferred unit: formazin turbidity unit, formazin nephelometric units' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, water' - slot_uri: MIXS:0000191 - water_content: - is_a: environment field - aliases: - - water content - description: Water content measurement - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: gram per gram or cubic centimeter per cubic centimeter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 3 packages: microbial mat_biofilm, sediment, soil' - slot_uri: MIXS:0000185 - water_current: - is_a: environment field - aliases: - - water current - description: Measurement of magnitude and direction of flow within a fluid - range: quantity value - examples: - - value: 10 cubic meter per second - comments: - - 'Expected value: measurement value' - - 'Preferred unit: cubic meter per second, knots' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: miscellaneous natural or artificial environment, - water' - slot_uri: MIXS:0000203 - air_temp_regm: - is_a: environment field - aliases: - - air temperature regimen - description: Information about treatment involving an exposure to varying temperatures; - should include the temperature, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include different temperature regimens - range: string - examples: - - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: temperature value;treatment interval and duration' - - 'Preferred unit: degree Celsius' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000551 - antibiotic_regm: - is_a: environment field - aliases: - - antibiotic regimen - description: Information about treatment involving antibiotic administration; - should include the name of antibiotic, amount administered, treatment regimen - including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - antibiotic regimens - range: string - examples: - - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: antibiotic name;antibiotic amount;treatment interval and duration' - - 'Preferred unit: milligram' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000553 - biotic_regm: - is_a: environment field - aliases: - - biotic regimen - description: Information about treatment(s) involving use of biotic factors, such - as bacteria, viruses or fungi. - range: string - examples: - - value: sample inoculated with Rhizobium spp. Culture - comments: - - 'Expected value: free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text}' - slot_uri: MIXS:0001038 - chem_mutagen: - is_a: environment field - aliases: - - chemical mutagen - description: Treatment involving use of mutagens; should include the name of mutagen, - amount administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple mutagen regimens - range: string - examples: - - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: mutagen name;mutagen amount;treatment interval and duration' - - 'Preferred unit: milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000555 - climate_environment: - is_a: environment field - aliases: - - climate environment - description: Treatment involving an exposure to a particular climate; treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - climates - range: string - examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: climate name;treatment interval and duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001040 - cult_root_med: - is_a: environment field - aliases: - - culture rooting medium - description: Name or reference for the hydroponic or in vitro culture rooting - medium; can be the name of a commonly used medium or reference to a specific - medium, e.g. Murashige and Skoog medium. If the medium has not been formally - published, use the rooting medium descriptors. - range: string - examples: - - value: http://himedialabs.com/TD/PT158.pdf - comments: - - 'Expected value: name, PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text}|{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0001041 - fertilizer_regm: - is_a: environment field - aliases: - - fertilizer regimen - description: Information about treatment involving the use of fertilizers; should - include the name of fertilizer, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple fertilizer - regimens - range: string - examples: - - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: fertilizer name;fertilizer amount;treatment interval and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000556 - fungicide_regm: - is_a: environment field - aliases: - - fungicide regimen - description: Information about treatment involving use of fungicides; should include - the name of fungicide, amount administered, treatment regimen including how - many times the treatment was repeated, how long each treatment lasted, and the - start and end time of the entire treatment; can include multiple fungicide regimens - range: string - examples: - - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: fungicide name;fungicide amount;treatment interval and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000557 - gaseous_environment: - is_a: environment field - aliases: - - gaseous environment - description: Use of conditions with differing gaseous environments; should include - the name of gaseous compound, amount administered, treatment duration, interval - and total experimental duration; can include multiple gaseous environment regimens - range: string - examples: - - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: gaseous compound name;gaseous compound amount;treatment interval - and duration' - - 'Preferred unit: micromole per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000558 - gravity: - is_a: environment field - aliases: - - gravity - description: Information about treatment involving use of gravity factor to study - various types of responses in presence, absence or modified levels of gravity; - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple treatments - range: string - examples: - - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: gravity factor value;treatment interval and duration' - - 'Preferred unit: meter per square second, g' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000559 - growth_facil: - is_a: environment field - aliases: - - growth facility - description: 'Type of facility where the sampled plant was grown; controlled vocabulary: - growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively - use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' - range: string - examples: - - value: Growth chamber [CO_715:0000189] - comments: - - 'Expected value: free text or CO' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text}|{termLabel} {[termID]}' - slot_uri: MIXS:0001043 - growth_habit: - is_a: environment field - aliases: - - growth habit - description: Characteristic shape, appearance or growth form of a plant species - range: growth_habit_enum - examples: - - value: spreading - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '[erect|semi-erect|spreading|prostrate]' - slot_uri: MIXS:0001044 - growth_hormone_regm: - is_a: environment field - aliases: - - growth hormone regimen - description: Information about treatment involving use of growth hormones; should - include the name of growth hormone, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple growth - hormone regimens - range: string - examples: - - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: growth hormone name;growth hormone amount;treatment interval - and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000560 - herbicide_regm: - is_a: environment field - aliases: - - herbicide regimen - description: Information about treatment involving use of herbicides; information - about treatment involving use of growth hormones; should include the name of - herbicide, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple regimens - range: string - examples: - - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: herbicide name;herbicide amount;treatment interval and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000561 - host_wet_mass: - is_a: environment field - aliases: - - host wet mass - description: Measurement of wet mass - range: quantity value - examples: - - value: 1500 gram - comments: - - 'Expected value: measurement value' - - 'Preferred unit: kilogram, gram' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - slot_uri: MIXS:0000567 - humidity_regm: - is_a: environment field - aliases: - - humidity regimen - description: Information about treatment involving an exposure to varying degree - of humidity; information about treatment involving use of growth hormones; should - include amount of humidity administered, treatment regimen including how many - times the treatment was repeated, how long each treatment lasted, and the start - and end time of the entire treatment; can include multiple regimens - range: string - examples: - - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: humidity value;treatment interval and duration' - - 'Preferred unit: gram per cubic meter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000568 - light_regm: - is_a: environment field - aliases: - - light regimen - description: Information about treatment(s) involving exposure to light, including - both light intensity and quality. - range: string - examples: - - value: incandescant light;10 lux;450 nanometer - comments: - - 'Expected value: exposure type;light intensity;light quality' - - 'Preferred unit: lux; micrometer, nanometer, angstrom' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{float} {unit}' - slot_uri: MIXS:0000569 - mechanical_damage: - is_a: environment field - aliases: - - mechanical damage - description: Information about any mechanical damage exerted on the plant; can - include multiple damages and sites - range: string - examples: - - value: pruning;bark - comments: - - 'Expected value: damage type;body site' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{text}' - slot_uri: MIXS:0001052 - mineral_nutr_regm: - is_a: environment field - aliases: - - mineral nutrient regimen - description: Information about treatment involving the use of mineral supplements; - should include the name of mineral nutrient, amount administered, treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - mineral nutrient regimens - range: string - examples: - - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: mineral nutrient name;mineral nutrient amount;treatment interval - and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000570 - non_mineral_nutr_regm: - is_a: environment field - aliases: - - non-mineral nutrient regimen - description: Information about treatment involving the exposure of plant to non-mineral - nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral - nutrient, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple non-mineral nutrient regimens - range: string - examples: - - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: non-mineral nutrient name;non-mineral nutrient amount;treatment - interval and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000571 - ph_regm: - is_a: environment field - aliases: - - pH regimen - description: Information about treatment involving exposure of plants to varying - levels of ph of the growth media, treatment regimen including how many times - the treatment was repeated, how long each treatment lasted, and the start and - end time of the entire treatment; can include multiple regimen - range: string - examples: - - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: measurement value;treatment interval and duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001056 - pesticide_regm: - is_a: environment field - aliases: - - pesticide regimen - description: Information about treatment involving use of insecticides; should - include the name of pesticide, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple pesticide - regimens - range: string - examples: - - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: pesticide name;pesticide amount;treatment interval and duration' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000573 - plant_growth_med: - is_a: environment field - aliases: - - plant growth medium - description: Specification of the media for growing the plants or tissue cultured - samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in - vitro liquid culture medium. Recommended value is a specific value from EO:plant - growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) - or other controlled vocabulary - range: plant_growth_med_enum - examples: - - value: hydroponic plant culture media [EO:0007067] - comments: - - 'Expected value: EO or enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{termLabel} {[termID]} or [husk|other artificial liquid medium|other - artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' - slot_uri: MIXS:0001057 - plant_product: - is_a: environment field - aliases: - - plant product - description: Substance produced by the plant, where the sample was obtained from - range: string - examples: - - value: xylem sap [PO:0025539] - comments: - - 'Expected value: product name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text}' - slot_uri: MIXS:0001058 - plant_sex: - is_a: environment field - aliases: - - plant sex - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, - staminate, monoecieous, hermaphrodite. - range: plant_sex_enum - examples: - - value: Hermaphroditic - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]' - slot_uri: MIXS:0001059 - plant_struc: - is_a: environment field - aliases: - - plant structure - description: Name of plant structure the sample was obtained from; for Plant Ontology - (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, - e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the - sex of it can be recorded here. - range: string - examples: - - value: epidermis [PO:0005679] - comments: - - 'Expected value: PO' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{termLabel} {[termID]}' - slot_uri: MIXS:0001060 - radiation_regm: - is_a: environment field - aliases: - - radiation regimen - description: Information about treatment involving exposure of plant or a plant - part to a particular radiation regimen; should include the radiation type, amount - or intensity administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple radiation regimens - range: string - examples: - - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: radiation type name;radiation amount;treatment interval and - duration' - - 'Preferred unit: rad, gray' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000575 - rainfall_regm: - is_a: environment field - aliases: - - rainfall regimen - description: Information about treatment involving an exposure to a given amount - of rainfall, treatment regimen including how many times the treatment was repeated, - how long each treatment lasted, and the start and end time of the entire treatment; - can include multiple regimens - range: string - examples: - - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: measurement value;treatment interval and duration' - - 'Preferred unit: millimeter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000576 - root_cond: - is_a: environment field - aliases: - - rooting conditions - description: Relevant rooting conditions such as field plot size, sowing density, - container dimensions, number of plants per container. - range: string - examples: - - value: http://himedialabs.com/TD/PT158.pdf - comments: - - 'Expected value: PMID,DOI,url or free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001061 - root_med_carbon: - is_a: environment field - aliases: - - rooting medium carbon - description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - range: string - examples: - - value: sucrose - comments: - - 'Expected value: carbon source name;measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000577 - root_med_macronutr: - is_a: environment field - aliases: - - rooting medium macronutrients - description: "Measurement of the culture rooting medium macronutrients (N,P, K,\ - \ Ca, Mg, S); e.g. KH2PO4 (170\xAC\u2020mg/L)." - range: string - examples: - - value: "KH2PO4;170\xAC\u2020milligram per liter" - comments: - - 'Expected value: macronutrient name;measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000578 - root_med_micronutr: - is_a: environment field - aliases: - - rooting medium micronutrients - description: "Measurement of the culture rooting medium micronutrients (Fe, Mn,\ - \ Zn, B, Cu, Mo); e.g. H3BO3 (6.2\xAC\u2020mg/L)." - range: string - examples: - - value: "H3BO3;6.2\xAC\u2020milligram per liter" - comments: - - 'Expected value: micronutrient name;measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000579 - root_med_suppl: - is_a: environment field - aliases: - - rooting medium organic supplements - description: "Organic supplements of the culture rooting medium, such as vitamins,\ - \ amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic\ - \ acid (0.5\xAC\u2020mg/L)." - range: string - examples: - - value: nicotinic acid;0.5 milligram per liter - comments: - - 'Expected value: supplement name;measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000580 - root_med_ph: - is_a: environment field - aliases: - - rooting medium pH - description: pH measurement of the culture rooting medium; e.g. 5.5. - range: double - examples: - - value: '7.5' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - slot_uri: MIXS:0001062 - root_med_regl: - is_a: environment field - aliases: - - rooting medium regulators - description: "Growth regulators in the culture rooting medium such as cytokinins,\ - \ auxins, gybberellins, abscisic acid; e.g. 0.5\xAC\u2020mg/L NAA." - range: string - examples: - - value: abscisic acid;0.75 milligram per liter - comments: - - 'Expected value: regulator name;measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000581 - root_med_solid: - is_a: environment field - aliases: - - rooting medium solidifier - description: Specification of the solidifying agent in the culture rooting medium; - e.g. agar. - range: string - examples: - - value: agar - comments: - - 'Expected value: name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text}' - slot_uri: MIXS:0001063 - salt_regm: - is_a: environment field - aliases: - - salt regimen - description: Information about treatment involving use of salts as supplement - to liquid and soil growth media; should include the name of salt, amount administered, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple salt regimens - range: string - examples: - - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: salt name;salt amount;treatment interval and duration' - - 'Preferred unit: gram, microgram, mole per liter, gram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000582 - season_environment: - is_a: environment field - aliases: - - seasonal environment - description: Treatment involving an exposure to a particular season (e.g. Winter, - summer, rabi, rainy etc.), treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment - range: string - examples: - - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: seasonal environment name;treatment interval and duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001068 - standing_water_regm: - is_a: environment field - aliases: - - standing water regimen - description: Treatment involving an exposure to standing water during a plant's - life span, types can be flood water or standing water, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple regimens - range: string - examples: - - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: standing water type;treatment interval and duration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001069 - tiss_cult_growth_med: - is_a: environment field - aliases: - - tissue culture growth media - description: Description of plant tissue culture growth media used - range: string - examples: - - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf - comments: - - 'Expected value: PMID,DOI,url or free text' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001070 - water_temp_regm: - is_a: environment field - aliases: - - water temperature regimen - description: Information about treatment involving an exposure to water with varying - degree of temperature, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple regimens - range: string - examples: - - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: measurement value;treatment interval and duration' - - 'Preferred unit: degree Celsius' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000590 - watering_regm: - is_a: environment field - aliases: - - watering regimen - description: Information about treatment involving an exposure to watering frequencies, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple regimens - range: string - examples: - - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - comments: - - 'Expected value: measurement value;treatment interval and duration' - - 'Preferred unit: milliliter, liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: plant-associated' - pattern: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000591 - particle_class: - is_a: environment field - aliases: - - particle classification - description: Particles are classified, based on their size, into six general categories:clay, - silt, sand, gravel, cobbles, and boulders; should include amount of particle - preceded by the name of the particle type; can include multiple values - range: string - examples: - - value: '' - comments: - - 'Expected value: particle name;measurement value' - - 'Preferred unit: micrometer' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: sediment' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000206 - sediment_type: - is_a: environment field - aliases: - - sediment type - description: Information about the sediment type based on major constituents - range: sediment_type_enum - examples: - - value: biogenous - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: sediment' - pattern: '[biogenous|cosmogenous|hydrogenous|lithogenous]' - slot_uri: MIXS:0001078 - tidal_stage: - is_a: environment field - aliases: - - tidal stage - description: Stage of tide - range: tidal_stage_enum - examples: - - value: high tide - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: sediment, water' - pattern: '[low tide|ebb tide|flood tide|high tide]' - slot_uri: MIXS:0000750 - tot_depth_water_col: - is_a: environment field - aliases: - - total depth of water column - description: Measurement of total depth of water column - range: quantity value - examples: - - value: 500 meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: meter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used in: 2 packages: sediment, water' - slot_uri: MIXS:0000634 - cur_land_use: - is_a: environment field - aliases: - - current land use - description: Present state of sample site - range: cur_land_use_enum - examples: - - value: conifers - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: soil' - pattern: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt - flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small - grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands - (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands - used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub - land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional - shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub - crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers - (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed - hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest - receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water - body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery - trees)]' - slot_uri: MIXS:0001080 - cur_vegetation: - is_a: environment field - aliases: - - current vegetation - description: Vegetation classification from one or more standard classification - systems, or agricultural crop - range: string - examples: - - value: '' - comments: - - 'Expected value: current vegetation type' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 2' - - 'This field is used uniquely in: soil' - pattern: '{text}' - slot_uri: MIXS:0000312 - cur_vegetation_meth: - is_a: environment field - aliases: - - current vegetation method - description: Reference or method used in vegetation classification - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 3' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000314 - previous_land_use: - is_a: environment field - aliases: - - history/previous land use - description: Previous land use and dates - range: string - examples: - - value: '' - comments: - - 'Expected value: land use name;date' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 4' - - 'This field is used uniquely in: soil' - pattern: '{text};{timestamp}' - slot_uri: MIXS:0000315 - previous_land_use_meth: - is_a: environment field - aliases: - - history/previous land use method - description: Reference or method used in determining previous land use and dates - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 5' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000316 - crop_rotation: - is_a: environment field - aliases: - - history/crop rotation - description: Whether or not crop is rotated, and if yes, rotation schedule - range: string - examples: - - value: yes;R2/2017-01-01/2018-12-31/P6M - comments: - - 'Expected value: crop rotation status;schedule' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 6' - - 'This field is used uniquely in: soil' - pattern: '{boolean};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000318 - agrochem_addition: - is_a: environment field - aliases: - - history/agrochemical additions - description: Addition of fertilizers, pesticides, etc. - amount and time of applications - range: string - examples: - - value: roundup;5 milligram per liter;2018-06-21 - comments: - - 'Expected value: agrochemical name;agrochemical amount;timestamp' - - 'Preferred unit: gram, mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 7' - - 'This field is used uniquely in: soil' - pattern: '{text};{float} {unit};{timestamp}' - slot_uri: MIXS:0000639 - tillage: - is_a: environment field - aliases: - - history/tillage - description: Note method(s) used for tilling - range: tillage_enum - examples: - - value: chisel - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 8' - - 'This field is used uniquely in: soil' - pattern: '[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc - plough]' - slot_uri: MIXS:0001081 - fire: - is_a: environment field - aliases: - - history/fire - description: Historical and/or physical evidence of fire - range: string - examples: - - value: '' - comments: - - 'Expected value: date' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 9' - - 'This field is used uniquely in: soil' - pattern: '{timestamp}' - slot_uri: MIXS:0001086 - flooding: - is_a: environment field - aliases: - - history/flooding - description: Historical and/or physical evidence of flooding - range: string - examples: - - value: '' - comments: - - 'Expected value: date' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 10' - - 'This field is used uniquely in: soil' - pattern: '{timestamp}' - slot_uri: MIXS:0000319 - extreme_event: - is_a: environment field - aliases: - - history/extreme events - description: Unusual physical events that may have affected microbial populations - range: string - examples: - - value: '' - comments: - - 'Expected value: date' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 11' - - 'This field is used uniquely in: soil' - pattern: '{timestamp}' - slot_uri: MIXS:0000320 - horizon: - is_a: environment field - aliases: - - horizon - description: Specific layer in the land area which measures parallel to the soil - surface and possesses physical characteristics which differ from the layers - above and beneath - range: horizon_enum - examples: - - value: A horizon - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 12' - - 'This field is used uniquely in: soil' - pattern: '[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]' - slot_uri: MIXS:0001082 - horizon_meth: - is_a: environment field - aliases: - - horizon method - description: Reference or method used in determining the horizon - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 13' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - sieving: - is_a: environment field - aliases: - - composite design/sieving (if any) - description: Collection design of pooled samples and/or sieve size and amount - of sample sieved - range: string - examples: - - value: '' - comments: - - 'Expected value: design name and/or size;amount' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 14' - - 'This field is used uniquely in: soil' - pattern: '{{text}|{float} {unit}};{float} {unit}' - slot_uri: MIXS:0000322 - water_content_soil_meth: - is_a: environment field - aliases: - - water content method - description: Reference or method used in determining the water content of soil - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 16' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000323 - pool_dna_extracts: - is_a: environment field - aliases: - - pooling of DNA extracts (if done) - description: Indicate whether multiple DNA extractions were mixed. If the answer - yes, the number of extracts that were pooled should be given - range: string - examples: - - value: yes;5 - comments: - - 'Expected value: pooling status;number of pooled extracts' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 18' - - 'This field is used uniquely in: soil' - pattern: '{boolean};{integer}' - slot_uri: MIXS:0000325 - store_cond: - is_a: environment field - aliases: - - storage conditions (fresh/frozen/other) - description: Explain how and for how long the soil sample was stored before DNA - extraction - range: string - examples: - - value: -20 degree Celsius freezer;P2Y10D - comments: - - 'Expected value: storage condition type;duration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 19' - - 'This field is used uniquely in: soil' - pattern: '{text};{duration}' - slot_uri: MIXS:0000327 - link_climate_info: - is_a: environment field - aliases: - - link to climate information - description: Link to climate resource - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 20' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000328 - annual_temp: - is_a: environment field - aliases: - - mean annual temperature - description: Mean annual temperature - range: quantity value - examples: - - value: 12.5 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 21' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000642 - season_temp: - is_a: environment field - aliases: - - mean seasonal temperature - description: Mean seasonal temperature - range: quantity value - examples: - - value: 18 degree Celsius - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree Celsius' - - 'Occurrence: 1' - - 'Position: 22' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000643 - annual_precpt: - is_a: environment field - aliases: - - mean annual precipitation - description: The average of all annual precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps. - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millimeter' - - 'Occurrence: 1' - - 'Position: 23' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000644 - season_precpt: - is_a: environment field - aliases: - - mean seasonal precipitation - description: The average of all seasonal precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps. - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millimeter' - - 'Occurrence: 1' - - 'Position: 24' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000645 - link_class_info: - is_a: environment field - aliases: - - link to classification information - description: Link to digitized soil maps or other soil classification information - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 25' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000329 - fao_class: - is_a: environment field - aliases: - - soil_taxonomic/FAO classification - description: Soil classification from the FAO World Reference Database for Soil - Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - range: fao_class_enum - examples: - - value: Luvisols - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 26' - - 'This field is used uniquely in: soil' - pattern: '[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]' - slot_uri: MIXS:0001083 - local_class: - is_a: environment field - aliases: - - soil_taxonomic/local classification - description: Soil classification based on local soil classification system - range: string - examples: - - value: '' - comments: - - 'Expected value: local classification name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 27' - - 'This field is used uniquely in: soil' - pattern: '{text}' - slot_uri: MIXS:0000330 - local_class_meth: - is_a: environment field - aliases: - - soil_taxonomic/local classification method - description: Reference or method used in determining the local soil classification - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 28' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000331 - soil_type: - is_a: environment field - aliases: - - soil type - description: Soil series name or other lower-level classification - range: string - examples: - - value: '' - comments: - - 'Expected value: soil type name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 29' - - 'This field is used uniquely in: soil' - pattern: '{text}' - slot_uri: MIXS:0000332 - soil_type_meth: - is_a: environment field - aliases: - - soil type method - description: Reference or method used in determining soil series name or other - lower-level classification - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 30' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000334 - slope_gradient: - is_a: environment field - aliases: - - slope gradient - description: Commonly called 'slope'. The angle between ground surface and a horizontal - line (in percent). This is the direction that overland water would flow. This - measure is usually taken with a hand level meter or clinometer - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 31' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000646 - slope_aspect: - is_a: environment field - aliases: - - slope aspect - description: The direction a slope faces. While looking down a slope use a compass - to record the direction you are facing (direction or degrees); e.g., nw or 315 - degrees. This measure provides an indication of sun and wind exposure that will - influence soil temperature and evapotranspiration. - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: degree' - - 'Occurrence: 1' - - 'Position: 32' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000647 - profile_position: - is_a: environment field - aliases: - - profile position - description: Cross-sectional position in the hillslope where sample was collected.sample - area position in relation to surrounding areas - range: profile_position_enum - examples: - - value: summit - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 33' - - 'This field is used uniquely in: soil' - pattern: '[summit|shoulder|backslope|footslope|toeslope]' - slot_uri: MIXS:0001084 - drainage_class: - is_a: environment field - aliases: - - drainage classification - description: Drainage classification from a standard system such as the USDA system - range: drainage_class_enum - examples: - - value: well - comments: - - 'Expected value: enumeration' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 34' - - 'This field is used uniquely in: soil' - pattern: '[very poorly|poorly|somewhat poorly|moderately well|well|excessively - drained]' - slot_uri: MIXS:0001085 - texture: - is_a: environment field - aliases: - - texture - description: The relative proportion of different grain sizes of mineral particles - in a soil, as described using a standard system; express as % sand (50 um to - 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty - clay loam) optional. - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 35' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000335 - texture_meth: - is_a: environment field - aliases: - - texture method - description: Reference or method used in determining soil texture - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 36' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000336 - ph_meth: - is_a: environment field - aliases: - - pH method - description: Reference or method used in determining ph - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 38' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0001106 - tot_org_c_meth: - is_a: environment field - aliases: - - total organic carbon method - description: Reference or method used in determining total organic carbon - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 40' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000337 - tot_nitro_content_meth: - is_a: environment field - aliases: - - total nitrogen content method - description: Reference or method used in determining the total nitrogen - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 42' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000338 - microbial_biomass: - is_a: environment field - aliases: - - microbial biomass - description: The part of the organic matter in the soil that constitutes living - microorganisms smaller than 5-10 micrometer. If you keep this, you would need - to have correction factors used for conversion to the final units - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: ton, kilogram, gram per kilogram soil' - - 'Occurrence: 1' - - 'Position: 43' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000650 - microbial_biomass_meth: - is_a: environment field - aliases: - - microbial biomass method - description: Reference or method used in determining microbial biomass - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 44' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000339 - link_addit_analys: - is_a: environment field - aliases: - - links to additional analysis - description: Link to additional analysis results performed on the sample - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 45' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000340 - extreme_salinity: - is_a: environment field - aliases: - - extreme_unusual_properties/salinity - description: Measured salinity - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: millisiemens per meter' - - 'Occurrence: 1' - - 'Position: 46' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000651 - salinity_meth: - is_a: environment field - aliases: - - extreme_unusual_properties/salinity method - description: Reference or method used in determining salinity - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 47' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000341 - heavy_metals: - is_a: environment field - aliases: - - extreme_unusual_properties/heavy metals - description: Heavy metals present and concentrationsany drug used by subject and - the frequency of usage; can include multiple heavy metals and concentrations - range: string - examples: - - value: '' - comments: - - 'Expected value: heavy metal name;measurement value' - - 'Preferred unit: microgram per gram' - - 'Occurrence: m' - - 'Position: 48' - - 'This field is used uniquely in: soil' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000652 - heavy_metals_meth: - is_a: environment field - aliases: - - extreme_unusual_properties/heavy metals method - description: Reference or method used in determining heavy metals - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or url' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 49' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000343 - al_sat: - is_a: environment field - aliases: - - extreme_unusual_properties/Al saturation - description: Aluminum saturation (esp. For tropical soils) - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 50' - - 'This field is used uniquely in: soil' - slot_uri: MIXS:0000607 - al_sat_meth: - is_a: environment field - aliases: - - extreme_unusual_properties/Al saturation method - description: Reference or method used in determining Al saturation - range: string - examples: - - value: '' - comments: - - 'Expected value: PMID,DOI or URL' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 51' - - 'This field is used uniquely in: soil' - pattern: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000324 - biochem_oxygen_dem: - is_a: environment field - aliases: - - biochemical oxygen demand - description: Amount of dissolved oxygen needed by aerobic biological organisms - in a body of water to break down organic material present in a given water sample - at certain temperature over a specific time period - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000653 - chem_oxygen_dem: - is_a: environment field - aliases: - - chemical oxygen demand - description: A measure of the capacity of water to consume oxygen during the decomposition - of organic matter and the oxidation of inorganic chemicals such as ammonia and - nitrite - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000656 - efficiency_percent: - is_a: environment field - aliases: - - efficiency percent - description: Percentage of volatile solids removed from the anaerobic digestor - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000657 - emulsions: - is_a: environment field - aliases: - - emulsions - description: Amount or concentration of substances such as paints, adhesives, - mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion - types - range: string - examples: - - value: '' - comments: - - 'Expected value: emulsion name;measurement value' - - 'Preferred unit: gram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000660 - gaseous_substances: - is_a: environment field - aliases: - - gaseous substances - description: Amount or concentration of substances such as hydrogen sulfide, carbon - dioxide, methane, etc.; can include multiple substances - range: string - examples: - - value: '' - comments: - - 'Expected value: gaseous substance name;measurement value' - - 'Preferred unit: micromole per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000661 - indust_eff_percent: - is_a: environment field - aliases: - - industrial effluent percent - description: Percentage of industrial effluents received by wastewater treatment - plant - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: percentage' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000662 - inorg_particles: - is_a: environment field - aliases: - - inorganic particles - description: Concentration of particles such as sand, grit, metal particles, ceramics, - etc.; can include multiple particles - range: string - examples: - - value: '' - comments: - - 'Expected value: inorganic particle name;measurement value' - - 'Preferred unit: mole per liter, milligram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000664 - org_particles: - is_a: environment field - aliases: - - organic particles - description: Concentration of particles such as faeces, hairs, food, vomit, paper - fibers, plant material, humus, etc. - range: string - examples: - - value: '' - comments: - - 'Expected value: particle name;measurement value' - - 'Preferred unit: gram per liter' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000665 - pre_treatment: - is_a: environment field - aliases: - - pre-treatment - description: The process of pre-treatment removes materials that can be easily - collected from the raw wastewater - range: string - examples: - - value: '' - comments: - - 'Expected value: pre-treatment type' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000348 - primary_treatment: - is_a: environment field - aliases: - - primary treatment - description: The process to produce both a generally homogeneous liquid capable - of being treated biologically and a sludge that can be separately treated or - processed - range: string - examples: - - value: '' - comments: - - 'Expected value: primary treatment type' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000349 - reactor_type: - is_a: environment field - aliases: - - reactor type - description: Anaerobic digesters can be designed and engineered to operate using - a number of different process configurations, as batch or continuous, mesophilic, - high solid or low solid, and single stage or multistage - range: string - examples: - - value: '' - comments: - - 'Expected value: reactor type name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000350 - secondary_treatment: - is_a: environment field - aliases: - - secondary treatment - description: The process for substantially degrading the biological content of - the sewage - range: string - examples: - - value: '' - comments: - - 'Expected value: secondary treatment type' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000351 - sewage_type: - is_a: environment field - aliases: - - sewage type - description: Type of wastewater treatment plant as municipial or industrial - range: string - examples: - - value: '' - comments: - - 'Expected value: sewage type name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000215 - sludge_retent_time: - is_a: environment field - aliases: - - sludge retention time - description: The time activated sludge remains in reactor - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: hours' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000669 - soluble_inorg_mat: - is_a: environment field - aliases: - - soluble inorganic material - description: Concentration of substances such as ammonia, road-salt, sea-salt, - cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - range: string - examples: - - value: '' - comments: - - 'Expected value: soluble inorganic material name;measurement value' - - 'Preferred unit: gram, microgram, mole per liter, gram per liter, parts per - million' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000672 - soluble_org_mat: - is_a: environment field - aliases: - - soluble organic material - description: Concentration of substances such as urea, fruit sugars, soluble proteins, - drugs, pharmaceuticals, etc. - range: string - examples: - - value: '' - comments: - - 'Expected value: soluble organic material name;measurement value' - - 'Preferred unit: gram, microgram, mole per liter, gram per liter, parts per - million' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0000673 - tertiary_treatment: - is_a: environment field - aliases: - - tertiary treatment - description: The process providing a final treatment stage to raise the effluent - quality before it is discharged to the receiving environment - range: string - examples: - - value: '' - comments: - - 'Expected value: tertiary treatment type' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000352 - tot_phosphate: - is_a: environment field - aliases: - - total phosphate - description: Total amount or concentration of phosphate - range: quantity value - examples: - - value: '' - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - slot_uri: MIXS:0000689 - wastewater_type: - is_a: environment field - aliases: - - wastewater type - description: The origin of wastewater such as human waste, rainfall, storm drains, - etc. - range: string - examples: - - value: '' - comments: - - 'Expected value: wastewater type name' - - 'Preferred unit: ' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: wastewater_sludge' - pattern: '{text}' - slot_uri: MIXS:0000353 - atmospheric_data: - is_a: environment field - aliases: - - atmospheric data - description: Measurement of atmospheric data; can include multiple data - range: string - examples: - - value: wind speed;9 knots - comments: - - 'Expected value: atmospheric data name;measurement value' - - 'Preferred unit: ' - - 'Occurrence: m' - - 'Position: 1' - - 'This field is used uniquely in: water' - pattern: '{text};{float} {unit}' - slot_uri: MIXS:0001097 - bac_prod: - is_a: environment field - aliases: - - bacterial production - description: Bacterial production in the water column measured by isotope uptake - range: quantity value - examples: - - value: 5 milligram per cubic meter per day - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per cubic meter per day' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000683 - bac_resp: - is_a: environment field - aliases: - - bacterial respiration - description: Measurement of bacterial respiration in the water column - range: quantity value - examples: - - value: 300 micromole oxygen per liter per hour - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per cubic meter per day, micromole oxygen per liter - per hour' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000684 - conduc: - is_a: environment field - aliases: - - conductivity - description: Electrical conductivity of water - range: quantity value - examples: - - value: 10 milliSiemens per centimeter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milliSiemens per centimeter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000692 - diss_inorg_nitro: - is_a: environment field - aliases: - - dissolved inorganic nitrogen - description: Concentration of dissolved inorganic nitrogen - range: quantity value - examples: - - value: 761 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000698 - down_par: - is_a: environment field - aliases: - - downward PAR - description: Visible waveband radiance and irradiance measurements in the water - column - range: quantity value - examples: - - value: 28.71 microEinstein per square meter per second - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microEinstein per square meter per second, microEinstein per - square centimeter per second' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000703 - fluor: - is_a: environment field - aliases: - - fluorescence - description: Raw or converted fluorescence of water - range: quantity value - examples: - - value: 2.5 volts - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram chlorophyll a per cubic meter, volts' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000704 - light_intensity: - is_a: environment field - aliases: - - light intensity - description: Measurement of light intensity - range: quantity value - examples: - - value: 0.3 lux - comments: - - 'Expected value: measurement value' - - 'Preferred unit: lux' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000706 - part_org_nitro: - is_a: environment field - aliases: - - particulate organic nitrogen - description: Concentration of particulate organic nitrogen - range: quantity value - examples: - - value: 0.3 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000719 - photon_flux: - is_a: environment field - aliases: - - photon flux - description: Measurement of photon flux - range: quantity value - examples: - - value: 3.926 micromole photons per second per square meter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: number of photons per second per unit area' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000725 - primary_prod: - is_a: environment field - aliases: - - primary production - description: Measurement of primary production, generally measured as isotope - uptake - range: quantity value - examples: - - value: 100 milligram per cubic meter per day - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per cubic meter per day, gram per square meter per - day' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000728 - size_frac_low: - is_a: environment field - aliases: - - size-fraction lower threshold - description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. - Materials larger than the size threshold are excluded from the sample - range: quantity value - examples: - - value: 0.2 micrometer - comments: - - 'Expected value: value' - - 'Preferred unit: micrometer' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000735 - size_frac_up: - is_a: environment field - aliases: - - size-fraction upper threshold - description: Refers to the mesh/pore size used to retain the sample. Materials - smaller than the size threshold are excluded from the sample - range: quantity value - examples: - - value: 20 micrometer - comments: - - 'Expected value: value' - - 'Preferred unit: micrometer' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000736 - soluble_react_phosp: - is_a: environment field - aliases: - - soluble reactive phosphorus - description: Concentration of soluble reactive phosphorus - range: quantity value - examples: - - value: 0.1 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: micromole per liter, milligram per liter, parts per million' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000738 - suspend_part_matter: - is_a: environment field - aliases: - - suspended particulate matter - description: Concentration of suspended particulate matter - range: quantity value - examples: - - value: 0.5 milligram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: milligram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000741 - tot_diss_nitro: - is_a: environment field - aliases: - - total dissolved nitrogen - description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured - by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' - range: quantity value - examples: - - value: 40 microgram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000744 - tot_inorg_nitro: - is_a: environment field - aliases: - - total inorganic nitrogen - description: Total inorganic nitrogen content - range: quantity value - examples: - - value: 40 microgram per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000745 - tot_part_carb: - is_a: environment field - aliases: - - total particulate carbon - description: Total particulate carbon content - range: quantity value - examples: - - value: 35 micromole per liter - comments: - - 'Expected value: measurement value' - - 'Preferred unit: microgram per liter, micromole per liter' - - 'Occurrence: 1' - - 'Position: 1' - - 'This field is used uniquely in: water' - slot_uri: MIXS:0000747 -classes: - quantity value: - description: used to record a measurement - attributes: - has unit: - description: Example "m" - has numeric value: - range: double - has raw value: - string_serialization: '{has numeric value} {has unit}' - MIGS eukaryote: - mixin: true - description: 'Minimal Information about a Genome Sequence: eukaryote' - aliases: - - MIGS.eu - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - ploidy - - num_replicons - - extrachrom_elements - - estimated_size - - ref_biomaterial - - source_mat_id - - pathogenicity - - biotic_relationship - - specific_host - - host_spec_range - - health_disease_stat - - trophic_level - - propagation - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - compl_score - - compl_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - ploidy: - required: 'False' - num_replicons: - required: 'False' - extrachrom_elements: - required: 'False' - estimated_size: - required: 'False' - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - pathogenicity: - comments: - - conditional mandatory - biotic_relationship: - required: 'False' - specific_host: - required: 'False' - host_spec_range: - required: 'False' - health_disease_stat: - required: 'False' - trophic_level: - comments: - - conditional mandatory - propagation: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - required: 'False' - samp_size: - required: 'False' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - required: 'False' - lib_reads_seqd: - required: 'False' - lib_layout: - required: 'False' - lib_vector: - required: 'False' - lib_screen: - required: 'False' - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - comments: - - conditional mandatory - assembly_qual: - required: 'True' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - comments: - - conditional mandatory - number_contig: - required: 'True' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - compl_score: - required: 'False' - compl_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIGS bacteria: - mixin: true - description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' - aliases: - - MIGS.ba - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - num_replicons - - extrachrom_elements - - estimated_size - - ref_biomaterial - - source_mat_id - - pathogenicity - - biotic_relationship - - specific_host - - host_spec_range - - health_disease_stat - - trophic_level - - encoded_traits - - rel_to_oxygen - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - compl_score - - compl_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - num_replicons: - required: 'True' - extrachrom_elements: - comments: - - conditional mandatory - estimated_size: - required: 'False' - ref_biomaterial: - required: 'True' - source_mat_id: - comments: - - conditional mandatory - pathogenicity: - comments: - - conditional mandatory - biotic_relationship: - comments: - - conditional mandatory - specific_host: - comments: - - conditional mandatory - host_spec_range: - required: 'False' - health_disease_stat: - comments: - - conditional mandatory - trophic_level: - comments: - - conditional mandatory - encoded_traits: - required: 'False' - rel_to_oxygen: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - required: 'False' - samp_size: - required: 'False' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - required: 'False' - lib_reads_seqd: - required: 'False' - lib_layout: - required: 'False' - lib_vector: - required: 'False' - lib_screen: - required: 'False' - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - comments: - - conditional mandatory - assembly_qual: - required: 'True' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - comments: - - conditional mandatory - number_contig: - required: 'True' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - compl_score: - required: 'False' - compl_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIGS plant: - mixin: true - description: 'Minimal Information about a Genome Sequence: plant' - aliases: - - MIGS.pl - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - estimated_size - - ref_biomaterial - - source_mat_id - - specific_host - - host_spec_range - - propagation - - encoded_traits - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - compl_score - - compl_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - estimated_size: - required: 'False' - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - specific_host: - comments: - - conditional mandatory - host_spec_range: - required: 'False' - propagation: - required: 'True' - encoded_traits: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - required: 'False' - samp_size: - required: 'False' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - required: 'False' - lib_reads_seqd: - required: 'False' - lib_layout: - required: 'False' - lib_vector: - required: 'False' - lib_screen: - required: 'False' - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - comments: - - conditional mandatory - assembly_qual: - required: 'False' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - comments: - - conditional mandatory - number_contig: - required: 'False' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - compl_score: - required: 'False' - compl_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIGS virus: - mixin: true - description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' - aliases: - - MIGS.ba - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - num_replicons - - estimated_size - - ref_biomaterial - - source_mat_id - - pathogenicity - - biotic_relationship - - specific_host - - host_spec_range - - health_disease_stat - - propagation - - encoded_traits - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - virus_enrich_appr - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - compl_score - - compl_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - num_replicons: - comments: - - conditional mandatory - estimated_size: - required: 'False' - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - pathogenicity: - comments: - - conditional mandatory - biotic_relationship: - required: 'False' - specific_host: - comments: - - conditional mandatory - host_spec_range: - comments: - - conditional mandatory - health_disease_stat: - comments: - - conditional mandatory - propagation: - required: 'True' - encoded_traits: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - required: 'False' - samp_size: - required: 'False' - virus_enrich_appr: - comments: - - conditional mandatory - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - required: 'False' - lib_reads_seqd: - required: 'False' - lib_layout: - required: 'False' - lib_vector: - required: 'False' - lib_screen: - required: 'False' - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - comments: - - conditional mandatory - assembly_qual: - required: 'False' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - comments: - - conditional mandatory - number_contig: - required: 'False' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - compl_score: - required: 'False' - compl_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIGS org: - mixin: true - description: 'Minimal Information about a Genome Sequence: org' - aliases: - - MIGS.org - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - extrachrom_elements - - estimated_size - - ref_biomaterial - - source_mat_id - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - compl_score - - compl_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - extrachrom_elements: - comments: - - conditional mandatory - estimated_size: - required: 'False' - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - required: 'False' - samp_size: - required: 'False' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - required: 'False' - lib_reads_seqd: - required: 'False' - lib_layout: - required: 'False' - lib_vector: - required: 'False' - lib_screen: - required: 'False' - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - comments: - - conditional mandatory - assembly_qual: - required: 'False' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - comments: - - conditional mandatory - number_contig: - required: 'False' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - compl_score: - required: 'False' - compl_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - ME: - mixin: true - description: Metagenome or Environmental - aliases: - - ME - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - ref_biomaterial - - source_mat_id - - rel_to_oxygen - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - mid - - adapters - - seq_meth - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - comments: - - conditional mandatory - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - rel_to_oxygen: - required: 'False' - samp_collect_device: - comments: - - conditional mandatory - samp_mat_process: - comments: - - conditional mandatory - size_frac: - required: 'False' - samp_size: - comments: - - conditional mandatory - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - comments: - - conditional mandatory - lib_reads_seqd: - comments: - - conditional mandatory - lib_layout: - comments: - - conditional mandatory - lib_vector: - comments: - - conditional mandatory - lib_screen: - comments: - - conditional mandatory - mid: - comments: - - conditional mandatory - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - assembly_qual: - comments: - - conditional mandatory - assembly_name: - comments: - - conditional mandatory - assembly_software: - comments: - - conditional mandatory - annot: - comments: - - conditional mandatory - number_contig: - comments: - - conditional mandatory - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIMARKS specimen: - mixin: true - description: 'Minimal Information about a Marker Specimen: specimen' - aliases: - - MIMARKS.specimen - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - source_mat_id - - rel_to_oxygen - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - target_gene - - target_subfragment - - pcr_primers - - mid - - adapters - - pcr_cond - - seq_meth - - seq_quality_check - - chimera_check - - assembly_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - comments: - - conditional mandatory - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - source_mat_id: - comments: - - conditional mandatory - rel_to_oxygen: - required: 'False' - samp_collect_device: - comments: - - conditional mandatory - samp_mat_process: - comments: - - conditional mandatory - size_frac: - required: 'False' - samp_size: - comments: - - conditional mandatory - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - comments: - - conditional mandatory - lib_reads_seqd: - comments: - - conditional mandatory - lib_layout: - comments: - - conditional mandatory - lib_vector: - comments: - - conditional mandatory - lib_screen: - comments: - - conditional mandatory - target_gene: - required: 'True' - target_subfragment: - comments: - - conditional mandatory - pcr_primers: - comments: - - conditional mandatory - mid: - comments: - - conditional mandatory - adapters: - comments: - - conditional mandatory - pcr_cond: - comments: - - conditional mandatory - seq_meth: - required: 'True' - seq_quality_check: - comments: - - conditional mandatory - chimera_check: - comments: - - conditional mandatory - assembly_software: - comments: - - conditional mandatory - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIMARKS survey: - mixin: true - description: 'Minimal Information about a Marker Specimen: survey' - aliases: - - MIMARKS.survey - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - extrachrom_elements - - source_mat_id - - biotic_relationship - - trophic_level - - rel_to_oxygen - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - target_gene - - target_subfragment - - pcr_primers - - pcr_cond - - seq_meth - - seq_quality_check - - chimera_check - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - required: 'False' - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - subspecf_gen_lin: - comments: - - conditional mandatory - extrachrom_elements: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - biotic_relationship: - comments: - - conditional mandatory - trophic_level: - comments: - - conditional mandatory - rel_to_oxygen: - comments: - - conditional mandatory - isol_growth_condt: - required: 'True' - samp_collect_device: - required: 'False' - samp_mat_process: - comments: - - conditional mandatory - samp_size: - required: 'False' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - target_gene: - required: 'True' - target_subfragment: - comments: - - conditional mandatory - pcr_primers: - comments: - - conditional mandatory - pcr_cond: - comments: - - conditional mandatory - seq_meth: - required: 'True' - seq_quality_check: - comments: - - conditional mandatory - chimera_check: - comments: - - conditional mandatory - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MISAG: - mixin: true - description: Minimum Information About a Single Amplified Genome - aliases: - - MISAG - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - ref_biomaterial - - source_mat_id - - rel_to_oxygen - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - mid - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - x_16s_recover - - x_16s_recover_software - - trnas - - trna_ext_software - - compl_score - - compl_software - - compl_appr - - contam_score - - contam_screen_input - - contam_screen_param - - decontam_software - - sort_tech - - single_cell_lysis_appr - - single_cell_lysis_prot - - wga_amp_appr - - wga_amp_kit - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - comments: - - conditional mandatory - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - rel_to_oxygen: - required: 'False' - samp_collect_device: - comments: - - conditional mandatory - samp_mat_process: - comments: - - conditional mandatory - size_frac: - required: 'False' - samp_size: - comments: - - conditional mandatory - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - comments: - - conditional mandatory - lib_reads_seqd: - comments: - - conditional mandatory - lib_layout: - comments: - - conditional mandatory - lib_vector: - comments: - - conditional mandatory - lib_screen: - comments: - - conditional mandatory - mid: - comments: - - conditional mandatory - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - required: 'True' - assembly_qual: - required: 'True' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - required: 'False' - number_contig: - required: 'False' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - x_16s_recover: - required: 'False' - x_16s_recover_software: - required: 'False' - trnas: - required: 'False' - trna_ext_software: - required: 'False' - compl_score: - required: 'True' - compl_software: - required: 'True' - compl_appr: - required: 'False' - contam_score: - required: 'True' - contam_screen_input: - required: 'False' - contam_screen_param: - required: 'False' - decontam_software: - required: 'False' - sort_tech: - required: 'True' - single_cell_lysis_appr: - required: 'True' - single_cell_lysis_prot: - required: 'False' - wga_amp_appr: - required: 'True' - wga_amp_kit: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIMAG: - mixin: true - description: Minimum Information About a Metagenome-Assembled Genome - aliases: - - MIMAG - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - ref_biomaterial - - source_mat_id - - rel_to_oxygen - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - mid - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - x_16s_recover - - x_16s_recover_software - - trnas - - trna_ext_software - - compl_score - - compl_software - - compl_appr - - contam_score - - contam_screen_input - - contam_screen_param - - decontam_software - - bin_param - - bin_software - - reassembly_bin - - mag_cov_software - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - comments: - - conditional mandatory - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - rel_to_oxygen: - required: 'False' - samp_collect_device: - comments: - - conditional mandatory - samp_mat_process: - comments: - - conditional mandatory - size_frac: - required: 'False' - samp_size: - comments: - - conditional mandatory - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - comments: - - conditional mandatory - lib_reads_seqd: - comments: - - conditional mandatory - lib_layout: - comments: - - conditional mandatory - lib_vector: - comments: - - conditional mandatory - lib_screen: - comments: - - conditional mandatory - mid: - comments: - - conditional mandatory - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - required: 'True' - assembly_qual: - required: 'True' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - required: 'False' - number_contig: - required: 'False' - feat_pred: - required: 'False' - ref_db: - required: 'False' - sim_search_meth: - required: 'False' - tax_class: - required: 'False' - x_16s_recover: - required: 'False' - x_16s_recover_software: - required: 'False' - trnas: - required: 'False' - trna_ext_software: - required: 'False' - compl_score: - required: 'True' - compl_software: - required: 'True' - compl_appr: - required: 'False' - contam_score: - required: 'True' - contam_screen_input: - required: 'False' - contam_screen_param: - required: 'False' - decontam_software: - required: 'False' - bin_param: - required: 'True' - bin_software: - required: 'True' - reassembly_bin: - required: 'False' - mag_cov_software: - required: 'False' - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - MIUVIG: - mixin: true - description: Minimum Information About an Uncultivated Virus Genome - aliases: - - MIUVIG - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - estimated_size - - ref_biomaterial - - source_mat_id - - pathogenicity - - biotic_relationship - - specific_host - - host_spec_range - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - source_uvig - - virus_enrich_appr - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - mid - - adapters - - seq_meth - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - trnas - - trna_ext_software - - compl_score - - compl_software - - compl_appr - - sort_tech - - single_cell_lysis_appr - - single_cell_lysis_prot - - wga_amp_appr - - wga_amp_kit - - bin_param - - bin_software - - reassembly_bin - - mag_cov_software - - vir_ident_software - - pred_genome_type - - pred_genome_struc - - detec_type - - votu_class_appr - - votu_seq_comp_appr - - votu_db - - host_pred_appr - - host_pred_est_acc - - url - - sop - slot_usage: - submitted_to_insdc: - required: 'True' - investigation_type: - required: 'True' - sample_name: {} - project_name: - required: 'True' - experimental_factor: - comments: - - conditional mandatory - lat_lon: - required: 'True' - geo_loc_name: - required: 'True' - collection_date: - required: 'True' - env_broad_scale: - required: 'True' - env_local_scale: - required: 'True' - env_medium: - required: 'True' - env_package: - comments: - - conditional mandatory - estimated_size: - required: 'False' - ref_biomaterial: - required: 'False' - source_mat_id: - comments: - - conditional mandatory - pathogenicity: - required: 'False' - biotic_relationship: - required: 'False' - specific_host: - required: 'False' - host_spec_range: - required: 'False' - samp_collect_device: - comments: - - conditional mandatory - samp_mat_process: - comments: - - conditional mandatory - size_frac: - comments: - - conditional mandatory - samp_size: - comments: - - conditional mandatory - source_uvig: - required: 'True' - virus_enrich_appr: - required: 'True' - nucl_acid_ext: - comments: - - conditional mandatory - nucl_acid_amp: - comments: - - conditional mandatory - lib_size: - comments: - - conditional mandatory - lib_reads_seqd: - comments: - - conditional mandatory - lib_layout: - comments: - - conditional mandatory - lib_vector: - comments: - - conditional mandatory - lib_screen: - comments: - - conditional mandatory - mid: - comments: - - conditional mandatory - adapters: - comments: - - conditional mandatory - seq_meth: - required: 'True' - tax_ident: - required: 'False' - assembly_qual: - required: 'True' - assembly_name: - comments: - - conditional mandatory - assembly_software: - required: 'True' - annot: - required: 'False' - number_contig: - required: 'True' - feat_pred: - comments: - - conditional mandatory - ref_db: - comments: - - conditional mandatory - sim_search_meth: - comments: - - conditional mandatory - tax_class: - comments: - - conditional mandatory - trnas: - required: 'False' - trna_ext_software: - required: 'False' - compl_score: - comments: - - conditional mandatory - compl_software: - required: 'False' - compl_appr: - comments: - - conditional mandatory - sort_tech: - comments: - - conditional mandatory - single_cell_lysis_appr: - comments: - - conditional mandatory - single_cell_lysis_prot: - comments: - - conditional mandatory - wga_amp_appr: - comments: - - conditional mandatory - wga_amp_kit: - comments: - - conditional mandatory - bin_param: - comments: - - conditional mandatory - bin_software: - comments: - - conditional mandatory - reassembly_bin: - comments: - - conditional mandatory - mag_cov_software: - required: 'False' - vir_ident_software: - required: 'True' - pred_genome_type: - required: 'True' - pred_genome_struc: - required: 'True' - detec_type: - required: 'True' - votu_class_appr: - comments: - - conditional mandatory - votu_seq_comp_appr: - comments: - - conditional mandatory - votu_db: - comments: - - conditional mandatory - host_pred_appr: - comments: - - conditional mandatory - host_pred_est_acc: - comments: - - conditional mandatory - url: - comments: - - conditional mandatory - sop: - comments: - - conditional mandatory - core: - description: Core package. Do not use this directly, this is used to build other - packages - slots: - - submitted_to_insdc - - investigation_type - - sample_name - - project_name - - experimental_factor - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - subspecf_gen_lin - - ploidy - - num_replicons - - extrachrom_elements - - estimated_size - - ref_biomaterial - - source_mat_id - - pathogenicity - - biotic_relationship - - specific_host - - host_spec_range - - health_disease_stat - - trophic_level - - propagation - - encoded_traits - - rel_to_oxygen - - isol_growth_condt - - samp_collect_device - - samp_mat_process - - size_frac - - samp_size - - source_uvig - - virus_enrich_appr - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - target_gene - - target_subfragment - - pcr_primers - - mid - - adapters - - pcr_cond - - seq_meth - - seq_quality_check - - chimera_check - - tax_ident - - assembly_qual - - assembly_name - - assembly_software - - annot - - number_contig - - feat_pred - - ref_db - - sim_search_meth - - tax_class - - x_16s_recover - - x_16s_recover_software - - trnas - - trna_ext_software - - compl_score - - compl_software - - compl_appr - - contam_score - - contam_screen_input - - contam_screen_param - - decontam_software - - sort_tech - - single_cell_lysis_appr - - single_cell_lysis_prot - - wga_amp_appr - - wga_amp_kit - - bin_param - - bin_software - - reassembly_bin - - mag_cov_software - - vir_ident_software - - pred_genome_type - - pred_genome_struc - - detec_type - - votu_class_appr - - votu_seq_comp_appr - - votu_db - - host_pred_appr - - host_pred_est_acc - - url - - sop - air: - description: air - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - barometric_press - - carb_dioxide - - carb_monoxide - - chem_administration - - humidity - - methane - - misc_param - - organism_count - - oxygen - - oxy_stat_samp - - perturbation - - pollutants - - resp_part_matter - - samp_salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - solar_irradiance - - temp - - ventilation_rate - - ventilation_type - - volatile_org_comp - - wind_direction - - wind_speed - slot_usage: {} - built environment: - description: built environment - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - surf_material - - surf_air_cont - - rel_air_humidity - - abs_air_humidity - - surf_humidity - - air_temp - - surf_temp - - surf_moisture_ph - - build_occup_type - - surf_moisture - - dew_point - - carb_dioxide - - ventilation_type - - organism_count - - indoor_space - - indoor_surf - - filter_type - - heat_cool_type - - substructure_type - - building_setting - - light_type - - samp_sort_meth - - space_typ_state - - typ_occup_density - - occup_samp - - occup_density_samp - - address - - adj_room - - aero_struc - - amount_light - - arch_struc - - avg_occup - - avg_dew_point - - avg_temp - - bathroom_count - - bedroom_count - - built_struc_age - - built_struc_set - - built_struc_type - - ceil_area - - ceil_cond - - ceil_finish_mat - - ceil_water_mold - - ceil_struc - - ceil_texture - - ceil_thermal_mass - - ceil_type - - cool_syst_id - - date_last_rain - - build_docs - - door_size - - door_cond - - door_direct - - door_loc - - door_mat - - door_move - - door_water_mold - - door_type - - door_comp_type - - door_type_metal - - door_type_wood - - drawings - - elevator - - escalator - - exp_duct - - exp_pipe - - ext_door - - fireplace_type - - floor_age - - floor_area - - floor_cond - - floor_count - - floor_finish_mat - - floor_water_mold - - floor_struc - - floor_thermal_mass - - freq_clean - - freq_cook - - furniture - - gender_restroom - - hall_count - - handidness - - heat_deliv_loc - - heat_system_deliv_meth - - heat_system_id - - height_carper_fiber - - inside_lux - - int_wall_cond - - last_clean - - max_occup - - mech_struc - - number_plants - - number_pets - - number_resident - - occup_document - - ext_wall_orient - - ext_window_orient - - rel_humidity_out - - pres_animal - - quad_pos - - rel_samp_loc - - room_air_exch_rate - - room_architec_element - - room_condt - - room_count - - room_dim - - room_door_dist - - room_loc - - room_moist_damage_hist - - room_net_area - - room_occup - - room_samp_pos - - room_type - - room_vol - - room_window_count - - room_connected - - room_hallway - - room_door_share - - room_wall_share - - samp_weather - - samp_floor - - samp_room_id - - samp_time_out - - season - - season_use - - shading_device_cond - - shading_device_loc - - shading_device_mat - - shading_device_water_mold - - shading_device_type - - specific_humidity - - specific - - temp_out - - train_line - - train_stat_loc - - train_stop_loc - - vis_media - - wall_area - - wall_const_type - - wall_finish_mat - - wall_height - - wall_loc - - wall_water_mold - - wall_surf_treatment - - wall_texture - - wall_thermal_mass - - water_feat_size - - water_feat_type - - weekday - - window_size - - window_cond - - window_cover - - window_horiz_pos - - window_loc - - window_mat - - window_open_freq - - window_water_mold - - window_status - - window_type - - window_vert_pos - slot_usage: {} - host-associated: - description: host-associated - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - ances_data - - biol_stat - - genetic_mod - - host_common_name - - samp_capt_status - - samp_dis_stage - - host_taxid - - host_subject_id - - host_age - - host_life_stage - - host_sex - - host_disease_stat - - chem_administration - - host_body_habitat - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_length - - host_diet - - host_last_meal - - host_growth_cond - - host_substrate - - host_family_relationship - - host_infra_specific_name - - host_infra_specific_rank - - host_genotype - - host_phenotype - - host_body_temp - - host_dry_mass - - host_blood_press_diast - - host_blood_press_syst - - host_color - - host_shape - - gravidity - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_dur - - samp_store_loc - - misc_param - slot_usage: {} - human-associated: - description: human-associated - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_family_relationship - - host_genotype - - host_phenotype - - host_body_temp - - smoker - - host_hiv_stat - - drug_usage - - host_body_mass_index - - diet_last_six_month - - weight_loss_3_month - - ihmc_ethnicity - - host_occupation - - pet_farm_animal - - travel_out_six_month - - twin_sibling - - medic_hist_perform - - study_complt_stat - - pulmonary_disord - - nose_throat_disord - - blood_blood_disord - - host_pulse - - gestation_state - - maternal_health_stat - - foetal_health_stat - - amniotic_fluid_color - - urogenit_tract_disor - - urine_collect_meth - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_dur - - samp_store_loc - - misc_param - slot_usage: {} - human-gut: - description: human-gut - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - gastrointest_disord - - liver_disord - - special_diet - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_family_relationship - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ihmc_ethnicity - - host_occupation - - medic_hist_perform - - host_pulse - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_store_temp - - samp_vol_we_dna_ext - - samp_store_dur - - samp_store_loc - - misc_param - slot_usage: {} - human-oral: - description: human-oral - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - nose_mouth_teeth_throat_disord - - time_last_toothbrush - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_family_relationship - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ihmc_ethnicity - - host_occupation - - medic_hist_perform - - host_pulse - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_dur - - samp_store_loc - - misc_param - slot_usage: {} - human-skin: - description: human-skin - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - dermatology_disord - - time_since_last_wash - - dominant_hand - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_family_relationship - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ihmc_ethnicity - - host_occupation - - medic_hist_perform - - host_pulse - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_dur - - samp_store_loc - - misc_param - slot_usage: {} - human-vaginal: - description: human-vaginal - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - menarche - - sexual_act - - pregnancy - - douche - - birth_control - - menopause - - hrt - - hysterectomy - - gynecologic_disord - - urogenit_disord - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_family_relationship - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ihmc_ethnicity - - host_occupation - - medic_hist_perform - - host_pulse - - perturbation - - samp_salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_loc - - samp_store_dur - - misc_param - slot_usage: {} - hydrocarbon resources-cores: - description: hydrocarbon resources-cores - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - hcr - - hc_produced - - basin - - field - - reservoir - - hcr_temp - - tvdss_of_hcr_temp - - hcr_pressure - - tvdss_of_hcr_pressure - - permeability - - porosity - - lithology - - depos_env - - hcr_geol_age - - owc_tvdss - - hcr_fw_salinity - - sulfate_fw - - vfa_fw - - sr_kerog_type - - sr_lithology - - sr_dep_env - - sr_geol_age - - samp_well_name - - win - - samp_type - - samp_subtype - - temp - - pressure - - samp_tvdss - - samp_md - - oxy_stat_samp - - samp_transport_cond - - samp_store_temp - - samp_store_dur - - samp_store_loc - - samp_vol_we_dna_ext - - organism_count - - organism_count_qpcr_info - - ph - - samp_salinity - - alkalinity - - alkalinity_method - - sulfate - - sulfide - - tot_sulfur - - nitrate - - nitrite - - ammonium - - tot_nitro - - diss_iron - - sodium - - chloride - - potassium - - magnesium - - calcium - - tot_iron - - diss_org_carb - - diss_inorg_carb - - diss_inorg_phosp - - tot_phosp - - suspend_solids - - density - - diss_carb_dioxide - - diss_oxygen_fluid - - vfa - - benzene - - toluene - - ethylbenzene - - xylene - - api - - tan - - viscosity - - pour_point - - saturates_pc - - aromatics_pc - - resins_pc - - asphaltenes_pc - - misc_param - - additional_info - slot_usage: {} - hydrocarbon resources-fluids_swabs: - description: hydrocarbon resources-fluids/swabs - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - hcr - - hc_produced - - basin - - field - - reservoir - - hcr_temp - - tvdss_of_hcr_temp - - hcr_pressure - - tvdss_of_hcr_pressure - - lithology - - depos_env - - hcr_geol_age - - hcr_fw_salinity - - sulfate_fw - - vfa_fw - - prod_start_date - - prod_rate - - water_production_rate - - water_cut - - iwf - - add_recov_method - - iw_bt_date_well - - biocide - - biocide_admin_method - - chem_treatment - - chem_treatment_method - - samp_loc_corr_rate - - samp_well_name - - win - - samp_type - - samp_subtype - - samp_collection_point - - temp - - pressure - - oxy_stat_samp - - samp_preserv - - samp_transport_cond - - samp_store_temp - - samp_store_dur - - samp_store_loc - - samp_vol_we_dna_ext - - organism_count - - organism_count_qpcr_info - - ph - - samp_salinity - - alkalinity - - alkalinity_method - - sulfate - - sulfide - - tot_sulfur - - nitrate - - nitrite - - ammonium - - tot_nitro - - diss_iron - - sodium - - chloride - - potassium - - magnesium - - calcium - - tot_iron - - diss_org_carb - - diss_inorg_carb - - diss_inorg_phosp - - tot_phosp - - suspend_solids - - density - - diss_carb_dioxide - - diss_oxygen_fluid - - vfa - - benzene - - toluene - - ethylbenzene - - xylene - - api - - tan - - viscosity - - pour_point - - saturates_pc - - aromatics_pc - - resins_pc - - asphaltenes_pc - - misc_param - - additional_info - slot_usage: {} - microbial mat_biofilm: - description: microbial mat/biofilm - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - alkalinity - - alkyl_diethers - - aminopept_act - - ammonium - - bacteria_carb_prod - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - glucosidase_act - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - methane - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - part_org_carb - - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - potassium - - pressure - - redox_potential - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - silicate - - sodium - - sulfate - - sulfide - - temp - - tot_carb - - tot_nitro_content - - tot_org_carb - - turbidity - - water_content - slot_usage: {} - miscellaneous natural or artificial environment: - description: miscellaneous natural or artificial environment - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - alkalinity - - ammonium - - biomass - - bromide - - calcium - - chem_administration - - chloride - - chlorophyll - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_nitro - - diss_oxygen - - misc_param - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - perturbation - - phosphate - - phosplipid_fatt_acid - - potassium - - pressure - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - silicate - - sodium - - sulfate - - sulfide - - temp - - water_current - slot_usage: {} - plant-associated: - description: plant-associated - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - air_temp_regm - - ances_data - - antibiotic_regm - - biol_stat - - biotic_regm - - chem_administration - - chem_mutagen - - climate_environment - - cult_root_med - - fertilizer_regm - - fungicide_regm - - gaseous_environment - - genetic_mod - - gravity - - growth_facil - - growth_habit - - growth_hormone_regm - - herbicide_regm - - host_age - - host_common_name - - host_disease_stat - - host_dry_mass - - host_genotype - - host_height - - host_infra_specific_name - - host_infra_specific_rank - - host_length - - host_life_stage - - host_phenotype - - host_taxid - - host_tot_mass - - host_wet_mass - - humidity_regm - - light_regm - - mechanical_damage - - mineral_nutr_regm - - misc_param - - non_mineral_nutr_regm - - organism_count - - oxy_stat_samp - - ph_regm - - perturbation - - pesticide_regm - - plant_growth_med - - plant_product - - plant_sex - - plant_struc - - radiation_regm - - rainfall_regm - - root_cond - - root_med_carbon - - root_med_macronutr - - root_med_micronutr - - root_med_suppl - - root_med_ph - - root_med_regl - - root_med_solid - - salt_regm - - samp_capt_status - - samp_dis_stage - - samp_salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - season_environment - - standing_water_regm - - temp - - tiss_cult_growth_med - - water_temp_regm - - watering_regm - slot_usage: {} - sediment: - description: sediment - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - alkalinity - - alkyl_diethers - - aminopept_act - - ammonium - - bacteria_carb_prod - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - glucosidase_act - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - methane - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - particle_class - - part_org_carb - - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - porosity - - potassium - - pressure - - redox_potential - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - sediment_type - - silicate - - sodium - - sulfate - - sulfide - - temp - - tidal_stage - - tot_carb - - tot_depth_water_col - - tot_nitro_content - - tot_org_carb - - turbidity - - water_content - slot_usage: {} - soil: - description: soil - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - cur_land_use - - cur_vegetation - - cur_vegetation_meth - - previous_land_use - - previous_land_use_meth - - crop_rotation - - agrochem_addition - - tillage - - fire - - flooding - - extreme_event - - horizon - - horizon_meth - - sieving - - water_content - - water_content_soil_meth - - samp_vol_we_dna_ext - - pool_dna_extracts - - store_cond - - link_climate_info - - annual_temp - - season_temp - - annual_precpt - - season_precpt - - link_class_info - - fao_class - - local_class - - local_class_meth - - soil_type - - soil_type_meth - - slope_gradient - - slope_aspect - - profile_position - - drainage_class - - texture - - texture_meth - - ph - - ph_meth - - tot_org_carb - - tot_org_c_meth - - tot_nitro_content - - tot_nitro_content_meth - - microbial_biomass - - microbial_biomass_meth - - link_addit_analys - - extreme_salinity - - salinity_meth - - heavy_metals - - heavy_metals_meth - - al_sat - - al_sat_meth - - misc_param - slot_usage: {} - wastewater_sludge: - description: wastewater/sludge - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - alkalinity - - biochem_oxygen_dem - - chem_administration - - chem_oxygen_dem - - efficiency_percent - - emulsions - - gaseous_substances - - indust_eff_percent - - inorg_particles - - misc_param - - nitrate - - org_particles - - organism_count - - oxy_stat_samp - - ph - - perturbation - - phosphate - - pre_treatment - - primary_treatment - - reactor_type - - samp_salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - secondary_treatment - - sewage_type - - sludge_retent_time - - sodium - - soluble_inorg_mat - - soluble_org_mat - - suspend_solids - - temp - - tertiary_treatment - - tot_nitro - - tot_phosphate - - wastewater_type - slot_usage: {} - water: - description: water - mappings: [] - slots: - - lat_lon - - depth - - alt - - elev - - geo_loc_name - - collection_date - - env_broad_scale - - env_local_scale - - env_medium - - alkalinity - - alkalinity_method - - alkyl_diethers - - aminopept_act - - ammonium - - atmospheric_data - - bacteria_carb_prod - - bac_prod - - bac_resp - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - conduc - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_inorg_nitro - - diss_inorg_phosp - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - down_par - - fluor - - glucosidase_act - - light_intensity - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - part_org_carb - - part_org_nitro - - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - photon_flux - - potassium - - pressure - - primary_prod - - redox_potential - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - silicate - - size_frac_low - - size_frac_up - - sodium - - soluble_react_phosp - - sulfate - - sulfide - - suspend_part_matter - - temp - - tidal_stage - - tot_depth_water_col - - tot_diss_nitro - - tot_inorg_nitro - - tot_nitro - - tot_part_carb - - tot_phosp - - turbidity - - water_current - slot_usage: {} - air MIGS eukaryote: - is_a: air - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package air' - air MIGS bacteria: - is_a: air - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package air' - air MIGS plant: - is_a: air - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package air' - air MIGS virus: - is_a: air - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package air' - air MIGS org: - is_a: air - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package air' - air ME: - is_a: air - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package air - air MIMARKS specimen: - is_a: air - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package air' - air MIMARKS survey: - is_a: air - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package air' - air MISAG: - is_a: air - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package air - air MIMAG: - is_a: air - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package air - air MIUVIG: - is_a: air - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package air - built environment MIGS eukaryote: - is_a: built environment - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package built environment' - built environment MIGS bacteria: - is_a: built environment - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package built environment' - built environment MIGS plant: - is_a: built environment - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package built environment' - built environment MIGS virus: - is_a: built environment - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package built environment' - built environment MIGS org: - is_a: built environment - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package built environment' - built environment ME: - is_a: built environment - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package built environment - built environment MIMARKS specimen: - is_a: built environment - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package built environment' - built environment MIMARKS survey: - is_a: built environment - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package built environment' - built environment MISAG: - is_a: built environment - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package built environment - built environment MIMAG: - is_a: built environment - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package built environment - built environment MIUVIG: - is_a: built environment - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package built environment - host-associated MIGS eukaryote: - is_a: host-associated - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package host-associated' - host-associated MIGS bacteria: - is_a: host-associated - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package host-associated' - host-associated MIGS plant: - is_a: host-associated - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package host-associated' - host-associated MIGS virus: - is_a: host-associated - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package host-associated' - host-associated MIGS org: - is_a: host-associated - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package host-associated' - host-associated ME: - is_a: host-associated - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package host-associated - host-associated MIMARKS specimen: - is_a: host-associated - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package host-associated' - host-associated MIMARKS survey: - is_a: host-associated - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package host-associated' - host-associated MISAG: - is_a: host-associated - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package host-associated - host-associated MIMAG: - is_a: host-associated - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package host-associated - host-associated MIUVIG: - is_a: host-associated - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package host-associated - human-associated MIGS eukaryote: - is_a: human-associated - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package human-associated' - human-associated MIGS bacteria: - is_a: human-associated - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-associated' - human-associated MIGS plant: - is_a: human-associated - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package human-associated' - human-associated MIGS virus: - is_a: human-associated - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-associated' - human-associated MIGS org: - is_a: human-associated - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package human-associated' - human-associated ME: - is_a: human-associated - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package human-associated - human-associated MIMARKS specimen: - is_a: human-associated - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package human-associated' - human-associated MIMARKS survey: - is_a: human-associated - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package human-associated' - human-associated MISAG: - is_a: human-associated - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package human-associated - human-associated MIMAG: - is_a: human-associated - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package human-associated - human-associated MIUVIG: - is_a: human-associated - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package human-associated - human-gut MIGS eukaryote: - is_a: human-gut - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package human-gut' - human-gut MIGS bacteria: - is_a: human-gut - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-gut' - human-gut MIGS plant: - is_a: human-gut - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package human-gut' - human-gut MIGS virus: - is_a: human-gut - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-gut' - human-gut MIGS org: - is_a: human-gut - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package human-gut' - human-gut ME: - is_a: human-gut - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package human-gut - human-gut MIMARKS specimen: - is_a: human-gut - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package human-gut' - human-gut MIMARKS survey: - is_a: human-gut - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package human-gut' - human-gut MISAG: - is_a: human-gut - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package human-gut - human-gut MIMAG: - is_a: human-gut - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package human-gut - human-gut MIUVIG: - is_a: human-gut - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package human-gut - human-oral MIGS eukaryote: - is_a: human-oral - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package human-oral' - human-oral MIGS bacteria: - is_a: human-oral - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-oral' - human-oral MIGS plant: - is_a: human-oral - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package human-oral' - human-oral MIGS virus: - is_a: human-oral - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-oral' - human-oral MIGS org: - is_a: human-oral - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package human-oral' - human-oral ME: - is_a: human-oral - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package human-oral - human-oral MIMARKS specimen: - is_a: human-oral - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package human-oral' - human-oral MIMARKS survey: - is_a: human-oral - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package human-oral' - human-oral MISAG: - is_a: human-oral - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package human-oral - human-oral MIMAG: - is_a: human-oral - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package human-oral - human-oral MIUVIG: - is_a: human-oral - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package human-oral - human-skin MIGS eukaryote: - is_a: human-skin - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package human-skin' - human-skin MIGS bacteria: - is_a: human-skin - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-skin' - human-skin MIGS plant: - is_a: human-skin - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package human-skin' - human-skin MIGS virus: - is_a: human-skin - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-skin' - human-skin MIGS org: - is_a: human-skin - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package human-skin' - human-skin ME: - is_a: human-skin - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package human-skin - human-skin MIMARKS specimen: - is_a: human-skin - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package human-skin' - human-skin MIMARKS survey: - is_a: human-skin - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package human-skin' - human-skin MISAG: - is_a: human-skin - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package human-skin - human-skin MIMAG: - is_a: human-skin - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package human-skin - human-skin MIUVIG: - is_a: human-skin - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package human-skin - human-vaginal MIGS eukaryote: - is_a: human-vaginal - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package human-vaginal' - human-vaginal MIGS bacteria: - is_a: human-vaginal - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-vaginal' - human-vaginal MIGS plant: - is_a: human-vaginal - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package human-vaginal' - human-vaginal MIGS virus: - is_a: human-vaginal - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package human-vaginal' - human-vaginal MIGS org: - is_a: human-vaginal - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package human-vaginal' - human-vaginal ME: - is_a: human-vaginal - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package human-vaginal - human-vaginal MIMARKS specimen: - is_a: human-vaginal - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package human-vaginal' - human-vaginal MIMARKS survey: - is_a: human-vaginal - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package human-vaginal' - human-vaginal MISAG: - is_a: human-vaginal - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package human-vaginal - human-vaginal MIMAG: - is_a: human-vaginal - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package human-vaginal - human-vaginal MIUVIG: - is_a: human-vaginal - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package human-vaginal - hydrocarbon resources-cores MIGS eukaryote: - is_a: hydrocarbon resources-cores - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MIGS bacteria: - is_a: hydrocarbon resources-cores - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MIGS plant: - is_a: hydrocarbon resources-cores - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MIGS virus: - is_a: hydrocarbon resources-cores - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MIGS org: - is_a: hydrocarbon resources-cores - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores ME: - is_a: hydrocarbon resources-cores - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package hydrocarbon resources-cores - hydrocarbon resources-cores MIMARKS specimen: - is_a: hydrocarbon resources-cores - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MIMARKS survey: - is_a: hydrocarbon resources-cores - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package hydrocarbon resources-cores' - hydrocarbon resources-cores MISAG: - is_a: hydrocarbon resources-cores - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package hydrocarbon resources-cores - hydrocarbon resources-cores MIMAG: - is_a: hydrocarbon resources-cores - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package hydrocarbon resources-cores - hydrocarbon resources-cores MIUVIG: - is_a: hydrocarbon resources-cores - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package hydrocarbon resources-cores - hydrocarbon resources-fluids_swabs MIGS eukaryote: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MIGS bacteria: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MIGS plant: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MIGS virus: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MIGS org: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs ME: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package hydrocarbon resources-fluids_swabs - hydrocarbon resources-fluids_swabs MIMARKS specimen: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MIMARKS survey: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package hydrocarbon resources-fluids_swabs' - hydrocarbon resources-fluids_swabs MISAG: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package hydrocarbon resources-fluids_swabs - hydrocarbon resources-fluids_swabs MIMAG: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package hydrocarbon resources-fluids_swabs - hydrocarbon resources-fluids_swabs MIUVIG: - is_a: hydrocarbon resources-fluids_swabs - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package hydrocarbon resources-fluids_swabs - microbial mat_biofilm MIGS eukaryote: - is_a: microbial mat_biofilm - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package microbial mat_biofilm' - microbial mat_biofilm MIGS bacteria: - is_a: microbial mat_biofilm - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package microbial mat_biofilm' - microbial mat_biofilm MIGS plant: - is_a: microbial mat_biofilm - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package microbial mat_biofilm' - microbial mat_biofilm MIGS virus: - is_a: microbial mat_biofilm - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package microbial mat_biofilm' - microbial mat_biofilm MIGS org: - is_a: microbial mat_biofilm - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package microbial mat_biofilm' - microbial mat_biofilm ME: - is_a: microbial mat_biofilm - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package microbial mat_biofilm - microbial mat_biofilm MIMARKS specimen: - is_a: microbial mat_biofilm - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package microbial mat_biofilm' - microbial mat_biofilm MIMARKS survey: - is_a: microbial mat_biofilm - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package microbial mat_biofilm' - microbial mat_biofilm MISAG: - is_a: microbial mat_biofilm - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package microbial mat_biofilm - microbial mat_biofilm MIMAG: - is_a: microbial mat_biofilm - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package microbial mat_biofilm - microbial mat_biofilm MIUVIG: - is_a: microbial mat_biofilm - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package microbial mat_biofilm - miscellaneous natural or artificial environment MIGS eukaryote: - is_a: miscellaneous natural or artificial environment - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package miscellaneous natural or artificial environment' - miscellaneous natural or artificial environment MIGS bacteria: - is_a: miscellaneous natural or artificial environment - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package miscellaneous natural or - artificial environment' - miscellaneous natural or artificial environment MIGS plant: - is_a: miscellaneous natural or artificial environment - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package miscellaneous natural or artificial environment' - miscellaneous natural or artificial environment MIGS virus: - is_a: miscellaneous natural or artificial environment - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package miscellaneous natural or - artificial environment' - miscellaneous natural or artificial environment MIGS org: - is_a: miscellaneous natural or artificial environment - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package miscellaneous natural or artificial environment' - miscellaneous natural or artificial environment ME: - is_a: miscellaneous natural or artificial environment - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package miscellaneous natural or artificial environment - miscellaneous natural or artificial environment MIMARKS specimen: - is_a: miscellaneous natural or artificial environment - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package miscellaneous natural or artificial environment' - miscellaneous natural or artificial environment MIMARKS survey: - is_a: miscellaneous natural or artificial environment - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package miscellaneous natural or artificial environment' - miscellaneous natural or artificial environment MISAG: - is_a: miscellaneous natural or artificial environment - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package miscellaneous natural or artificial environment - miscellaneous natural or artificial environment MIMAG: - is_a: miscellaneous natural or artificial environment - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package miscellaneous natural or artificial environment - miscellaneous natural or artificial environment MIUVIG: - is_a: miscellaneous natural or artificial environment - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package miscellaneous natural or artificial - environment - plant-associated MIGS eukaryote: - is_a: plant-associated - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package plant-associated' - plant-associated MIGS bacteria: - is_a: plant-associated - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package plant-associated' - plant-associated MIGS plant: - is_a: plant-associated - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package plant-associated' - plant-associated MIGS virus: - is_a: plant-associated - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package plant-associated' - plant-associated MIGS org: - is_a: plant-associated - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package plant-associated' - plant-associated ME: - is_a: plant-associated - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package plant-associated - plant-associated MIMARKS specimen: - is_a: plant-associated - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package plant-associated' - plant-associated MIMARKS survey: - is_a: plant-associated - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package plant-associated' - plant-associated MISAG: - is_a: plant-associated - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package plant-associated - plant-associated MIMAG: - is_a: plant-associated - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package plant-associated - plant-associated MIUVIG: - is_a: plant-associated - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package plant-associated - sediment MIGS eukaryote: - is_a: sediment - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package sediment' - sediment MIGS bacteria: - is_a: sediment - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package sediment' - sediment MIGS plant: - is_a: sediment - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package sediment' - sediment MIGS virus: - is_a: sediment - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package sediment' - sediment MIGS org: - is_a: sediment - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package sediment' - sediment ME: - is_a: sediment - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package sediment - sediment MIMARKS specimen: - is_a: sediment - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package sediment' - sediment MIMARKS survey: - is_a: sediment - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package sediment' - sediment MISAG: - is_a: sediment - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package sediment - sediment MIMAG: - is_a: sediment - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package sediment - sediment MIUVIG: - is_a: sediment - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package sediment - soil MIGS eukaryote: - is_a: soil - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package soil' - soil MIGS bacteria: - is_a: soil - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package soil' - soil MIGS plant: - is_a: soil - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package soil' - soil MIGS virus: - is_a: soil - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package soil' - soil MIGS org: - is_a: soil - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package soil' - soil ME: - is_a: soil - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package soil - soil MIMARKS specimen: - is_a: soil - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package soil' - soil MIMARKS survey: - is_a: soil - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package soil' - soil MISAG: - is_a: soil - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package soil - soil MIMAG: - is_a: soil - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package soil - soil MIUVIG: - is_a: soil - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package soil - wastewater_sludge MIGS eukaryote: - is_a: wastewater_sludge - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package wastewater_sludge' - wastewater_sludge MIGS bacteria: - is_a: wastewater_sludge - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package wastewater_sludge' - wastewater_sludge MIGS plant: - is_a: wastewater_sludge - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package wastewater_sludge' - wastewater_sludge MIGS virus: - is_a: wastewater_sludge - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package wastewater_sludge' - wastewater_sludge MIGS org: - is_a: wastewater_sludge - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package wastewater_sludge' - wastewater_sludge ME: - is_a: wastewater_sludge - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package wastewater_sludge - wastewater_sludge MIMARKS specimen: - is_a: wastewater_sludge - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package wastewater_sludge' - wastewater_sludge MIMARKS survey: - is_a: wastewater_sludge - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package wastewater_sludge' - wastewater_sludge MISAG: - is_a: wastewater_sludge - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package wastewater_sludge - wastewater_sludge MIMAG: - is_a: wastewater_sludge - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package wastewater_sludge - wastewater_sludge MIUVIG: - is_a: wastewater_sludge - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package wastewater_sludge - water MIGS eukaryote: - is_a: water - mixins: - - MIGS eukaryote - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - eukaryote with environmental package water' - water MIGS bacteria: - is_a: water - mixins: - - MIGS bacteria - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package water' - water MIGS plant: - is_a: water - mixins: - - MIGS plant - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - plant with environmental package water' - water MIGS virus: - is_a: water - mixins: - - MIGS virus - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - cultured bacteria/archaea with environmental package water' - water MIGS org: - is_a: water - mixins: - - MIGS org - description: 'Combinatorial checklist Minimal Information about a Genome Sequence: - org with environmental package water' - water ME: - is_a: water - mixins: - - ME - description: Combinatorial checklist Metagenome or Environmental with environmental - package water - water MIMARKS specimen: - is_a: water - mixins: - - MIMARKS specimen - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - specimen with environmental package water' - water MIMARKS survey: - is_a: water - mixins: - - MIMARKS survey - description: 'Combinatorial checklist Minimal Information about a Marker Specimen: - survey with environmental package water' - water MISAG: - is_a: water - mixins: - - MISAG - description: Combinatorial checklist Minimum Information About a Single Amplified - Genome with environmental package water - water MIMAG: - is_a: water - mixins: - - MIMAG - description: Combinatorial checklist Minimum Information About a Metagenome-Assembled - Genome with environmental package water - water MIUVIG: - is_a: water - mixins: - - MIUVIG - description: Combinatorial checklist Minimum Information About an Uncultivated - Virus Genome with environmental package water +slots: {} +classes: {} subsets: {} -enums: - investigation_type_enum: - permissible_values: - eukaryote: {} - bacteria_archaea: {} - plasmid: {} - virus: {} - organelle: {} - metagenome: {} - metatranscriptome: {} - mimarks-survey: {} - mimarks-specimen: {} - misag: {} - mimag: {} - miuvig: {} - env_package_enum: - permissible_values: - air: {} - built environment: {} - host-associated: {} - human-associated: {} - human-skin: {} - human-oral: {} - human-gut: {} - human-vaginal: {} - hydrocarbon resources-cores: {} - hydrocarbon resources-fluids/swabs: {} - microbial mat/biofilm: {} - misc environment: {} - plant-associated: {} - sediment: {} - soil: {} - wastewater/sludge: {} - water: {} - biotic_relationship_enum: - permissible_values: - free living: {} - parasitism: {} - commensalism: {} - symbiotic: {} - mutualism: {} - health_disease_stat_enum: - permissible_values: - healthy: {} - diseased: {} - dead: {} - disease-free: {} - undetermined: {} - recovering: {} - resolving: {} - pre-existing condition: {} - pathological: {} - life threatening: {} - congenital: {} - trophic_level_enum: - permissible_values: - autotroph: {} - carboxydotroph: {} - chemoautotroph: {} - chemoheterotroph: {} - chemolithoautotroph: {} - chemolithotroph: {} - chemoorganoheterotroph: {} - chemoorganotroph: {} - chemosynthetic: {} - chemotroph: {} - copiotroph: {} - diazotroph: {} - facultative: {} - heterotroph: {} - lithoautotroph: {} - lithoheterotroph: {} - lithotroph: {} - methanotroph: {} - methylotroph: {} - mixotroph: {} - obligate: {} - chemoautolithotroph: {} - oligotroph: {} - organoheterotroph: {} - organotroph: {} - photoautotroph: {} - photoheterotroph: {} - photolithoautotroph: {} - photolithotroph: {} - photosynthetic: {} - phototroph: {} - rel_to_oxygen_enum: - permissible_values: - aerobe: {} - anaerobe: {} - facultative: {} - microaerophilic: {} - microanaerobe: {} - obligate aerobe: {} - obligate anaerobe: {} - source_uvig_enum: - permissible_values: - metagenome (not viral targeted): {} - viral fraction metagenome (virome): {} - sequence-targeted metagenome: {} - metatranscriptome (not viral targeted): {} - viral fraction RNA metagenome (RNA virome): {} - sequence-targeted RNA metagenome: {} - microbial single amplified genome (SAG): {} - viral single amplified genome (vSAG): {} - isolate microbial genome: {} - other: {} - virus_enrich_appr_enum: - permissible_values: - filtration: {} - ultrafiltration: {} - centrifugation: {} - ultracentrifugation: {} - PEG Precipitation: {} - FeCl Precipitation: {} - CsCl density gradient: {} - DNAse: {} - RNAse: {} - targeted sequence capture: {} - other: {} - none: {} - lib_layout_enum: - permissible_values: - paired: {} - single: {} - vector: {} - other: {} - seq_meth_enum: - permissible_values: - 454 GS: {} - 454 GS 20: {} - 454 GS FLX: {} - 454 GS FLX+: {} - 454 GS FLX Titanium: {} - 454 GS Junior: {} - AB 310 Genetic Analyzer: {} - AB 3130 Genetic Analyzer: {} - AB 3130xL Genetic Analyzer: {} - AB 3500 Genetic Analyzer: {} - AB 3500xL Genetic Analyzer: {} - AB 3730 Genetic Analyzer: {} - AB 3730xL Genetic Analyzer: {} - AB 5500 Genetic Analyzer: {} - AB 5500xl Genetic Analyzer: {} - AB 5500xl-W Genetic Analysis System: {} - AB SOLiD System: {} - AB SOLiD System 2.0: {} - AB SOLiD System 3.0: {} - AB SOLiD 3 Plus System: {} - AB SOLiD 4 System: {} - AB SOLiD 4hq System: {} - AB SOLiD PI System: {} - BGISEQ-500: {} - GridION: {} - Illumina Genome Analyzer: {} - Illumina Genome Analyzer II: {} - Illumina Genome Analyzer IIx: {} - Illumina HiSeq 1000: {} - Illumina HiSeq 1500: {} - Illumina HiSeq 2000: {} - Illumina HiSeq 2500: {} - Illumina HiSeq 3000: {} - Illumina HiSeq 4000: {} - Illumina HiScanSQ: {} - Illumina MiSeq: {} - Illumina HiSeq X Five: {} - Illumina HiSeq X Ten: {} - Illumina NextSeq 500: {} - Illumina NextSeq 550: {} - Ion Torrent PGM: {} - Ion Torrent Proton: {} - Ion Torrent S5: {} - Ion Torrent S5 XL: {} - MinION: {} - PacBio RS: {} - PacBio RS II: {} - PromethION: {} - Sequel: {} - tax_ident_enum: - permissible_values: - 16S rRNA gene: {} - multi-marker approach: {} - other: {} - assembly_qual_enum: - permissible_values: - Finished genome: {} - High-quality draft genome: {} - Medium-quality draft genome: {} - Low-quality draft genome: {} - Genome fragment(s): {} - compl_score_enum: - permissible_values: - high: {} - med: {} - low;{percentage}: {} - compl_appr_enum: - permissible_values: - marker gene: {} - reference based: {} - other: {} - contam_screen_param_enum: - permissible_values: - ref db: {} - kmer: {} - coverage: {} - combination;{text: {} - integer}: {} - decontam_software_enum: - permissible_values: - checkm/refinem: {} - anvi'o: {} - prodege: {} - bbtools:decontaminate.sh: {} - acdc: {} - combination: {} - sort_tech_enum: - permissible_values: - flow cytometric cell sorting: {} - microfluidics: {} - lazer-tweezing: {} - optical manipulation: {} - micromanipulation: {} - other: {} - single_cell_lysis_appr_enum: - permissible_values: - chemical: {} - enzymatic: {} - physical: {} - combination: {} - bin_param_enum: - permissible_values: - homology search: {} - kmer: {} - coverage: {} - codon usage: {} - combination: {} - bin_software_enum: - permissible_values: - metabat: {} - maxbin: {} - concoct: {} - groupm: {} - esom: {} - metawatt: {} - combination: {} - other: {} - mag_cov_software_enum: - permissible_values: - bwa: {} - bbmap: {} - bowtie: {} - other: {} - pred_genome_type_enum: - permissible_values: - DNA: {} - dsDNA: {} - ssDNA: {} - RNA: {} - dsRNA: {} - ssRNA: {} - ssRNA (+): {} - ssRNA (-): {} - mixed: {} - uncharacterized: {} - pred_genome_struc_enum: - permissible_values: - segmented: {} - non-segmented: {} - undetermined: {} - host_pred_appr_enum: - permissible_values: - provirus: {} - host sequence similarity: {} - CRISPR spacer match: {} - kmer similarity: {} - co-occurrence: {} - combination: {} - other: {} - organism_count_enum: - permissible_values: - ATP: {} - MPN: {} - other: {} - oxy_stat_samp_enum: - permissible_values: - aerobic: {} - anaerobic: {} - other: {} - surf_material_enum: - permissible_values: - adobe: {} - carpet: {} - cinder blocks: {} - concrete: {} - hay bales: {} - glass: {} - metal: {} - paint: {} - plastic: {} - stainless steel: {} - stone: {} - stucco: {} - tile: {} - vinyl: {} - wood: {} - surf_air_cont_enum: - permissible_values: - dust: {} - organic matter: {} - particulate matter: {} - volatile organic compounds: {} - biological contaminants: {} - radon: {} - nutrients: {} - biocides: {} - build_occup_type_enum: - permissible_values: - office: {} - market: {} - restaurant: {} - residence: {} - school: {} - residential: {} - commercial: {} - low rise: {} - high rise: {} - wood framed: {} - health care: {} - airport: {} - sports complex: {} - indoor_space_enum: - permissible_values: - bedroom: {} - office: {} - bathroom: {} - foyer: {} - kitchen: {} - locker room: {} - hallway: {} - elevator: {} - indoor_surf_enum: - permissible_values: - cabinet: {} - ceiling: {} - counter top: {} - door: {} - shelving: {} - vent cover: {} - window: {} - wall: {} - filter_type_enum: - permissible_values: - particulate air filter: {} - chemical air filter: {} - low-MERV pleated media: {} - HEPA: {} - electrostatic: {} - gas-phase or ultraviolet air treatments: {} - heat_cool_type_enum: - permissible_values: - radiant system: {} - heat pump: {} - forced air system: {} - steam forced heat: {} - wood stove: {} - substructure_type_enum: - permissible_values: - crawlspace: {} - slab on grade: {} - basement: {} - building_setting_enum: - permissible_values: - urban: {} - suburban: {} - exurban: {} - rural: {} - light_type_enum: - permissible_values: - natural light: {} - electric light: {} - desk lamp: {} - flourescent lights: {} - none: {} - arch_struc_enum: - permissible_values: - building: {} - shed: {} - home: {} - ceil_cond_enum: - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - ceil_finish_mat_enum: - permissible_values: - drywall: {} - mineral fibre: {} - tiles: {} - PVC: {} - plasterboard: {} - metal: {} - fiberglass: {} - stucco: {} - mineral wool/calcium silicate: {} - wood: {} - ceil_texture_enum: - permissible_values: - crows feet: {} - crows-foot stomp: {} - double skip: {} - hawk and trowel: {} - knockdown: {} - popcorn: {} - orange peel: {} - rosebud stomp: {} - Santa-Fe texture: {} - skip trowel: {} - smooth: {} - stomp knockdown: {} - swirl: {} - ceil_type_enum: - permissible_values: - cathedral: {} - dropped: {} - concave: {} - barrel-shaped: {} - coffered: {} - cove: {} - stretched: {} - build_docs_enum: - permissible_values: - building information model: {} - commissioning report: {} - complaint logs: {} - contract administration: {} - cost estimate: {} - janitorial schedules or logs: {} - maintenance plans: {} - schedule: {} - sections: {} - shop drawings: {} - submittals: {} - ventilation system: {} - windows: {} - door_cond_enum: - permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - door_direct_enum: - permissible_values: - inward: {} - outward: {} - sideways: {} - door_loc_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - door_mat_enum: - permissible_values: - aluminum: {} - cellular PVC: {} - engineered plastic: {} - fiberboard: {} - fiberglass: {} - metal: {} - thermoplastic alloy: {} - vinyl: {} - wood: {} - wood/plastic composite: {} - door_move_enum: - permissible_values: - collapsible: {} - folding: {} - revolving: {} - rolling shutter: {} - sliding: {} - swinging: {} - door_type_enum: - permissible_values: - composite: {} - metal: {} - wooden: {} - door_comp_type_enum: - permissible_values: - metal covered: {} - revolving: {} - sliding: {} - telescopic: {} - door_type_metal_enum: - permissible_values: - collapsible: {} - corrugated steel: {} - hollow: {} - rolling shutters: {} - steel plate: {} - door_type_wood_enum: - permissible_values: - bettened and ledged: {} - battened: {} - ledged and braced: {} - ledged and framed: {} - ledged, braced and frame: {} - framed and paneled: {} - glashed or sash: {} - flush: {} - louvered: {} - wire gauged: {} - drawings_enum: - permissible_values: - operation: {} - as built: {} - construction: {} - bid: {} - design: {} - building navigation map: {} - diagram: {} - sketch: {} - floor_cond_enum: - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - floor_finish_mat_enum: - permissible_values: - tile: {} - wood strip or parquet: {} - carpet: {} - rug: {} - laminate wood: {} - lineoleum: {} - vinyl composition tile: {} - sheet vinyl: {} - stone: {} - bamboo: {} - cork: {} - terrazo: {} - concrete: {} - none;specify unfinished: {} - sealed: {} - clear finish: {} - paint: {} - floor_water_mold_enum: - permissible_values: - mold odor: {} - wet floor: {} - water stains: {} - wall discoloration: {} - floor discoloration: {} - ceiling discoloration: {} - peeling paint or wallpaper: {} - bulging walls: {} - condensation: {} - floor_struc_enum: - permissible_values: - balcony: {} - floating floor: {} - glass floor: {} - raised floor: {} - sprung floor: {} - wood-framed: {} - concrete: {} - furniture_enum: - permissible_values: - cabinet: {} - chair: {} - desks: {} - handidness_enum: - permissible_values: - ambidexterity: {} - left handedness: {} - mixed-handedness: {} - right handedness: {} - heat_deliv_loc_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - int_wall_cond_enum: - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - mech_struc_enum: - permissible_values: - subway: {} - coach: {} - carriage: {} - elevator: {} - escalator: {} - boat: {} - train: {} - car: {} - bus: {} - occup_document_enum: - permissible_values: - automated count: {} - estimate: {} - manual count: {} - videos: {} - ext_wall_orient_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - northeast: {} - southeast: {} - southwest: {} - northwest: {} - ext_window_orient_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - northeast: {} - southeast: {} - southwest: {} - northwest: {} - pres_animal_enum: - permissible_values: - cat: {} - dog: {} - rodent: {} - snake: {} - other;{integer}: {} - quad_pos_enum: - permissible_values: - North side: {} - West side: {} - South side: {} - East side: {} - rel_samp_loc_enum: - permissible_values: - edge of car: {} - center of car: {} - under a seat: {} - room_condt_enum: - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - visible signs of mold/mildew: {} - room_loc_enum: - permissible_values: - corner room: {} - interior room: {} - exterior wall: {} - room_samp_pos_enum: - permissible_values: - north corner: {} - south corner: {} - west corner: {} - east corner: {} - northeast corner: {} - northwest corner: {} - southeast corner: {} - southwest corner: {} - center: {} - room_type_enum: - permissible_values: - attic: {} - bathroom: {} - closet: {} - conference room: {} - elevator: {} - examining room: {} - hallway: {} - kitchen: {} - mail room: {} - private office: {} - open office: {} - stairwell: {} - ',restroom': {} - lobby: {} - vestibule: {} - mechanical or electrical room: {} - data center: {} - laboratory_wet: {} - laboratory_dry: {} - gymnasium: {} - natatorium: {} - auditorium: {} - lockers: {} - cafe: {} - warehouse: {} - room_connected_enum: - permissible_values: - attic: {} - bathroom: {} - closet: {} - conference room: {} - elevator: {} - examining room: {} - hallway: {} - kitchen: {} - mail room: {} - office: {} - stairwell: {} - samp_weather_enum: - permissible_values: - clear sky: {} - cloudy: {} - foggy: {} - hail: {} - rain: {} - snow: {} - sleet: {} - sunny: {} - windy: {} - samp_floor_enum: - permissible_values: - 1st floor: {} - 2nd floor: {} - basement: {} - lobby: {} - season_use_enum: - permissible_values: - Spring: {} - Summer: {} - Fall: {} - Winter: {} - shading_device_cond_enum: - permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - shading_device_type_enum: - permissible_values: - bahama shutters: {} - exterior roll blind: {} - gambrel awning: {} - hood awning: {} - porchroller awning: {} - sarasota shutters: {} - slatted aluminum: {} - solid aluminum awning: {} - sun screen: {} - tree: {} - trellis: {} - venetian awning: {} - specific_enum: - permissible_values: - operation: {} - as built: {} - construction: {} - bid: {} - design: {} - photos: {} - train_line_enum: - permissible_values: - red: {} - green: {} - orange: {} - train_stat_loc_enum: - permissible_values: - south station above ground: {} - south station underground: {} - south station amtrak: {} - forest hills: {} - riverside: {} - train_stop_loc_enum: - permissible_values: - end: {} - mid: {} - downtown: {} - vis_media_enum: - permissible_values: - photos: {} - videos: {} - commonly of the building: {} - site context (adjacent buildings, vegetation, terrain, streets): {} - interiors: {} - equipment: {} - 3D scans: {} - wall_const_type_enum: - permissible_values: - frame construction: {} - joisted masonry: {} - light noncombustible: {} - masonry noncombustible: {} - modified fire resistive: {} - fire resistive: {} - wall_finish_mat_enum: - permissible_values: - plaster: {} - gypsum plaster: {} - veneer plaster: {} - gypsum board: {} - tile: {} - terrazzo: {} - stone facing: {} - acoustical treatment: {} - wood: {} - metal: {} - masonry: {} - wall_loc_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - wall_surf_treatment_enum: - permissible_values: - painted: {} - wall paper: {} - no treatment: {} - paneling: {} - stucco: {} - fabric: {} - wall_texture_enum: - permissible_values: - crows feet: {} - crows-foot stomp: {} - ? '' - : {} - double skip: {} - hawk and trowel: {} - knockdown: {} - popcorn: {} - orange peel: {} - rosebud stomp: {} - Santa-Fe texture: {} - skip trowel: {} - smooth: {} - stomp knockdown: {} - swirl: {} - water_feat_type_enum: - permissible_values: - fountain: {} - pool: {} - standing feature: {} - stream: {} - waterfall: {} - weekday_enum: - permissible_values: - Monday: {} - Tuesday: {} - Wednesday: {} - Thursday: {} - Friday: {} - Saturday: {} - Sunday: {} - window_cond_enum: - permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - window_cover_enum: - permissible_values: - blinds: {} - curtains: {} - none: {} - window_horiz_pos_enum: - permissible_values: - left: {} - middle: {} - right: {} - window_loc_enum: - permissible_values: - north: {} - south: {} - east: {} - west: {} - window_mat_enum: - permissible_values: - clad: {} - fiberglass: {} - metal: {} - vinyl: {} - wood: {} - window_type_enum: - permissible_values: - single-hung sash window: {} - horizontal sash window: {} - fixed window: {} - window_vert_pos_enum: - permissible_values: - bottom: {} - middle: {} - top: {} - low: {} - high: {} - biol_stat_enum: - permissible_values: - wild: {} - natural: {} - semi-natural: {} - inbred line: {} - breeder's line: {} - hybrid: {} - clonal selection: {} - mutant: {} - samp_capt_status_enum: - permissible_values: - active surveillance in response to an outbreak: {} - active surveillance not initiated by an outbreak: {} - farm sample: {} - market sample: {} - other: {} - host_sex_enum: - permissible_values: - male: {} - female: {} - neuter: {} - hermaphrodite: {} - not determined: {} - drug_usage_enum: - permissible_values: - month: {} - week: {} - day: {} - hour: {} - study_complt_stat_enum: - permissible_values: - non-compliance: {} - lost to follow up: {} - other-specify: {} - special_diet_enum: - permissible_values: - low carb: {} - reduced calorie: {} - vegetarian: {} - other(to be specified): {} - dominant_hand_enum: - permissible_values: - left: {} - right: {} - ambidextrous: {} - hcr_enum: - permissible_values: - Oil Reservoir: {} - Gas Reservoir: {} - Oil Sand: {} - Coalbed: {} - Shale: {} - Tight Oil Reservoir: {} - Tight Gas Reservoir: {} - other: {} - hc_produced_enum: - permissible_values: - Oil: {} - Gas-Condensate: {} - Gas: {} - Bitumen: {} - Coalbed Methane: {} - other: {} - lithology_enum: - permissible_values: - Basement: {} - Chalk: {} - Chert: {} - Coal: {} - Conglomerate: {} - Diatomite: {} - Dolomite: {} - Limestone: {} - Sandstone: {} - Shale: {} - Siltstone: {} - Volcanic: {} - other: {} - depos_env_enum: - permissible_values: - Continental - Alluvial: {} - Continental - Aeolian: {} - Continental - Fluvial: {} - Continental - Lacustrine: {} - Transitional - Deltaic: {} - Transitional - Tidal: {} - Transitional - Lagoonal: {} - Transitional - Beach: {} - Transitional - Lake: {} - Marine - Shallow: {} - Marine - Deep: {} - Marine - Reef: {} - Other - Evaporite: {} - Other - Glacial: {} - Other - Volcanic: {} - other: {} - hcr_geol_age_enum: - permissible_values: - Archean: {} - Cambrian: {} - Carboniferous: {} - Cenozoic: {} - Cretaceous: {} - Devonian: {} - Jurassic: {} - Mesozoic: {} - Neogene: {} - Ordovician: {} - Paleogene: {} - Paleozoic: {} - Permian: {} - Precambrian: {} - Proterozoic: {} - Silurian: {} - Triassic: {} - other: {} - sr_kerog_type_enum: - permissible_values: - Type I: {} - Type II: {} - Type III: {} - Type IV: {} - other: {} - sr_lithology_enum: - permissible_values: - Clastic: {} - Carbonate: {} - Coal: {} - Biosilicieous: {} - other: {} - sr_dep_env_enum: - permissible_values: - Lacustine: {} - Fluvioldeltaic: {} - Fluviomarine: {} - Marine: {} - other: {} - sr_geol_age_enum: - permissible_values: - Archean: {} - Cambrian: {} - Carboniferous: {} - Cenozoic: {} - Cretaceous: {} - Devonian: {} - Jurassic: {} - Mesozoic: {} - Neogene: {} - Ordovician: {} - Paleogene: {} - Paleozoic: {} - Permian: {} - Precambrian: {} - Proterozoic: {} - Silurian: {} - Triassic: {} - other: {} - samp_type_enum: - permissible_values: - core: {} - rock trimmings: {} - drill cuttings: {} - piping section: {} - coupon: {} - pigging debris: {} - solid deposit: {} - produced fluid: {} - produced water: {} - injected water: {} - water from treatment plant: {} - fresh water: {} - sea water: {} - drilling fluid: {} - procedural blank: {} - positive control: {} - negative control: {} - other: {} - samp_subtype_enum: - permissible_values: - oil phase: {} - water phase: {} - biofilm: {} - not applicable: {} - other: {} - samp_md_enum: - permissible_values: - DF: {} - RT: {} - KB: {} - MSL: {} - other: {} - add_recov_method_enum: - permissible_values: - Water Injection: {} - Dump Flood: {} - Gas Injection: {} - Wag Immiscible Injection: {} - Polymer Addition: {} - Surfactant Addition: {} - Not Applicable: {} - other;{timestamp}: {} - samp_collection_point_enum: - permissible_values: - well: {} - test well: {} - drilling rig: {} - wellhead: {} - separator: {} - storage tank: {} - other: {} - growth_habit_enum: - permissible_values: - erect: {} - semi-erect: {} - spreading: {} - prostrate: {} - plant_growth_med_enum: - permissible_values: - other artificial liquid medium: {} - other artificial solid medium: {} - peat moss: {} - perlite: {} - pumice: {} - sand: {} - soil: {} - vermiculite: {} - water: {} - plant_sex_enum: - permissible_values: - Androdioecious: {} - Androecious: {} - Androgynous: {} - Androgynomonoecious: {} - Andromonoecious: {} - Bisexual: {} - Dichogamous: {} - Diclinous: {} - Dioecious: {} - Gynodioecious: {} - Gynoecious: {} - Gynomonoecious: {} - Hermaphroditic: {} - Imperfect: {} - Monoclinous: {} - Monoecious: {} - Perfect: {} - Polygamodioecious: {} - Polygamomonoecious: {} - Polygamous: {} - Protandrous: {} - Protogynous: {} - Subandroecious: {} - Subdioecious: {} - Subgynoecious: {} - Synoecious: {} - Trimonoecious: {} - Trioecious: {} - Unisexual: {} - sediment_type_enum: - permissible_values: - biogenous: {} - cosmogenous: {} - hydrogenous: {} - lithogenous: {} - tidal_stage_enum: - permissible_values: - low tide: {} - ebb tide: {} - flood tide: {} - high tide: {} - cur_land_use_enum: - permissible_values: - cities: {} - farmstead: {} - industrial areas: {} - roads/railroads: {} - rock: {} - sand: {} - gravel: {} - mudflats: {} - salt flats: {} - badlands: {} - permanent snow or ice: {} - saline seeps: {} - mines/quarries: {} - oil waste areas: {} - small grains: {} - row crops: {} - vegetable crops: {} - horticultural plants (e.g. tulips): {} - marshlands (grass,sedges,rushes): {} - tundra (mosses,lichens): {} - rangeland: {} - pastureland (grasslands used for livestock grazing): {} - hayland: {} - meadows (grasses,alfalfa,fescue,bromegrass,timothy): {} - shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus): {} - successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries): {} - shrub crops (blueberries,nursery ornamentals,filberts): {} - vine crops (grapes): {} - conifers (e.g. pine,spruce,fir,cypress): {} - hardwoods (e.g. oak,hickory,elm,aspen): {} - intermixed hardwood and conifers: {} - tropical (e.g. mangrove,palms): {} - rainforest (evergreen forest receiving >406 cm annual rainfall): {} - swamp (permanent or semi-permanent water body dominated by woody plants): {} - crop trees (nuts,fruit,christmas trees,nursery trees): {} - tillage_enum: - permissible_values: - drill: {} - cutting disc: {} - ridge till: {} - strip tillage: {} - zonal tillage: {} - chisel: {} - tined: {} - mouldboard: {} - disc plough: {} - horizon_enum: - permissible_values: - O horizon: {} - A horizon: {} - E horizon: {} - B horizon: {} - C horizon: {} - R layer: {} - Permafrost: {} - fao_class_enum: - permissible_values: - Acrisols: {} - Andosols: {} - Arenosols: {} - Cambisols: {} - Chernozems: {} - Ferralsols: {} - Fluvisols: {} - Gleysols: {} - Greyzems: {} - Gypsisols: {} - Histosols: {} - Kastanozems: {} - Lithosols: {} - Luvisols: {} - Nitosols: {} - Phaeozems: {} - Planosols: {} - Podzols: {} - Podzoluvisols: {} - Rankers: {} - Regosols: {} - Rendzinas: {} - Solonchaks: {} - Solonetz: {} - Vertisols: {} - Yermosols: {} - profile_position_enum: - permissible_values: - summit: {} - shoulder: {} - backslope: {} - footslope: {} - toeslope: {} - drainage_class_enum: - permissible_values: - very poorly: {} - poorly: {} - somewhat poorly: {} - moderately well: {} - well: {} - excessively drained: {}